From af82dda19923a8ad2d4bbc04f19595a493a2293d Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Wed, 29 Feb 2012 13:57:20 -0800 Subject: [PATCH 01/22] Added add_attribute method to ClawData and some notes on things to do. --- src/python/clawutil/clawdata.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/python/clawutil/clawdata.py b/src/python/clawutil/clawdata.py index 3ac08dcd..8b6c8032 100755 --- a/src/python/clawutil/clawdata.py +++ b/src/python/clawutil/clawdata.py @@ -41,6 +41,8 @@ def __init__(self, attributes=None): for attr in attributes: self.__setattr__(attr,None) + def add_attribute(self, name, value=None, add_to_list=True): + setattr(self,name,value) # ======================== class ClawData(object): @@ -900,7 +902,7 @@ def write(self): make_userdatafile(self) -class GeoclawInputData(ClawData): +class GeoclawInputData(Data): r""" Object that will be written out to the various GeoClaw data files. """ From 0793ddd339de62887b2a7cbec062bbb484788baf Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Tue, 24 Apr 2012 15:37:30 +0200 Subject: [PATCH 02/22] fix to paths in imagediff --- src/python/clawutil/imagediff.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/python/clawutil/imagediff.py b/src/python/clawutil/imagediff.py index 03f82164..6540631f 100755 --- a/src/python/clawutil/imagediff.py +++ b/src/python/clawutil/imagediff.py @@ -65,6 +65,9 @@ def imagediff_dir(dir1, dir2, dir3="_image_diff", ext='.png', \ if dir1[-1] == '/': dir1 = dir1[:-1] if dir2[-1] == '/': dir2 = dir2[:-1] + dir1 = os.path.abspath(dir1) + dir2 = os.path.abspath(dir2) + files1 = glob.glob("%s/*%s" % (dir1,ext)) files1 = [f.replace(dir1+'/','') for f in files1] @@ -90,8 +93,7 @@ def imagediff_dir(dir1, dir2, dir3="_image_diff", ext='.png', \ os.system('mkdir -p %s' % dir3) startdir = os.getcwd() - dir1 = '../' + dir1 - dir2 = '../' + dir2 + os.chdir(dir3) From 9cab2f04e56fb66adf2aa2f235240474174a6910 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Fri, 11 May 2012 14:01:33 +0200 Subject: [PATCH 03/22] Modified imagediff.py to add a --relocatable option. This option copies figures from dir1 and dir2 to subdirectories of dir3 so the latter can be moved to a webpage for sharing with others. --- src/python/clawutil/imagediff.py | 47 +++++++++++++++++++++++++++----- 1 file changed, 40 insertions(+), 7 deletions(-) diff --git a/src/python/clawutil/imagediff.py b/src/python/clawutil/imagediff.py index 6540631f..971e33fa 100755 --- a/src/python/clawutil/imagediff.py +++ b/src/python/clawutil/imagediff.py @@ -4,15 +4,20 @@ Can by used from the command line via: python imagediff.py file1 file2 - python imagediff.py dir1 dir2 -Assumes dir1 and dir2 are subdirectories of working directory. + python imagediff.py dir1 dir2 [dir3] +In the latter case dir1 and dir2 are any two directories and all +images will be compared. The optional dir3 argument gives the directory +for the resulting diff's and html files. Default is '_image_diff'. Command line flags include: -v, --verbose = Verbose output + -r, --relocatable = Copy original image files to dir3 also -h, --help = Display this help """ -import os, sys, getopt +help_message = __doc__ + +import os, sys, getopt, shutil def imagediff_file(fname1, fname2, verbose): @@ -59,7 +64,7 @@ def make_imagediff(fname1,fname2,fname3='', verbose=False): def imagediff_dir(dir1, dir2, dir3="_image_diff", ext='.png', \ - overwrite=False, verbose=False): + relocatable=False, overwrite=False, verbose=False): import filecmp,glob @@ -82,7 +87,7 @@ def imagediff_dir(dir1, dir2, dir3="_image_diff", ext='.png', \ print "Comparing files in the directory: ", dir1 print " with the directory: ", dir2 - + if os.path.isdir(dir3): if (len(os.listdir(dir3)) > 0) and (not overwrite): ans = raw_input("Ok to overwrite files in %s ? " % dir3) @@ -110,6 +115,24 @@ def imagediff_dir(dir1, dir2, dir3="_image_diff", ext='.png', \ """ % (dir1,dir2,ext)) f_equal, f_diff, f_other = filecmp.cmpfiles(dir1,dir2,files,False) + + if relocatable: + # copy files from dir1 and dir2 into dir3 so the whole thing can + # be moved elsewhere, e.g. to post on web for discussion of a bug. + dir1copy = 'dir1' + dir2copy = 'dir2' + os.system('mkdir %s' % dir1copy) + os.system('mkdir %s' % dir2copy) + for f in files: + shutil.copy(os.path.join(dir1,f),dir1copy) + shutil.copy(os.path.join(dir2,f),dir2copy) + fhtml = os.path.splitext(f)[0] + '.html' ## Specific to Clawpack _plots + if not os.path.isfile(os.path.join(dir1,fhtml)): fhtml = f + shutil.copy(os.path.join(dir1,fhtml),dir1copy) + shutil.copy(os.path.join(dir2,fhtml),dir2copy) + dir1 = 'dir1' + dir2 = 'dir2' + for f in files: fhtml = os.path.splitext(f)[0] + '.html' ## Specific to Clawpack _plots @@ -174,31 +197,41 @@ class Usage(Exception): def __init__(self, msg): self.msg = msg + if __name__ == "__main__": # Parse input arguments argv = sys.argv try: try: - opts, args = getopt.getopt(argv[1:], "hv",["help","verbose"]) + opts, args = getopt.getopt(argv[1:], "hv",["help","verbose","relocatable"]) except getopt.error, msg: raise Usage(msg) # Default script parameter values verbose = False + relocatable = False # option processing for option, value in opts: # Script parameters if option in ("-v","--verbose"): verbose = True + if option in ("-r","--relocatable"): + relocatable = True if option in ("-h","--help"): raise Usage(help_message) + #import pdb; pdb.set_trace() # Run diff if os.path.isfile(args[0]) and os.path.isfile(args[1]): sys.exit(imagediff_file(args[0],args[1],verbose=verbose)) elif os.path.isdir(args[0]) and os.path.isdir(args[1]): - sys.exit(imagediff_dir(args[0],args[1],verbose=verbose)) + if len(args)==3: + sys.exit(imagediff_dir(args[0],args[1],args[2],verbose=verbose,\ + relocatable=relocatable)) + else: + sys.exit(imagediff_dir(args[0],args[1],verbose=verbose,\ + relocatable=relocatable)) else: raise Usage("Both paths must either be files or directories.") From c26dc7b27bcdef918348a0c4f677386d425e1ea3 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Fri, 11 May 2012 20:46:52 +0200 Subject: [PATCH 04/22] Rewriting clawdata.py, with bugs Want to redesign data_write function. --- src/python/clawutil/clawdata.py | 553 ++++++++++++-------------------- 1 file changed, 213 insertions(+), 340 deletions(-) diff --git a/src/python/clawutil/clawdata.py b/src/python/clawutil/clawdata.py index 8b6c8032..e04bc0cd 100755 --- a/src/python/clawutil/clawdata.py +++ b/src/python/clawutil/clawdata.py @@ -1,5 +1,3 @@ -#!/usr/bin/env python -# encoding: utf-8 r""" Data Module @@ -11,16 +9,7 @@ data classes are now subclasses of ClawData, which checks if attributes already exist before setting. - -:Authors: - Kyle T. Mandli and Randall J. LeVeque - """ -# ============================================================================ -# Distributed under the terms of the Berkeley Software Distribution (BSD) -# license -# http://www.opensource.org/licenses/ -# ============================================================================ import os import logging @@ -197,26 +186,21 @@ class ClawInputData(ClawData): r""" Object that will be written out to claw.data. """ - def __init__(self, ndim): + def __init__(self, num_dim): super(ClawInputData,self).__init__() - self.add_attribute('ndim',ndim) # Set default values: - self.add_attribute('mx',100) - self.add_attribute('meqn',1) - self.add_attribute('mwaves',1) - self.add_attribute('maux',0) + self.add_attribute('num_dim',num_dim) + self.add_attribute('num_eqn',1) + self.add_attribute('num_waves',1) + self.add_attribute('num_aux',0) self.add_attribute('output_style',1) - self.add_attribute('output_ntimes',1) - self.add_attribute('output_times',[1.]) - self.add_attribute('output_step_interval',10) - self.add_attribute('total_steps',5) - self.add_attribute('output_time_interval',1.) + self.add_attribute('output_times',[]) + self.add_attribute('output_steps',[]) self.add_attribute('output_format',1) self.add_attribute('output_q_components','all') self.add_attribute('output_aux_components',[]) self.add_attribute('output_aux_onlyonce',True) - self.add_attribute('tfinal',1.0) self.add_attribute('dt_initial',1.e-5) self.add_attribute('dt_max',1.e99) @@ -225,44 +209,42 @@ def __init__(self, ndim): self.add_attribute('cfl_max',1.0) self.add_attribute('steps_max',50000) self.add_attribute('order',2) - self.add_attribute('order_trans',0) + self.add_attribute('transverse_waves',2) self.add_attribute('dimensional_split',0) self.add_attribute('verbosity',0) self.add_attribute('verbosity_regrid',0) - self.add_attribute('src_split',0) - self.add_attribute('mcapa',0) + self.add_attribute('source_split',0) + self.add_attribute('capa_index',0) self.add_attribute('limiter',[4]) self.add_attribute('t0',0.) - self.add_attribute('xlower',0.) - self.add_attribute('xupper',1.) self.add_attribute('num_ghost',2) - self.add_attribute('bc_xlower',1) - self.add_attribute('bc_xupper',1) - self.add_attribute('restart',0) - self.add_attribute('restart_frame',0) self.add_attribute('fwave',False) self.add_attribute('restart',False) + self.add_attribute('restart_frame',0) self.add_attribute('restart_file','') self.add_attribute('regions',[]) self.add_attribute('gauges',[]) - - if ndim >= 2: - self.add_attribute('my',100) - self.add_attribute('ylower',0.) - self.add_attribute('yupper',1.) - self.add_attribute('bc_ylower',1) - self.add_attribute('bc_yupper',1) - - if ndim == 3: - self.add_attribute('mz',100) - self.add_attribute('zlower',0.) - self.add_attribute('zupper',1.) - self.add_attribute('bc_zlower',1) - self.add_attribute('bc_zupper',1) - - if ndim not in [1,2,3]: - raise ValueError("Only ndim=1, 2, or 3 supported ") + if num_dim == 1: + self.add_attribute('lower',[0.]) + self.add_attribute('upper',[1.]) + self.add_attribute('num_cells',[100]) + self.add_attribute('bc_lower',[0]) + self.add_attribute('bc_upper',[0]) + elif num_dim == 2: + self.add_attribute('lower',[0.,0.]) + self.add_attribute('upper',[1.,1.]) + self.add_attribute('num_cells',[100,100]) + self.add_attribute('bc_lower',[0,0]) + self.add_attribute('bc_upper',[0,0]) + elif num_dim == 3: + self.add_attribute('lower',[0.,0.,0.]) + self.add_attribute('upper',[1.,1.,1.]) + self.add_attribute('num_cells',[100,100,100]) + self.add_attribute('bc_lower',[0,0,0]) + self.add_attribute('bc_upper',[0,0,0]) + else: + raise ValueError("Only num_dim=1, 2, or 3 supported ") def write(self): print 'Creating data file claw.data for use with xclaw' @@ -273,28 +255,34 @@ class AmrclawInputData(ClawInputData): r""" Object that will be written out to amrclaw.data. """ - def __init__(self, ndim): + def __init__(self, num_dim): # Set default values: # Some defaults are inherited from ClawInputData: - super(AmrclawInputData,self).__init__(ndim) + super(AmrclawInputData,self).__init__(num_dim) - self.add_attribute('amrlevels_max',1) + self.add_attribute('amr_levels_max',1) self.add_attribute('refinement_ratio_x',[1]) + self.add_attribute('refinement_ratio_y',[1]) + if num_dim == 3: + self.add_attribute('refinement_ratio_z',[1]) + if num_dim == 1: + raise Exception("*** 1d AMR not yet supported") + self.add_attribute('variable_dt_refinement_ratios',False) + self.add_attribute('refinement_ratio_t',[1]) - self.add_attribute('auxtype',[]) + self.add_attribute('aux_type',[]) self.add_attribute('checkpt_style',1) self.add_attribute('checkpt_interval',1000) self.add_attribute('checkpt_time_interval',1000.) self.add_attribute('checkpt_times',[1000.]) - self.add_attribute('checkpt_ntimes',1) self.add_attribute('flag_richardson',False) self.add_attribute('flag_richardson_tol',1.0) - self.add_attribute('flag_gradient',True) - self.add_attribute('flag_gradient_tol',0.05) + self.add_attribute('flag2refine',True) + self.add_attribute('flag2refine_tol',0.05) self.add_attribute('regrid_interval',2) self.add_attribute('regrid_buffer_width',3) self.add_attribute('clustering_cutoff',0.7) @@ -313,8 +301,7 @@ def __init__(self, ndim): self.add_attribute('uprint',False) - - if ndim == 1: + if num_dim == 1: # attributes needed only because 1d AMR is done using 2d amrclaw: self.add_attribute('my',1) @@ -324,14 +311,6 @@ def __init__(self, ndim): self.add_attribute('bc_yupper',1) self.add_attribute('refinement_ratio_y',[1,1,1,1,1,1]) - elif ndim >= 2: - - self.add_attribute('refinement_ratio_y',[1]) - - - if ndim not in [1,2]: - print '*** Error: only ndim=1 or 2 supported so far ***' - raise AttributeError("Only ndim=1 or 2 supported so far") def write(self): print 'Creating data file amrclaw.data for use with xamr' @@ -418,125 +397,150 @@ def make_clawdatafile(clawdata): # open file and write a warning header: file = open_datafile('claw.data') - ndim = clawdata.ndim - data_write(file, clawdata, 'ndim', '(number of dimensions)') - data_write(file, clawdata, 'mx', '(cells in x direction)') - if ndim > 1: - data_write(file, clawdata, 'my', '(cells in y direction)') - if ndim == 3: - data_write(file, clawdata, 'mz', '(cells in z direction)') + write_clawdata_noamr(clawdata, file) + file.close() + + +def write_clawdata_noamr(clawdata, file): + r""" + Write out the Clawpack parameters that are used both for Classic and AMR. + """ + + import pdb; pdb.set_trace() + num_dim = clawdata.num_dim + data_write(file, clawdata, 'num_dim') + data_write(file, clawdata, 'lower[0]') + if num_dim > 1: + data_write(file, clawdata, 'lower[1]') + if num_dim == 3: + data_write(file, clawdata, 'lower[2]') data_write(file, clawdata, None) # writes blank line - data_write(file, clawdata, 'meqn', '(number of equations)') - data_write(file, clawdata, 'mwaves', '(number of waves)') - data_write(file, clawdata, 'maux', '(number of aux variables)') + data_write(file, clawdata, 'num_eqn') + data_write(file, clawdata, 'num_waves') + data_write(file, clawdata, 'num_aux') data_write(file, clawdata, None) # writes blank line - data_write(file, clawdata, 'output_style', '(style of specifying output times)') - if clawdata.output_style == 1: - data_write(file, clawdata, 'output_ntimes', '(number of output times)') - data_write(file, clawdata, 'tfinal', '(final time)') - elif clawdata.output_style == 2: - clawdata.output_ntimes = len(clawdata.output_times) - data_write(file, clawdata, 'output_ntimes', '(number of output times)') - data_write(file, clawdata, 'output_times', '(output times)') - elif clawdata.output_style == 3: - data_write(file, clawdata, 'output_step_interval', '(timesteps between output)') - data_write(file, clawdata, 'total_steps', '(number of output times)') - elif clawdata.output_style == 4: - data_write(file, clawdata, 'output_time_interval', '(output interval)') - data_write(file, clawdata, 'tfinal', '(final time)') - else: - print '*** Error: unrecognized output_style' - raise - return + clawdata._num_output_times = len(clawdata.output_times) + data_write(file, clawdata, 'num_output_times') + if clawdata._num_output_times > 0: + data_write(file, clawdata, 'output_times') + + clawdata._num_output_steps = len(clawdata.output_steps) + data_write(file, clawdata, 'num_output_steps') + if clawdata._num_output_steps > 0: + data_write(file, clawdata, 'output_steps') data_write(file, clawdata, None) if clawdata.output_format in [1,'ascii']: clawdata.output_format = 1 - elif clawdata.output_format in [2,'binary']: + elif clawdata.output_format in [2,'netcdf']: clawdata.output_format = 2 else: raise ValueError("*** Error in data parameter: " + \ "output_format unrecognized: ",clawdata.output_format) - data_write(file, clawdata, 'output_format', '(output format)') - clawdata._iout_q = clawdata.meqn * [1] + data_write(file, clawdata, 'output_format') + + clawdata._iout_q = clawdata.num_eqn * [1] if clawdata.output_q_components != 'all': - for i in range(clawdata.meqn): + for i in range(clawdata.num_eqn): if i+1 not in clawdata.output_q_components: clawdata._iout_q[i] = 0 - data_write(file, clawdata, '_iout_q', '(which components of q)') - if clawdata.maux > 0: - clawdata._iout_aux = clawdata.maux * [1] + data_write(file, clawdata, '_iout_q') + + if clawdata.num_aux > 0: + clawdata._iout_aux = clawdata.num_aux * [1] if clawdata.output_aux_components != 'all': - for i in range(clawdata.maux): + for i in range(clawdata.num_aux): if i+1 not in clawdata.output_aux_components: clawdata._iout_aux[i] = 0 - data_write(file, clawdata, '_iout_aux', '(which components of aux)') - data_write(file, clawdata, 'output_aux_onlyonce', '(only once?)') + data_write(file, clawdata, '_iout_aux') + data_write(file, clawdata, 'output_aux_onlyonce') + data_write(file, clawdata, None) - data_write(file, clawdata, 'dt_initial', '(initial time step dt)') - data_write(file, clawdata, 'dt_max', '(max allowable dt)') - data_write(file, clawdata, 'cfl_max', '(max allowable Courant number)') - data_write(file, clawdata, 'cfl_desired', '(desired Courant number)') - data_write(file, clawdata, 'steps_max', '(max time steps per call to claw)') + data_write(file, clawdata, 'dt_initial') + data_write(file, clawdata, 'dt_max') + data_write(file, clawdata, 'cfl_max') + data_write(file, clawdata, 'cfl_desired') + data_write(file, clawdata, 'steps_max') data_write(file, clawdata, None) - data_write(file, clawdata, 'dt_variable', '(1 for variable dt, 0 for fixed)') - data_write(file, clawdata, 'order', '(1 or 2)') - if ndim == 1: - #data_write(file, clawdata, 'order_trans', '(not used in 1d)') + data_write(file, clawdata, 'dt_variable') + data_write(file, clawdata, 'order') + if num_dim == 1: pass else: - data_write(file, clawdata, 'order_trans', '(transverse order)') - data_write(file, clawdata, 'dimensional_split', '(use dimensional splitting?)') + if clawdata.transverse_waves == 'none': + clawdata.transverse_waves = 0 + elif clawdata.transverse_waves == 'increment': + clawdata.transverse_waves = 1 + elif clawdata.transverse_waves == 'all': + clawdata.transverse_waves = 2 + else: + raise AttributeError("Unrecognized transverse_waves: %s" \ + % clawdata.transverse_waves) + data_write(file, clawdata, 'transverse_waves') + + if clawdata.dimensional_split == 'unsplit': + clawdata.dimensional_split = 0 + elif clawdata.dimensional_split == 'godunov': + clawdata.dimensional_split = 1 + elif clawdata.dimensional_split == 'strang': + clawdata.dimensional_split = 2 + else: + raise AttributeError("Unrecognized dimensional_split: %s" \ + % clawdata.dimensional_split) + data_write(file, clawdata, 'dimensional_split') - data_write(file, clawdata, 'verbosity', '(verbosity of output)') - data_write(file, clawdata, 'src_split', '(source term splitting)') - data_write(file, clawdata, 'mcapa', '(aux index for capacity fcn)') + data_write(file, clawdata, 'verbosity') + data_write(file, clawdata, 'source_split') + data_write(file, clawdata, 'capa_index') + data_write(file, clawdata, 'fwave') data_write(file, clawdata, None) - data_write(file, clawdata, 'limiter', '(limiter choice for each wave)') + for i in range(len(limiter)): + if clawdata.limiter[i] == 'none': clawdata.limiter[i] = 0 + elif clawdata.limiter[i] == 'minmod': clawdata.limiter[i] = 1 + elif clawdata.limiter[i] == 'superbee': clawdata.limiter[i] = 2 + elif clawdata.limiter[i] == 'mc': clawdata.limiter[i] = 3 + elif clawdata.limiter[i] == 'vanleer': clawdata.limiter[i] = 4 + else: + raise AttributeError("Unrecognized limiter: %s" \ + % clawdata.limiter[i]) + data_write(file, clawdata, 'limiter') + data_write(file, clawdata, None) - data_write(file, clawdata, 't0', '(initial time)') - data_write(file, clawdata, 'xlower', '(xlower)') - data_write(file, clawdata, 'xupper', '(xupper)') - if ndim > 1: - data_write(file, clawdata, 'ylower', '(ylower)') - data_write(file, clawdata, 'yupper', '(yupper)') - if ndim == 3: - data_write(file, clawdata, 'zlower', '(zlower)') - data_write(file, clawdata, 'zupper', '(zupper)') + data_write(file, clawdata, 't0') + data_write(file, clawdata, 'lower') + data_write(file, clawdata, 'upper') data_write(file, clawdata, None) - data_write(file, clawdata, 'num_ghost', '(number of ghost cells)') - - for bdry in ['xlower','xupper','ylower','yupper','zlower','zupper']: - bc = getattr(clawdata, 'bc_'+bdry, None) - if bc == 'user': - setattr(clawdata, 'bc_'+bdry, 0) - if bc == 'extrap': - setattr(clawdata, 'bc_'+bdry, 1) - if bc == 'periodic': - setattr(clawdata, 'bc_'+bdry, 2) - if bc == 'wall': - setattr(clawdata, 'bc_'+bdry, 3) - - data_write(file, clawdata, 'bc_xlower', '(type of BC at xlower)') - data_write(file, clawdata, 'bc_xupper', '(type of BC at xupper)') - if ndim > 1: - data_write(file, clawdata, 'bc_ylower', '(type of BC at ylower)') - data_write(file, clawdata, 'bc_yupper', '(type of BC at yupper)') - if ndim == 3: - data_write(file, clawdata, 'bc_zlower', '(type of BC at zlower)') - data_write(file, clawdata, 'bc_zupper', '(type of BC at zupper)') + data_write(file, clawdata, 'num_ghost') + for i in range(num_dim): + if clawdata.bc_lower[i] == 'user': clawdata.bc_lower[i] = 0 + elif clawdata.bc_lower[i] == 'extrap': clawdata.bc_lower[i] = 1 + elif clawdata.bc_lower[i] == 'periodic': clawdata.bc_lower[i] = 2 + elif clawdata.bc_lower[i] == 'wall': clawdata.bc_lower[i] = 3 + else: + raise AttributeError("Unrecognized bc_lower: %s" \ + % clawdata.bc_lower[i]) + data_write(file, clawdata, 'bc_lower') + + for i in range(num_dim): + if clawdata.bc_upper[i] == 'user': clawdata.bc_upper[i] = 0 + elif clawdata.bc_upper[i] == 'extrap': clawdata.bc_upper[i] = 1 + elif clawdata.bc_upper[i] == 'periodic': clawdata.bc_upper[i] = 2 + elif clawdata.bc_upper[i] == 'wall': clawdata.bc_upper[i] = 3 + else: + raise AttributeError("Unrecognized bc_upper: %s" \ + % clawdata.bc_upper[i]) + data_write(file, clawdata, 'bc_upper') data_write(file, clawdata, None) - data_write(file, clawdata, 'restart', '(T to restart from a past run)') - data_write(file, clawdata, 'restart_frame', '(which frame to restart from)') + data_write(file, clawdata, 'restart') + data_write(file, clawdata, 'restart_frame') data_write(file, clawdata, None) - file.close() def make_amrclawdatafile(clawdata): r""" @@ -548,205 +552,75 @@ def make_amrclawdatafile(clawdata): # open file and write a warning header: file = open_datafile('amrclaw.data') - ndim = clawdata.ndim - data_write(file, clawdata, 'ndim', '(number of dimensions)') - data_write(file, clawdata, 'mx', '(cells in x direction)') - data_write(file, clawdata, 'my', '(cells in y direction)') - if ndim == 3: - data_write(file, clawdata, 'mz', '(cells in z direction)') + write_clawdata_noamr(clawdata, file) + write_clawdata_amr(clawdata, file) + file.close() - data_write(file, clawdata, 'amrlevels_max', '(max number of grid levels)') - if len(clawdata.refinement_ratio_x) < max(abs(clawdata.amrlevels_max)-1, 1): + +def write_clawdata_amr(clawdata, file): + r""" + Write the input parameters only used by AMRClaw. + """ + + data_write(file, clawdata, 'amr_levels_max') + + num_ratios = max(abs(clawdata.amr_levels_max)-1, 1) + if len(clawdata.refinement_ratio_x) < num_ratios: raise ValueError("*** Error in data parameter: " + \ - "require len(refinement_ratio_x) >= %s " % max(abs(clawdata.amrlevels_max) - 1, 1)) - if len(clawdata.refinement_ratio_y) < max(abs(clawdata.amrlevels_max)-1, 1): + "require len(refinement_ratio_x) >= %s " % num_ratios) + if len(clawdata.refinement_ratio_y) < num_ratios: raise ValueError("*** Error in data parameter: " + \ - "require len(refinement_ratio_y) >= %s " % max(abs(clawdata.amrlevels_max) - 1, 1)) - data_write(file, clawdata, 'refinement_ratio_x', '(refinement ratios)') - data_write(file, clawdata, 'refinement_ratio_y', '(refinement ratios)') - if ndim == 3: - if len(clawdata.refinement_ratio_z) < max(abs(clawdata.amrlevels_max)-1, 1): + "require len(refinement_ratio_y) >= %s " % num_ratios) + data_write(file, clawdata, 'refinement_ratio_x') + data_write(file, clawdata, 'refinement_ratio_y') + if num_dim == 3: + if len(clawdata.refinement_ratio_z) < num_ratios: raise ValueError("*** Error in data parameter: " + \ - "require len(refinement_ratio_z) >= %s " % max(abs(clawdata.amrlevels_max) - 1, 1)) - data_write(file, clawdata, 'refinement_ratio_z', '(refinement ratios)') - if len(clawdata.refinement_ratio_t) < max(abs(clawdata.amrlevels_max)-1, 1): + "require len(refinement_ratio_z) >= %s " % num_ratios) + data_write(file, clawdata, 'refinement_ratio_z') + if len(clawdata.refinement_ratio_t) < num_ratios: raise ValueError("*** Error in data parameter: " + \ - "require len(refinement_ratio_t) >= %s " % max(abs(clawdata.amrlevels_max) - 1, 1)) - data_write(file, clawdata, 'refinement_ratio_t', '(refinement ratios)') + "require len(refinement_ratio_t) >= %s " % num_ratios) + data_write(file, clawdata, 'refinement_ratio_t') data_write(file, clawdata, None) # writes blank line - data_write(file, clawdata, 't0', '(initial time)') - - data_write(file, clawdata, 'output_style', '(style of specifying output times)') - if clawdata.output_style == 1: - data_write(file, clawdata, 'output_ntimes', '(number of output times)') - data_write(file, clawdata, 'tfinal', '(final time)') - elif clawdata.output_style == 2: - clawdata.output_ntimes = len(clawdata.output_times) - data_write(file, clawdata, 'output_ntimes', '(number of output times)') - data_write(file, clawdata, 'output_times', '(output times)') - elif clawdata.output_style == 3: - data_write(file, clawdata, 'output_step_interval', '(output every output_step_interval steps)') - data_write(file, clawdata, 'total_steps', '(number of steps to take)') - elif clawdata.output_style == 4: - data_write(file, clawdata, 'output_time_interval', '(time between outputs)') - data_write(file, clawdata, 'tfinal', '(final time)') - else: - print '*** Error: unrecognized output_style = ',output_style - raise - return - - data_write(file, clawdata, None) - data_write(file, clawdata, 'dt_initial', '(initial time step dt)') - data_write(file, clawdata, 'dt_max', '(max allowable dt)') - data_write(file, clawdata, 'cfl_max', '(max allowable Courant number)') - data_write(file, clawdata, 'cfl_desired', '(desired Courant number)') - data_write(file, clawdata, 'steps_max', '(max time steps per call to claw)') - data_write(file, clawdata, None) - data_write(file, clawdata, 'dt_variable', '(1 for variable dt, 0 for fixed)') - data_write(file, clawdata, 'order', '(1 or 2)') - if ndim == 1: - data_write(file, clawdata, 'order_trans', '(not used in 1d)') - else: - data_write(file, clawdata, 'order_trans', '(transverse order)') - data_write(file, clawdata, 'dimensional_split', '(use dimensional splitting?)') - - data_write(file, clawdata, 'verbosity', '(verbosity of output)') - data_write(file, clawdata, 'src_split', '(source term splitting)') - data_write(file, clawdata, 'mcapa', '(aux index for capacity fcn)') - data_write(file, clawdata, 'maux', '(number of aux variables)') - if len(clawdata.auxtype) != clawdata.maux: - file.close() - print "*** Error: An auxtype array must be specified of length maux" - raise AttributeError, "require len(clawdata.auxtype) == clawdata.maux" - for i in range(clawdata.maux): - file.write("'%s'\n" % clawdata.auxtype[i]) - data_write(file, clawdata, None) - - data_write(file, clawdata, 'meqn', '(number of equations)') - data_write(file, clawdata, 'mwaves', '(number of waves)') - data_write(file, clawdata, 'limiter', '(limiter choice for each wave)') - if clawdata.fwave: - clawdata.add_attribute('ifwave',1) - else: - clawdata.add_attribute('ifwave',0) - data_write(file, clawdata, 'ifwave', '(use f-wave form?)') - data_write(file, clawdata, None) - - data_write(file, clawdata, 'xlower', '(xlower)') - data_write(file, clawdata, 'xupper', '(xupper)') - data_write(file, clawdata, 'ylower', '(ylower)') - data_write(file, clawdata, 'yupper', '(yupper)') - if ndim == 3: - data_write(file, clawdata, 'zlower', '(zlower)') - data_write(file, clawdata, 'zupper', '(zupper)') - data_write(file, clawdata, None) - for bdry in ['xlower','xupper','ylower','yupper','zlower','zupper']: - bc = getattr(clawdata, 'bc_'+bdry, None) - if bc == 'user': - setattr(clawdata, 'bc_'+bdry, 0) - if bc == 'extrap': - setattr(clawdata, 'bc_'+bdry, 1) - if bc == 'periodic': - setattr(clawdata, 'bc_'+bdry, 2) - if bc == 'wall': - setattr(clawdata, 'bc_'+bdry, 3) - - data_write(file, clawdata, 'num_ghost', '(number of ghost cells)') - data_write(file, clawdata, 'bc_xlower', '(type of BC at xlower)') - data_write(file, clawdata, 'bc_xupper', '(type of BC at xupper)') - data_write(file, clawdata, 'bc_ylower', '(type of BC at ylower)') - data_write(file, clawdata, 'bc_yupper', '(type of BC at yupper)') - if ndim == 3: - data_write(file, clawdata, 'bc_zlower', '(type of BC at zlower)') - data_write(file, clawdata, 'bc_zupper', '(type of BC at zupper)') - data_write(file, clawdata, None) - - data_write(file, clawdata, 'restart', '(1 to restart from a past run)') - data_write(file, clawdata, 'checkpt_style', '(how checkpoints specified)') - - if clawdata.checkpt_style == 2: - clawdata.checkpt_ntimes = len(clawdata.checkpt_times) - data_write(file, clawdata, 'checkpt_ntimes', '(number of checkpoint times)') - data_write(file, clawdata, 'checkpt_times', '(checkpoint times)') - elif clawdata.checkpt_style == 3: - data_write(file, clawdata, 'checkpt_interval', '(step interval for checkpoint)') - elif clawdata.checkpt_style == 4: - print "*** Error: checkpt_style==4 not yet implemented" - raise ValueError("Invalid checkpt_style") - data_write(file, clawdata, 'checkpt_time_interval', '(time interval for checkpoint)') - else: - print "*** Error, unrecognized checkpt_style = ",clawdata.checkpt_style - print "*** Require: 0,2,3, or 4" - raise ValueError("Unrecognized checkpt_style") - return + data_write(file, clawdata, 'flag_richardson') + data_write(file, clawdata, 'flag_richardson_tol') + data_write(file, clawdata, 'flag2refine') + data_write(file, clawdata, 'flag2refine_tol') + data_write(file, clawdata, 'regrid_interval') + data_write(file, clawdata, 'regrid_buffer_width') + data_write(file, clawdata, 'clustering_cutoff') + data_write(file, clawdata, 'verbosity_regrid') data_write(file, clawdata, None) - data_write(file, clawdata, 'flag_richardson', '(use Richardson extrap?)') - data_write(file, clawdata, 'flag_richardson_tol', '(tolerance for Richardson)') - data_write(file, clawdata, 'flag_gradient', '(use gradient flagging?)') - data_write(file, clawdata, 'flag_gradient_tol', '(tolerance used for gradient)') - data_write(file, clawdata, 'regrid_interval', '(how often to regrid)') - data_write(file, clawdata, 'regrid_buffer_width', '(buffer zone around flagged pts)') - data_write(file, clawdata, 'clustering_cutoff', '(efficiency cutoff for clustering)') - data_write(file, clawdata, 'verbosity_regrid', '(what levels to print grid info)') - data_write(file, clawdata, None) - - if clawdata.output_format == 'ascii': - clawdata.output_format = 1 - elif clawdata.output_format == 'binary': - clawdata.output_format = 2 - else: - if clawdata.output_format not in [1,2]: - print "*** Unrecognized output_format: ",clawdata.output_format - raise - return - data_write(file, clawdata, 'output_format', '(format for fort.q files)') - - if clawdata.output_q_components=='all': - clawdata.output_q_components = range(1,clawdata.meqn+1) - - nq_components = len(clawdata.output_q_components) - clawdata.add_attribute('output_nq_components',nq_components) - data_write(file, clawdata, 'output_nq_components', '(number of q vals to print)') - if clawdata.output_nq_components > 0: - data_write(file, clawdata, 'output_q_components', '(which components of q)') - - if clawdata.output_aux_components=='all': - clawdata.output_aux_components = range(1,clawdata.maux+1) - - naux_components = len(clawdata.output_aux_components) - clawdata.add_attribute('output_naux_components',naux_components) - data_write(file, clawdata, 'output_naux_components', '(number of aux vals to print)') - if clawdata.output_naux_components > 0: - data_write(file, clawdata, 'output_aux_components', '(which components of aux)') - data_write(file, clawdata, 'output_aux_onlyonce', '(only at t0?)') - - - data_write(file, clawdata, None) - data_write(file, clawdata, 'dprint', '(print domain flags)') - data_write(file, clawdata, 'eprint', '(print err est flags)') - data_write(file, clawdata, 'edebug', '(even more err est flags)') - data_write(file, clawdata, 'gprint', '(grid bisection/clustering)') - data_write(file, clawdata, 'nprint', '(proper nesting output)') - data_write(file, clawdata, 'pprint', '(proj. of tagged points)') - data_write(file, clawdata, 'rprint', '(print regridding summary)') - data_write(file, clawdata, 'sprint', '(space/memory output)') - data_write(file, clawdata, 'tprint', '(time step reporting each level)') - data_write(file, clawdata, 'uprint', '(update/upbnd reporting)') + data_write(file, clawdata, 'dprint') + data_write(file, clawdata, 'eprint') + data_write(file, clawdata, 'edebug') + data_write(file, clawdata, 'gprint') + data_write(file, clawdata, 'nprint') + data_write(file, clawdata, 'pprint') + data_write(file, clawdata, 'rprint') + data_write(file, clawdata, 'sprint') + data_write(file, clawdata, 'tprint') + data_write(file, clawdata, 'uprint') data_write(file, clawdata, None) +def regions_and_gauges(): + r""" + Placeholder... where to put these? + """ clawdata.add_attribute('nregions', len(clawdata.regions)) - data_write(file, clawdata, 'nregions', '(nregions)') + data_write(file, clawdata, 'nregions') for regions in clawdata.regions: file.write(8*" %g" % tuple(regions) +"\n") clawdata.add_attribute('ngauges', len(clawdata.gauges)) - data_write(file, clawdata, 'ngauges', '(ngauges)') + data_write(file, clawdata, 'ngauges') gaugeno_used = [] for gauge in clawdata.gauges: gaugeno = gauge[0] @@ -758,7 +632,6 @@ def make_amrclawdatafile(clawdata): #file.write("%4i %19.10e %17.10e %13.6e %13.6e\n" % tuple(gauge)) file.write(5*" %g" % tuple(gauge) +"\n") - file.close() def make_userdatafile(userdata): r""" @@ -812,10 +685,10 @@ class ClawRunData(ClawData): r""" Object that will be written out to claw.data. """ - def __init__(self, pkg, ndim): + def __init__(self, pkg, num_dim): super(ClawRunData,self).__init__() self.add_attribute('pkg',pkg) - self.add_attribute('ndim',ndim) + self.add_attribute('num_dim',num_dim) self.add_attribute('datalist',[]) @@ -823,7 +696,7 @@ def __init__(self, pkg, ndim): self.add_attribute('xclawcmd', 'xclaw') # Required data set for basic run parameters: - clawdata = ClawInputData(ndim) + clawdata = ClawInputData(num_dim) self.add_attribute('clawdata', clawdata) self.datalist.append(clawdata) @@ -831,7 +704,7 @@ def __init__(self, pkg, ndim): self.add_attribute('xclawcmd', 'xamr') # Required data set for basic run parameters: - clawdata = AmrclawInputData(ndim) + clawdata = AmrclawInputData(num_dim) self.add_attribute('clawdata', clawdata) self.datalist.append(clawdata) @@ -839,10 +712,10 @@ def __init__(self, pkg, ndim): self.add_attribute('xclawcmd', 'xgeoclaw') # Required data set for basic run parameters: - clawdata = AmrclawInputData(ndim) + clawdata = AmrclawInputData(num_dim) self.add_attribute('clawdata', clawdata) self.datalist.append(clawdata) - geodata = GeoclawInputData(ndim) + geodata = GeoclawInputData(num_dim) self.add_attribute('geodata', geodata) self.datalist.append(geodata) @@ -865,7 +738,7 @@ def add_GaugeData(self): r""" Create a gaugedata attribute for writing to gauges.data. """ - gaugedata = GaugeData(self.ndim) + gaugedata = GaugeData(self.num_dim) self.datalist.append(gaugedata) self.gaugedata = gaugedata return gaugedata @@ -906,7 +779,7 @@ class GeoclawInputData(Data): r""" Object that will be written out to the various GeoClaw data files. """ - def __init__(self, ndim): + def __init__(self, num_dim): super(GeoclawInputData,self).__init__() # Set default values: From c5d1b93accbf13e843ca4843d3a25e11be487036 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Fri, 11 May 2012 23:47:03 +0200 Subject: [PATCH 05/22] New clawdata.py writing output file for amrclaw example --- src/python/clawutil/clawdata.py | 231 +++++++++++++++++++------------- 1 file changed, 138 insertions(+), 93 deletions(-) mode change 100755 => 100644 src/python/clawutil/clawdata.py diff --git a/src/python/clawutil/clawdata.py b/src/python/clawutil/clawdata.py old mode 100755 new mode 100644 index e04bc0cd..4e9780dd --- a/src/python/clawutil/clawdata.py +++ b/src/python/clawutil/clawdata.py @@ -346,7 +346,7 @@ def open_datafile(name, datasource='setrun.py'): return file -def data_write(file, dataobj, name=None, descr=''): +def data_write_old(file, dataobj, name=None, descr=''): r""" Write out value to data file, in the form :: @@ -386,6 +386,43 @@ def data_write(file, dataobj, name=None, descr=''): padded_name = string.ljust(name, 12) file.write('%s =: %s %s\n' % (padded_value, padded_name, descr)) +def data_write(file, value, name=None, description=''): + r""" + Write out value to data file, in the form :: + + value # name [description] + + Remove brackets and commas from lists, and replace booleans by T/F. + + :Input: + - *name* - (string) normally a string defining the variable, + ``if name==None``, write a blank line. + - *description* - (string) optional description + """ + + import string + from numpy import ndarray + if name is None: + file.write('\n') + else: + # Convert value to an appropriate string repr + if isinstance(value,ndarray): + value = list(value) + if isinstance(value,tuple) | isinstance(value,list): + # Remove [], (), and ',' + string_value = repr(value)[1:-1] + string_value = string_value.replace(',','') + elif isinstance(value,bool): + if value: + string_value = 'T' + else: + string_value = 'F' + else: + string_value = repr(value) + padded_value = string.ljust(string_value, 40) + #padded_name = string.ljust(name, 12) + file.write('%s # %s %s\n' % (padded_value, name, description)) + def make_clawdatafile(clawdata): r""" @@ -406,29 +443,29 @@ def write_clawdata_noamr(clawdata, file): Write out the Clawpack parameters that are used both for Classic and AMR. """ - import pdb; pdb.set_trace() + #import pdb; pdb.set_trace() num_dim = clawdata.num_dim - data_write(file, clawdata, 'num_dim') - data_write(file, clawdata, 'lower[0]') - if num_dim > 1: - data_write(file, clawdata, 'lower[1]') - if num_dim == 3: - data_write(file, clawdata, 'lower[2]') + data_write(file, clawdata.num_dim, 'num_dim') + data_write(file, clawdata.lower, 'lower') + data_write(file, clawdata.upper, 'upper') + data_write(file, clawdata.num_cells, 'num_cells') data_write(file, clawdata, None) # writes blank line - data_write(file, clawdata, 'num_eqn') - data_write(file, clawdata, 'num_waves') - data_write(file, clawdata, 'num_aux') + data_write(file, clawdata.num_eqn, 'num_eqn') + data_write(file, clawdata.num_waves, 'num_waves') + data_write(file, clawdata.num_aux, 'num_aux') data_write(file, clawdata, None) # writes blank line - clawdata._num_output_times = len(clawdata.output_times) - data_write(file, clawdata, 'num_output_times') - if clawdata._num_output_times > 0: - data_write(file, clawdata, 'output_times') + data_write(file, clawdata.t0, 't0') + data_write(file, clawdata, None) + num_output_times = len(clawdata.output_times) + data_write(file, num_output_times, 'num_output_times') + if num_output_times > 0: + data_write(file, clawdata.output_times, 'output_times') - clawdata._num_output_steps = len(clawdata.output_steps) - data_write(file, clawdata, 'num_output_steps') - if clawdata._num_output_steps > 0: - data_write(file, clawdata, 'output_steps') + num_output_steps = len(clawdata.output_steps) + data_write(file, num_output_steps, 'num_output_steps') + if num_output_steps > 0: + data_write(file, clawdata.output_steps, 'output_steps') data_write(file, clawdata, None) if clawdata.output_format in [1,'ascii']: @@ -439,14 +476,14 @@ def write_clawdata_noamr(clawdata, file): raise ValueError("*** Error in data parameter: " + \ "output_format unrecognized: ",clawdata.output_format) - data_write(file, clawdata, 'output_format') + data_write(file, clawdata.output_format, 'output_format') clawdata._iout_q = clawdata.num_eqn * [1] if clawdata.output_q_components != 'all': for i in range(clawdata.num_eqn): if i+1 not in clawdata.output_q_components: clawdata._iout_q[i] = 0 - data_write(file, clawdata, '_iout_q') + data_write(file, clawdata._iout_q, '_iout_q') if clawdata.num_aux > 0: clawdata._iout_aux = clawdata.num_aux * [1] @@ -454,91 +491,98 @@ def write_clawdata_noamr(clawdata, file): for i in range(clawdata.num_aux): if i+1 not in clawdata.output_aux_components: clawdata._iout_aux[i] = 0 - data_write(file, clawdata, '_iout_aux') - data_write(file, clawdata, 'output_aux_onlyonce') + data_write(file, clawdata._iout_aux, '_iout_aux') + data_write(file, clawdata.output_aux_onlyonce, 'output_aux_onlyonce') data_write(file, clawdata, None) - data_write(file, clawdata, 'dt_initial') - data_write(file, clawdata, 'dt_max') - data_write(file, clawdata, 'cfl_max') - data_write(file, clawdata, 'cfl_desired') - data_write(file, clawdata, 'steps_max') + data_write(file, clawdata.dt_initial, 'dt_initial') + data_write(file, clawdata.dt_max, 'dt_max') + data_write(file, clawdata.cfl_max, 'cfl_max') + data_write(file, clawdata.cfl_desired, 'cfl_desired') + data_write(file, clawdata.steps_max, 'steps_max') data_write(file, clawdata, None) - data_write(file, clawdata, 'dt_variable') - data_write(file, clawdata, 'order') + data_write(file, clawdata.dt_variable, 'dt_variable') + data_write(file, clawdata.order, 'order') if num_dim == 1: pass else: - if clawdata.transverse_waves == 'none': + if clawdata.transverse_waves in [0,'none']: clawdata.transverse_waves = 0 - elif clawdata.transverse_waves == 'increment': + elif clawdata.transverse_waves in [1,'increment']: clawdata.transverse_waves = 1 - elif clawdata.transverse_waves == 'all': + elif clawdata.transverse_waves in [2,'all']: clawdata.transverse_waves = 2 else: raise AttributeError("Unrecognized transverse_waves: %s" \ % clawdata.transverse_waves) - data_write(file, clawdata, 'transverse_waves') + data_write(file, clawdata.transverse_waves, 'transverse_waves') - if clawdata.dimensional_split == 'unsplit': + if clawdata.dimensional_split in [0,'unsplit']: clawdata.dimensional_split = 0 - elif clawdata.dimensional_split == 'godunov': + elif clawdata.dimensional_split in [1,'godunov']: clawdata.dimensional_split = 1 - elif clawdata.dimensional_split == 'strang': + elif clawdata.dimensional_split in [2,'strang']: clawdata.dimensional_split = 2 else: raise AttributeError("Unrecognized dimensional_split: %s" \ % clawdata.dimensional_split) - data_write(file, clawdata, 'dimensional_split') + data_write(file, clawdata.dimensional_split, 'dimensional_split') - data_write(file, clawdata, 'verbosity') - data_write(file, clawdata, 'source_split') - data_write(file, clawdata, 'capa_index') - data_write(file, clawdata, 'fwave') + data_write(file, clawdata.verbosity, 'verbosity') + + if clawdata.source_split in [0,'none']: + clawdata.source_split = 0 + elif clawdata.source_split in [1,'godunov']: + clawdata.source_split = 1 + elif clawdata.source_split in [2,'strang']: + clawdata.source_split = 2 + else: + raise AttributeError("Unrecognized source_split: %s" \ + % clawdata.source_split) + data_write(file, clawdata.source_split, 'source_split') + + data_write(file, clawdata.capa_index, 'capa_index') + data_write(file, clawdata.fwave, 'fwave') data_write(file, clawdata, None) - for i in range(len(limiter)): - if clawdata.limiter[i] == 'none': clawdata.limiter[i] = 0 - elif clawdata.limiter[i] == 'minmod': clawdata.limiter[i] = 1 - elif clawdata.limiter[i] == 'superbee': clawdata.limiter[i] = 2 - elif clawdata.limiter[i] == 'mc': clawdata.limiter[i] = 3 - elif clawdata.limiter[i] == 'vanleer': clawdata.limiter[i] = 4 + for i in range(len(clawdata.limiter)): + if clawdata.limiter[i] in [0,'none']: clawdata.limiter[i] = 0 + elif clawdata.limiter[i] in [1,'minmod']: clawdata.limiter[i] = 1 + elif clawdata.limiter[i] in [2,'superbee']: clawdata.limiter[i] = 2 + elif clawdata.limiter[i] in [3,'mc']: clawdata.limiter[i] = 3 + elif clawdata.limiter[i] in [4,'vanleer']: clawdata.limiter[i] = 4 else: raise AttributeError("Unrecognized limiter: %s" \ % clawdata.limiter[i]) - data_write(file, clawdata, 'limiter') + data_write(file, clawdata.limiter, 'limiter') data_write(file, clawdata, None) - data_write(file, clawdata, 't0') - data_write(file, clawdata, 'lower') - data_write(file, clawdata, 'upper') - data_write(file, clawdata, None) - data_write(file, clawdata, 'num_ghost') + data_write(file, clawdata.num_ghost, 'num_ghost') for i in range(num_dim): - if clawdata.bc_lower[i] == 'user': clawdata.bc_lower[i] = 0 - elif clawdata.bc_lower[i] == 'extrap': clawdata.bc_lower[i] = 1 - elif clawdata.bc_lower[i] == 'periodic': clawdata.bc_lower[i] = 2 - elif clawdata.bc_lower[i] == 'wall': clawdata.bc_lower[i] = 3 + if clawdata.bc_lower[i] in [0,'user']: clawdata.bc_lower[i] = 0 + elif clawdata.bc_lower[i] in [1,'extrap']: clawdata.bc_lower[i] = 1 + elif clawdata.bc_lower[i] in [2,'periodic']: clawdata.bc_lower[i] = 2 + elif clawdata.bc_lower[i] in [3,'wall']: clawdata.bc_lower[i] = 3 else: raise AttributeError("Unrecognized bc_lower: %s" \ % clawdata.bc_lower[i]) - data_write(file, clawdata, 'bc_lower') + data_write(file, clawdata.bc_lower, 'bc_lower') for i in range(num_dim): - if clawdata.bc_upper[i] == 'user': clawdata.bc_upper[i] = 0 - elif clawdata.bc_upper[i] == 'extrap': clawdata.bc_upper[i] = 1 - elif clawdata.bc_upper[i] == 'periodic': clawdata.bc_upper[i] = 2 - elif clawdata.bc_upper[i] == 'wall': clawdata.bc_upper[i] = 3 + if clawdata.bc_upper[i] in [0,'user']: clawdata.bc_upper[i] = 0 + elif clawdata.bc_upper[i] in [1,'extrap']: clawdata.bc_upper[i] = 1 + elif clawdata.bc_upper[i] in [2,'periodic']: clawdata.bc_upper[i] = 2 + elif clawdata.bc_upper[i] in [3,'wall']: clawdata.bc_upper[i] = 3 else: raise AttributeError("Unrecognized bc_upper: %s" \ % clawdata.bc_upper[i]) - data_write(file, clawdata, 'bc_upper') + data_write(file, clawdata.bc_upper, 'bc_upper') data_write(file, clawdata, None) - data_write(file, clawdata, 'restart') - data_write(file, clawdata, 'restart_frame') + data_write(file, clawdata.restart, 'restart') + data_write(file, clawdata.restart_frame, 'restart_frame') data_write(file, clawdata, None) @@ -562,7 +606,8 @@ def write_clawdata_amr(clawdata, file): Write the input parameters only used by AMRClaw. """ - data_write(file, clawdata, 'amr_levels_max') + num_dim = clawdata.num_dim + data_write(file, clawdata.amr_levels_max, 'amr_levels_max') num_ratios = max(abs(clawdata.amr_levels_max)-1, 1) if len(clawdata.refinement_ratio_x) < num_ratios: @@ -571,43 +616,43 @@ def write_clawdata_amr(clawdata, file): if len(clawdata.refinement_ratio_y) < num_ratios: raise ValueError("*** Error in data parameter: " + \ "require len(refinement_ratio_y) >= %s " % num_ratios) - data_write(file, clawdata, 'refinement_ratio_x') - data_write(file, clawdata, 'refinement_ratio_y') + data_write(file, clawdata.refinement_ratio_x, 'refinement_ratio_x') + data_write(file, clawdata.refinement_ratio_y, 'refinement_ratio_y') if num_dim == 3: if len(clawdata.refinement_ratio_z) < num_ratios: raise ValueError("*** Error in data parameter: " + \ "require len(refinement_ratio_z) >= %s " % num_ratios) - data_write(file, clawdata, 'refinement_ratio_z') + data_write(file, clawdata.refinement_ratio_z, 'refinement_ratio_z') if len(clawdata.refinement_ratio_t) < num_ratios: raise ValueError("*** Error in data parameter: " + \ "require len(refinement_ratio_t) >= %s " % num_ratios) - data_write(file, clawdata, 'refinement_ratio_t') + data_write(file, clawdata.refinement_ratio_t, 'refinement_ratio_t') data_write(file, clawdata, None) # writes blank line - data_write(file, clawdata, 'flag_richardson') - data_write(file, clawdata, 'flag_richardson_tol') - data_write(file, clawdata, 'flag2refine') - data_write(file, clawdata, 'flag2refine_tol') - data_write(file, clawdata, 'regrid_interval') - data_write(file, clawdata, 'regrid_buffer_width') - data_write(file, clawdata, 'clustering_cutoff') - data_write(file, clawdata, 'verbosity_regrid') + data_write(file, clawdata.flag_richardson, 'flag_richardson') + data_write(file, clawdata.flag_richardson_tol, 'flag_richardson_tol') + data_write(file, clawdata.flag2refine, 'flag2refine') + data_write(file, clawdata.flag2refine_tol, 'flag2refine_tol') + data_write(file, clawdata.regrid_interval, 'regrid_interval') + data_write(file, clawdata.regrid_buffer_width, 'regrid_buffer_width') + data_write(file, clawdata.clustering_cutoff, 'clustering_cutoff') + data_write(file, clawdata.verbosity_regrid, 'verbosity_regrid') data_write(file, clawdata, None) data_write(file, clawdata, None) - data_write(file, clawdata, 'dprint') - data_write(file, clawdata, 'eprint') - data_write(file, clawdata, 'edebug') - data_write(file, clawdata, 'gprint') - data_write(file, clawdata, 'nprint') - data_write(file, clawdata, 'pprint') - data_write(file, clawdata, 'rprint') - data_write(file, clawdata, 'sprint') - data_write(file, clawdata, 'tprint') - data_write(file, clawdata, 'uprint') + data_write(file, clawdata.dprint, 'dprint') + data_write(file, clawdata.eprint, 'eprint') + data_write(file, clawdata.edebug, 'edebug') + data_write(file, clawdata.gprint, 'gprint') + data_write(file, clawdata.nprint, 'nprint') + data_write(file, clawdata.pprint, 'pprint') + data_write(file, clawdata.rprint, 'rprint') + data_write(file, clawdata.sprint, 'sprint') + data_write(file, clawdata.tprint, 'tprint') + data_write(file, clawdata.uprint, 'uprint') data_write(file, clawdata, None) def regions_and_gauges(): @@ -615,12 +660,12 @@ def regions_and_gauges(): Placeholder... where to put these? """ clawdata.add_attribute('nregions', len(clawdata.regions)) - data_write(file, clawdata, 'nregions') + data_write(file, clawdata.nregions, 'nregions') for regions in clawdata.regions: file.write(8*" %g" % tuple(regions) +"\n") clawdata.add_attribute('ngauges', len(clawdata.gauges)) - data_write(file, clawdata, 'ngauges') + data_write(file, clawdata.ngauges, 'ngauges') gaugeno_used = [] for gauge in clawdata.gauges: gaugeno = gauge[0] @@ -647,8 +692,8 @@ def make_userdatafile(userdata): # write all the parameters: for param in userdata._attributes: - data_write(file, userdata, param, \ - userdata.__descr__[param]) + descr = userdata.__descr__.get(param, '') + data_write(file, getattr(userdata,param), param, descr) file.close() From f7bc61f208e3482ffd50cece7ad850a7f6ac5f23 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Tue, 15 May 2012 17:03:50 +0200 Subject: [PATCH 06/22] New input params works on example1 --- src/python/clawutil/clawdata.py | 75 ++++++++++++++++++++++----------- 1 file changed, 51 insertions(+), 24 deletions(-) diff --git a/src/python/clawutil/clawdata.py b/src/python/clawutil/clawdata.py index 4e9780dd..a7a723ea 100644 --- a/src/python/clawutil/clawdata.py +++ b/src/python/clawutil/clawdata.py @@ -13,7 +13,8 @@ import os import logging - + +import numpy as np # ======================== @@ -196,7 +197,11 @@ def __init__(self, num_dim): self.add_attribute('num_aux',0) self.add_attribute('output_style',1) self.add_attribute('output_times',[]) - self.add_attribute('output_steps',[]) + self.add_attribute('num_output_times',None) + self.add_attribute('output_t0',True) + self.add_attribute('output_step_interval',None) + self.add_attribute('total_steps',None) + self.add_attribute('tfinal',None) self.add_attribute('output_format',1) self.add_attribute('output_q_components','all') self.add_attribute('output_aux_components',[]) @@ -220,7 +225,6 @@ def __init__(self, num_dim): self.add_attribute('num_ghost',2) self.add_attribute('fwave',False) self.add_attribute('restart',False) - self.add_attribute('restart_frame',0) self.add_attribute('restart_file','') self.add_attribute('regions',[]) self.add_attribute('gauges',[]) @@ -457,15 +461,24 @@ def write_clawdata_noamr(clawdata, file): data_write(file, clawdata.t0, 't0') data_write(file, clawdata, None) - num_output_times = len(clawdata.output_times) - data_write(file, num_output_times, 'num_output_times') - if num_output_times > 0: + data_write(file, clawdata.output_style, 'output_style') + + if clawdata.output_style==1: + data_write(file, clawdata.num_output_times, 'num_output_times') + data_write(file, clawdata.tfinal, 'tfinal') + data_write(file, clawdata.output_t0, 'output_t0') + elif clawdata.output_style==2: + clawdata.num_output_times = len(clawdata.output_times) + data_write(file, clawdata.num_output_times, 'num_output_times') data_write(file, clawdata.output_times, 'output_times') - - num_output_steps = len(clawdata.output_steps) - data_write(file, num_output_steps, 'num_output_steps') - if num_output_steps > 0: - data_write(file, clawdata.output_steps, 'output_steps') + elif clawdata.output_style==3: + data_write(file, clawdata.output_step_interval, 'output_step_interval') + data_write(file, clawdata.total_steps, 'total_steps') + data_write(file, clawdata.output_t0, 'output_t0') + else: + raise AttributeError("*** Unrecognized output_style: %s"\ + % clawdata.output_style) + data_write(file, clawdata, None) if clawdata.output_format in [1,'ascii']: @@ -478,20 +491,23 @@ def write_clawdata_noamr(clawdata, file): data_write(file, clawdata.output_format, 'output_format') - clawdata._iout_q = clawdata.num_eqn * [1] - if clawdata.output_q_components != 'all': - for i in range(clawdata.num_eqn): - if i+1 not in clawdata.output_q_components: - clawdata._iout_q[i] = 0 - data_write(file, clawdata._iout_q, '_iout_q') + if clawdata.output_q_components == 'all': + iout_q = clawdata.num_eqn * [1] + elif clawdata.output_q_components == 'none': + iout_q = clawdata.num_eqn * [0] + else: + iout_q = np.where(clawdata.output_q_components, 1, 0) + + data_write(file, iout_q, 'iout_q') if clawdata.num_aux > 0: - clawdata._iout_aux = clawdata.num_aux * [1] - if clawdata.output_aux_components != 'all': - for i in range(clawdata.num_aux): - if i+1 not in clawdata.output_aux_components: - clawdata._iout_aux[i] = 0 - data_write(file, clawdata._iout_aux, '_iout_aux') + if clawdata.output_aux_components == 'all': + iout_aux = clawdata.num_aux * [1] + elif clawdata.output_aux_components == 'none': + iout_aux = clawdata.num_aux * [0] + else: + iout_aux = np.where(clawdata.output_aux_components, 1, 0) + data_write(file, iout_aux, 'iout_aux') data_write(file, clawdata.output_aux_onlyonce, 'output_aux_onlyonce') data_write(file, clawdata, None) @@ -582,7 +598,18 @@ def write_clawdata_noamr(clawdata, file): data_write(file, clawdata, None) data_write(file, clawdata.restart, 'restart') - data_write(file, clawdata.restart_frame, 'restart_frame') + data_write(file, clawdata.restart_file, 'restart_file') + data_write(file, clawdata.checkpt_style, 'checkpt_style') + if clawdata.checkpt_style==2: + num_checkpt_times = len(clawdata.checkpt_times) + data_write(file, num_checkpt_times, 'num_checkpt_times') + data_write(file, clawdata.checkpt_times, 'checkpt_times') + elif clawdata.checkpt_style==3: + data_write(file, checkpt_interval, 'checkpt_interval') + elif clawdata.checkpt_style not in [1,2]: + raise AttributeError("*** Unrecognized checkpt_style: %s"\ + % clawdata.checkpt_style) + data_write(file, clawdata, None) From cb0c253becfff4394f963e227bca0d31fa1982d7 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Tue, 15 May 2012 17:04:38 +0200 Subject: [PATCH 07/22] Modified verbose output in chardiff --- src/python/clawutil/chardiff.py | 20 +++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/src/python/clawutil/chardiff.py b/src/python/clawutil/chardiff.py index b11440c1..dd44747c 100755 --- a/src/python/clawutil/chardiff.py +++ b/src/python/clawutil/chardiff.py @@ -34,6 +34,8 @@ def chardiff_file(fname1, fname2, print_all_lines=True, hfile1='', \ if (len(f1) != len(f2)) and verbose: print "*** files have different number of lines" + print " %s: %s lines" % (fname1,len(f1)) + print " %s: %s lines" % (fname2,len(f2)) flen = min(len(f1), len(f2)) table1 = [] @@ -114,9 +116,6 @@ def chardiff_file(fname1, fname2, print_all_lines=True, hfile1='', \ numchanges = sum(changed) html = open(hfile1,"w") - if verbose: - print "Point your browser to: " - print " view all %s lines with diffs: %s" % (flen, hfile1) hf2 = os.path.split(hfile2)[1] html.write(""" @@ -154,8 +153,6 @@ def chardiff_file(fname1, fname2, print_all_lines=True, hfile1='', \ # Only changed lines: html = open(hfile2,"w") - if verbose: - print " view only %s lines with changes: %s" % (numchanges, hfile2) hf1 = os.path.split(hfile1)[1] html.write(""" @@ -211,7 +208,7 @@ def chardiff_dir(dir1, dir2, file_pattern='all', dir3="_char_diff", checkfiles = filecmp.dircmp(dir1,dir2) allsame = (checkfiles.diff_files==[]) and (checkfiles.left_list == checkfiles.right_list) - if allsame and verbose: + if allsame: print "*All* files in the two directories are equal" elif verbose: if len(checkfiles.diff_files)>0: @@ -343,7 +340,16 @@ def __init__(self, msg): # Run diff if os.path.isfile(args[0]) and os.path.isfile(args[1]): - sys.exit(chardiff_file(args[0],args[1],verbose=verbose)) + try: + hfile1 = "diff_all_lines.html" + hfile2 = "diff_changed_lines.html" + (flen,numchanges) = chardiff_file(args[0],args[1],\ + hfile1=hfile1,hfile2=hfile2,verbose=verbose) + print "View all %s lines with diffs: %s" % (flen, hfile1) + print "View only %s lines with changes: %s" % (numchanges, hfile2) + sys.exit(0) + except: + sys.exit(1) elif os.path.isdir(args[0]) and os.path.isdir(args[1]): if len(args) > 2: if args[2][0] == '[': From d0448549f8da46033120bb03b4ff958e48b96b2e Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Fri, 25 May 2012 15:07:16 +0200 Subject: [PATCH 08/22] Fixes to clawdata.py for new inputs --- src/python/clawutil/clawdata.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/python/clawutil/clawdata.py b/src/python/clawutil/clawdata.py index a7a723ea..10b2976f 100644 --- a/src/python/clawutil/clawdata.py +++ b/src/python/clawutil/clawdata.py @@ -468,6 +468,9 @@ def write_clawdata_noamr(clawdata, file): data_write(file, clawdata.tfinal, 'tfinal') data_write(file, clawdata.output_t0, 'output_t0') elif clawdata.output_style==2: + if len(clawdata.output_times) == 0: + raise AttributeError("*** output_style==2 requires nonempty list" \ + + " of output times") clawdata.num_output_times = len(clawdata.output_times) data_write(file, clawdata.num_output_times, 'num_output_times') data_write(file, clawdata.output_times, 'output_times') @@ -605,7 +608,7 @@ def write_clawdata_noamr(clawdata, file): data_write(file, num_checkpt_times, 'num_checkpt_times') data_write(file, clawdata.checkpt_times, 'checkpt_times') elif clawdata.checkpt_style==3: - data_write(file, checkpt_interval, 'checkpt_interval') + data_write(file, clawdata.checkpt_interval, 'checkpt_interval') elif clawdata.checkpt_style not in [1,2]: raise AttributeError("*** Unrecognized checkpt_style: %s"\ % clawdata.checkpt_style) From c63f30714bbe0bb36f743a171eb9c4376e6c0e74 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Fri, 25 May 2012 15:47:50 +0200 Subject: [PATCH 09/22] Changed some macro names in Makefile.common --- src/Makefile.common | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/src/Makefile.common b/src/Makefile.common index 52c8a892..eb488d1f 100644 --- a/src/Makefile.common +++ b/src/Makefile.common @@ -26,8 +26,8 @@ CLAW_PYTHON ?= $(PYTHON) # Default values if not set: CLAW_EXE ?= xclaw CLAW_PKG ?= classic -OUT_DIR ?= _output -PLOT_DIR ?= _plots +OUTDIR ?= _output +PLOTDIR ?= _plots LIB_PATHS ?= $(CURDIR)/ OVERWRITE ?= True RESTART ?= False @@ -176,9 +176,9 @@ data: $(MAKEFILE_LIST); # runclaw will execute setrun.py to create data files and determine # what executable to run, e.g. xclaw or xamr. .output: $(CLAW_EXE) .data $(MAKEFILE_LIST); - $(CLAW_PYTHON) $(CLAW)/clawutil/src/python/clawutil/runclaw.py $(CLAW_EXE) $(OUT_DIR) \ + $(CLAW_PYTHON) $(CLAW)/clawutil/src/python/clawutil/runclaw.py $(CLAW_EXE) $(OUTDIR) \ $(OVERWRITE) $(RESTART) - @echo $(OUT_DIR) > .output + @echo $(OUTDIR) > .output #---------------------------------------------------------------------------- # Run the code without checking dependencies: @@ -194,12 +194,12 @@ output: $(MAKEFILE_LIST); # Plotting command PLOTCMD ?= $(CLAW_PYTHON) $(VISCLAW)/src/python/visclaw/plotclaw.py -# Rule to make the plots into subdirectory specified by PLOT_DIR, -# using data in subdirectory specified by OUT_DIR and the plotting +# Rule to make the plots into subdirectory specified by PLOTDIR, +# using data in subdirectory specified by OUTDIR and the plotting # commands specified in CLAW_SETPLOT. .plots: .output $(SETPLOT_FILE) $(MAKEFILE_LIST) ; - $(PLOTCMD) $(OUT_DIR) $(PLOT_DIR) $(SETPLOT_FILE) - @echo $(PLOT_DIR) > .plots + $(PLOTCMD) $(OUTDIR) $(PLOTDIR) $(SETPLOT_FILE) + @echo $(PLOTDIR) > .plots # Make the plots without checking dependencies: plots: $(SETPLOT_FILE) $(MAKEFILE_LIST); @@ -241,7 +241,7 @@ clobber: -rm -f $(MODULE_OBJECTS) -rm -f $(MODULE_FILES) -rm -f fort.* *.pyc pyclaw.log - -rm -f -r $(OUT_DIR) $(PLOT_DIR) + -rm -f -r $(OUTDIR) $(PLOTDIR) #---------------------------------------------------------------------------- From 4a6acf027738866e9521a24056599109359bdffd Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Fri, 25 May 2012 15:48:33 +0200 Subject: [PATCH 10/22] Fixed messages printed by runclaw.py --- src/python/clawutil/runclaw.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/python/clawutil/runclaw.py b/src/python/clawutil/runclaw.py index 06bc6108..d872ed04 100644 --- a/src/python/clawutil/runclaw.py +++ b/src/python/clawutil/runclaw.py @@ -22,7 +22,7 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=False, """ import os,glob,shutil,time - verbose = False + verbose = True xclawout = None xclawerr = None @@ -47,11 +47,11 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=False, if rundir is None: rundir = os.getcwd() rundir = os.path.abspath(rundir) - print "Will take data from ", rundir + print "==> runclaw: Will take data from ", rundir # directory for fort.* files: outdir = os.path.abspath(outdir) - print '== runclaw: Will write output to ',outdir + print '==> runclaw: Will write output to ',outdir #returncode = clawjob.runxclaw() From e865ca9e46c475a570da125dfd109e60bc4d498c Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Tue, 2 Oct 2012 14:48:59 -0400 Subject: [PATCH 11/22] Changed behavior of .plots and .output back to what was originally intended --- src/Makefile.common | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/src/Makefile.common b/src/Makefile.common index eb488d1f..5e8cf296 100644 --- a/src/Makefile.common +++ b/src/Makefile.common @@ -164,27 +164,27 @@ Makefile.html : Makefile ; $(CC2HTML) $< # Make data files needed by Fortran code: .data: $(SETRUN_FILE) $(MAKEFILE_LIST) ; - $(CLAW_PYTHON) $(SETRUN_FILE) $(CLAW_PKG) - touch .data + $(MAKE) data data: $(MAKEFILE_LIST); -rm -f .data - $(MAKE) .data + $(CLAW_PYTHON) $(SETRUN_FILE) $(CLAW_PKG) + touch .data #---------------------------------------------------------------------------- # Run the code and put fort.* files into subdirectory named output: # runclaw will execute setrun.py to create data files and determine # what executable to run, e.g. xclaw or xamr. .output: $(CLAW_EXE) .data $(MAKEFILE_LIST); - $(CLAW_PYTHON) $(CLAW)/clawutil/src/python/clawutil/runclaw.py $(CLAW_EXE) $(OUTDIR) \ - $(OVERWRITE) $(RESTART) - @echo $(OUTDIR) > .output + $(MAKE) output #---------------------------------------------------------------------------- # Run the code without checking dependencies: output: $(MAKEFILE_LIST); -rm -f .output - $(MAKE) .output + $(CLAW_PYTHON) $(CLAW)/clawutil/src/python/clawutil/runclaw.py $(CLAW_EXE) $(OUT_DIR) \ + $(OVERWRITE) $(RESTART) + @echo $(OUT_DIR) > .output #---------------------------------------------------------------------------- @@ -194,17 +194,18 @@ output: $(MAKEFILE_LIST); # Plotting command PLOTCMD ?= $(CLAW_PYTHON) $(VISCLAW)/src/python/visclaw/plotclaw.py -# Rule to make the plots into subdirectory specified by PLOTDIR, -# using data in subdirectory specified by OUTDIR and the plotting +# Rule to make the plots into subdirectory specified by PLOT_DIR, +# using data in subdirectory specified by OUT_DIR and the plotting # commands specified in CLAW_SETPLOT. .plots: .output $(SETPLOT_FILE) $(MAKEFILE_LIST) ; - $(PLOTCMD) $(OUTDIR) $(PLOTDIR) $(SETPLOT_FILE) - @echo $(PLOTDIR) > .plots + $(MAKE) plots # Make the plots without checking dependencies: plots: $(SETPLOT_FILE) $(MAKEFILE_LIST); -rm -f .plots - $(MAKE) .plots + $(PLOTCMD) $(OUT_DIR) $(PLOT_DIR) $(SETPLOT_FILE) + @echo $(PLOT_DIR) > .plots + #---------------------------------------------------------------------------- From 3f1717b2964ea90d908908383d94527e5d53dfe2 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Tue, 2 Oct 2012 15:29:39 -0400 Subject: [PATCH 12/22] Changed names in Makefile_common, runclaw. Switched to OUTDIR, EXE, etc. Changed format of backup _output when OVERWRITE=False. --- src/Makefile.common | 30 +++++++++++++++--------------- src/python/clawutil/runclaw.py | 2 +- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/src/Makefile.common b/src/Makefile.common index 5e8cf296..1e1137f9 100644 --- a/src/Makefile.common +++ b/src/Makefile.common @@ -24,7 +24,7 @@ CLAW_PYTHON ?= $(PYTHON) # Variables below should be set in Makefile that "includes" this one. # Default values if not set: -CLAW_EXE ?= xclaw +EXE ?= xclaw CLAW_PKG ?= classic OUTDIR ?= _output PLOTDIR ?= _plots @@ -115,10 +115,10 @@ endif .objs: $(MODULE_FILES) $(OBJECTS); # The order here is to again build the module files correctly -$(CLAW_EXE): $(MODULE_FILES) $(MODULE_OBJECTS) $(OBJECTS) $(MAKEFILE_LIST) ; - $(LINK) $(MODULE_OBJECTS) $(OBJECTS) $(ALL_INCLUDE) $(ALL_LFLAGS) -o $(CLAW_EXE) +$(EXE): $(MODULE_FILES) $(MODULE_OBJECTS) $(OBJECTS) $(MAKEFILE_LIST) ; + $(LINK) $(MODULE_OBJECTS) $(OBJECTS) $(ALL_INCLUDE) $(ALL_LFLAGS) -o $(EXE) -.exe: $(CLAW_EXE) +.exe: $(EXE) debug: @echo 'debugging -- MODULES:' @@ -175,16 +175,16 @@ data: $(MAKEFILE_LIST); # Run the code and put fort.* files into subdirectory named output: # runclaw will execute setrun.py to create data files and determine # what executable to run, e.g. xclaw or xamr. -.output: $(CLAW_EXE) .data $(MAKEFILE_LIST); +.output: $(EXE) .data $(MAKEFILE_LIST); $(MAKE) output #---------------------------------------------------------------------------- # Run the code without checking dependencies: output: $(MAKEFILE_LIST); -rm -f .output - $(CLAW_PYTHON) $(CLAW)/clawutil/src/python/clawutil/runclaw.py $(CLAW_EXE) $(OUT_DIR) \ + $(CLAW_PYTHON) $(CLAW)/clawutil/src/python/clawutil/runclaw.py $(EXE) $(OUTDIR) \ $(OVERWRITE) $(RESTART) - @echo $(OUT_DIR) > .output + @echo $(OUTDIR) > .output #---------------------------------------------------------------------------- @@ -194,17 +194,17 @@ output: $(MAKEFILE_LIST); # Plotting command PLOTCMD ?= $(CLAW_PYTHON) $(VISCLAW)/src/python/visclaw/plotclaw.py -# Rule to make the plots into subdirectory specified by PLOT_DIR, -# using data in subdirectory specified by OUT_DIR and the plotting -# commands specified in CLAW_SETPLOT. +# Rule to make the plots into subdirectory specified by PLOTDIR, +# using data in subdirectory specified by OUTDIR and the plotting +# commands specified in SETPLOT_FILE. .plots: .output $(SETPLOT_FILE) $(MAKEFILE_LIST) ; $(MAKE) plots # Make the plots without checking dependencies: plots: $(SETPLOT_FILE) $(MAKEFILE_LIST); -rm -f .plots - $(PLOTCMD) $(OUT_DIR) $(PLOT_DIR) $(SETPLOT_FILE) - @echo $(PLOT_DIR) > .plots + $(PLOTCMD) $(OUTDIR) $(PLOTDIR) $(SETPLOT_FILE) + @echo $(PLOTDIR) > .plots #---------------------------------------------------------------------------- @@ -227,13 +227,13 @@ new: -rm -f $(OBJECTS) -rm -f $(MODULE_OBJECTS) -rm -f $(MODULE_FILES) - -rm -f $(CLAW_EXE) - $(MAKE) $(CLAW_EXE) MAKELEVEL=0 + -rm -f $(EXE) + $(MAKE) $(EXE) MAKELEVEL=0 # Clean up options: clean: - -rm -f $(CLAW_EXE) $(HTML) + -rm -f $(EXE) $(HTML) -rm -f .data .output .plots .htmls clobber: diff --git a/src/python/clawutil/runclaw.py b/src/python/clawutil/runclaw.py index d872ed04..009244c7 100644 --- a/src/python/clawutil/runclaw.py +++ b/src/python/clawutil/runclaw.py @@ -83,7 +83,7 @@ def runclaw(xclawcmd=None, outdir=None, overwrite=True, restart=False, hour = str(tm[3]).zfill(2) minute = str(tm[4]).zfill(2) second = str(tm[5]).zfill(2) - outdir_backup = outdir + '_%s%s%s-%s%s%s' \ + outdir_backup = outdir + '_%s-%s-%s-%s%s%s' \ % (year,month,day,hour,minute,second) if verbose: print "==> runclaw: Directory already exists: ",os.path.split(outdir)[1] From c0627393e09b1582792c40d3076ce0c5faa70051 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Tue, 2 Oct 2012 15:34:26 -0400 Subject: [PATCH 13/22] Fixed to allow checkpt_style==0 --- src/python/clawutil/clawdata.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/python/clawutil/clawdata.py b/src/python/clawutil/clawdata.py index 10b2976f..e8590713 100644 --- a/src/python/clawutil/clawdata.py +++ b/src/python/clawutil/clawdata.py @@ -609,7 +609,7 @@ def write_clawdata_noamr(clawdata, file): data_write(file, clawdata.checkpt_times, 'checkpt_times') elif clawdata.checkpt_style==3: data_write(file, clawdata.checkpt_interval, 'checkpt_interval') - elif clawdata.checkpt_style not in [1,2]: + elif clawdata.checkpt_style not in [0,1]: raise AttributeError("*** Unrecognized checkpt_style: %s"\ % clawdata.checkpt_style) From 8d4d8563b859d33fee9307f70bf9e582bd858d7e Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Tue, 2 Oct 2012 22:37:27 -0400 Subject: [PATCH 14/22] Changed refinement_ratio to _ratios --- src/python/clawutil/clawdata.py | 34 ++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/src/python/clawutil/clawdata.py b/src/python/clawutil/clawdata.py index e8590713..2bf2ae7c 100644 --- a/src/python/clawutil/clawdata.py +++ b/src/python/clawutil/clawdata.py @@ -267,15 +267,15 @@ def __init__(self, num_dim): super(AmrclawInputData,self).__init__(num_dim) self.add_attribute('amr_levels_max',1) - self.add_attribute('refinement_ratio_x',[1]) - self.add_attribute('refinement_ratio_y',[1]) + self.add_attribute('refinement_ratios_x',[1]) + self.add_attribute('refinement_ratios_y',[1]) if num_dim == 3: - self.add_attribute('refinement_ratio_z',[1]) + self.add_attribute('refinement_ratios_z',[1]) if num_dim == 1: raise Exception("*** 1d AMR not yet supported") self.add_attribute('variable_dt_refinement_ratios',False) - self.add_attribute('refinement_ratio_t',[1]) + self.add_attribute('refinement_ratios_t',[1]) self.add_attribute('aux_type',[]) self.add_attribute('checkpt_style',1) @@ -313,7 +313,7 @@ def __init__(self, num_dim): self.add_attribute('yupper',1.) self.add_attribute('bc_ylower',1) self.add_attribute('bc_yupper',1) - self.add_attribute('refinement_ratio_y',[1,1,1,1,1,1]) + self.add_attribute('refinement_ratios_y',[1,1,1,1,1,1]) def write(self): @@ -640,23 +640,23 @@ def write_clawdata_amr(clawdata, file): data_write(file, clawdata.amr_levels_max, 'amr_levels_max') num_ratios = max(abs(clawdata.amr_levels_max)-1, 1) - if len(clawdata.refinement_ratio_x) < num_ratios: + if len(clawdata.refinement_ratios_x) < num_ratios: raise ValueError("*** Error in data parameter: " + \ - "require len(refinement_ratio_x) >= %s " % num_ratios) - if len(clawdata.refinement_ratio_y) < num_ratios: + "require len(refinement_ratios_x) >= %s " % num_ratios) + if len(clawdata.refinement_ratios_y) < num_ratios: raise ValueError("*** Error in data parameter: " + \ - "require len(refinement_ratio_y) >= %s " % num_ratios) - data_write(file, clawdata.refinement_ratio_x, 'refinement_ratio_x') - data_write(file, clawdata.refinement_ratio_y, 'refinement_ratio_y') + "require len(refinement_ratios_y) >= %s " % num_ratios) + data_write(file, clawdata.refinement_ratios_x, 'refinement_ratios_x') + data_write(file, clawdata.refinement_ratios_y, 'refinement_ratios_y') if num_dim == 3: - if len(clawdata.refinement_ratio_z) < num_ratios: + if len(clawdata.refinement_ratios_z) < num_ratios: raise ValueError("*** Error in data parameter: " + \ - "require len(refinement_ratio_z) >= %s " % num_ratios) - data_write(file, clawdata.refinement_ratio_z, 'refinement_ratio_z') - if len(clawdata.refinement_ratio_t) < num_ratios: + "require len(refinement_ratios_z) >= %s " % num_ratios) + data_write(file, clawdata.refinement_ratios_z, 'refinement_ratios_z') + if len(clawdata.refinement_ratios_t) < num_ratios: raise ValueError("*** Error in data parameter: " + \ - "require len(refinement_ratio_t) >= %s " % num_ratios) - data_write(file, clawdata.refinement_ratio_t, 'refinement_ratio_t') + "require len(refinement_ratios_t) >= %s " % num_ratios) + data_write(file, clawdata.refinement_ratios_t, 'refinement_ratios_t') data_write(file, clawdata, None) # writes blank line From 20fa4cb2a98a1a632823260547154ca9c90e051a Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Wed, 3 Oct 2012 20:51:35 -0400 Subject: [PATCH 15/22] Fixed aux_type omission and added conversion routine for 2d amrclaw setrun.py. --- src/python/clawutil/clawdata.py | 2 + .../conversion/convert_setrun_amrclaw_2d.py | 95 +++++ .../conversion/setrun_template_amrclaw_2d.py | 326 ++++++++++++++++++ 3 files changed, 423 insertions(+) create mode 100644 src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py create mode 100644 src/python/clawutil/conversion/setrun_template_amrclaw_2d.py diff --git a/src/python/clawutil/clawdata.py b/src/python/clawutil/clawdata.py index 2bf2ae7c..6af9d5ac 100644 --- a/src/python/clawutil/clawdata.py +++ b/src/python/clawutil/clawdata.py @@ -561,6 +561,8 @@ def write_clawdata_noamr(clawdata, file): data_write(file, clawdata.source_split, 'source_split') data_write(file, clawdata.capa_index, 'capa_index') + if clawdata.num_aux > 0: + data_write(file, clawdata.aux_type, 'aux_type') data_write(file, clawdata.fwave, 'fwave') data_write(file, clawdata, None) diff --git a/src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py b/src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py new file mode 100644 index 00000000..4efec909 --- /dev/null +++ b/src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py @@ -0,0 +1,95 @@ +""" +Conversion module for 2d amrclaw setrun.py file from 4.6 to 5.0 format. +""" + + +import os,sys + +clawutil = os.environ['CLAWUTIL'] + '/src/python/clawutil' +template = open(clawutil + '/conversion/setrun_template_amrclaw_2d.py').read() + +sys.path.insert(0,os.getcwd()) + +def convert(setrun_file='setrun.py'): + + setrun_module = os.path.splitext(setrun_file)[0] + exec('from %s import setrun' % setrun_module) + + rundata = setrun() + c = rundata.clawdata + + limiter_map = {0:'none',1:'minmod',2:'superbee',3:'mc',4:'vanleer'} + limiter = [limiter_map.get(i,i) for i in c.mthlim] + print "limiter: ", c.mthlim, limiter + + + bc_map = {0:'user', 1:'extrap', 2:'periodic', 3:'wall'} + for b in ['xlower','xupper','ylower','yupper']: + exec("s = bc_map.get(c.mthbc_%s, c.mthbc_%s)" % (b,b)) + if type(s) is str: + exec("""mthbc_%s = "'%s'" """ % (b,s)) + else: + exec("mthbc_%s = '%s'" % (b,s)) + + + mapping = { + 'xlower': c.xlower, + 'xupper': c.xupper, + 'ylower': c.ylower, + 'yupper': c.yupper, + 'mx': c.mx, + 'my': c.my, + 'num_eqn': c.meqn, + 'num_aux': c.maux, + 'capa_index': c.mcapa, + 't0': c.t0, + 'num_output_times': c.nout, + 'tfinal': c.tfinal, + 'dt_variable': str(c.dt_variable==1), + 'dt_initial': c.dt_initial, + 'dt_max': c.dt_max, + 'cfl_desired': c.cfl_desired, + 'cfl_max': c.cfl_max, + 'steps_max': c.max_steps, + 'order': c.order, + 'transverse_waves': c.order_trans, + 'num_waves': c.mwaves, + 'limiter': str(limiter), + 'source_split': c.src_split, + 'num_ghost': c.mbc, + 'mthbc_xlower': mthbc_xlower, + 'mthbc_xupper': mthbc_xupper, + 'mthbc_ylower': mthbc_ylower, + 'mthbc_yupper': mthbc_yupper, + 'amr_levels_max': abs(c.mxnest), + 'refinement_ratios_x': str(c.inratx), + 'refinement_ratios_y': str(c.inraty), + 'refinement_ratios_t': str(c.inratt), + 'aux_type': str(c.auxtype), + 'flag_richardson': str(c.tol > 0.), + 'flag_richardson_tol': abs(c.tol), + 'flag2refine': str(c.tolsp > 0.), + 'flag2refine_tol': c.tolsp, + 'regrid_interval': c.kcheck, + 'regrid_buffer_width': c.ibuff, + 'clustering_cutoff': c.cutoff, + } + + newtext = template.format(**mapping) + new_setrun_file = 'new_' + setrun_file + + setrun_text = open(setrun_file).readlines() + for line in setrun_text: + if "new_UserData" in line: + if line.strip()[0] != '#': + print "*** Warning: call to new_UserData detected..." + print line + print "*** User data lines from %s have NOT been copied to %s"\ + % (setrun_file, new_setrun_file) + + + open(new_setrun_file,'w').write(newtext) + print 'Created ', new_setrun_file + +if __name__ == "__main__": + convert(*sys.argv[1:]) diff --git a/src/python/clawutil/conversion/setrun_template_amrclaw_2d.py b/src/python/clawutil/conversion/setrun_template_amrclaw_2d.py new file mode 100644 index 00000000..94226805 --- /dev/null +++ b/src/python/clawutil/conversion/setrun_template_amrclaw_2d.py @@ -0,0 +1,326 @@ +""" +Module to set up run time parameters for Clawpack. + +The values set in the function setrun are then written out to data files +that will be read in by the Fortran code. + +""" + +import os +import numpy as np + +#------------------------------ +def setrun(claw_pkg='amrclaw'): +#------------------------------ + + """ + Define the parameters used for running Clawpack. + + INPUT: + claw_pkg expected to be "amrclaw" for this setrun. + + OUTPUT: + rundata - object of class ClawRunData + + """ + + from clawpack.clawutil import clawdata + + + assert claw_pkg.lower() == 'amrclaw', "Expected claw_pkg = 'amrclaw'" + + num_dim = 2 + rundata = clawdata.ClawRunData(claw_pkg, num_dim) + + #------------------------------------------------------------------ + # Problem-specific parameters to be written to setprob.data: + #------------------------------------------------------------------ + # Sample setup to write one line to setprob.data ... + #probdata = rundata.new_UserData(name='probdata',fname='setprob.data') + #probdata.add_param('u', 0.5, 'ubar advection velocity') + + #------------------------------------------------------------------ + # Standard Clawpack parameters to be written to claw.data: + # (or to amrclaw.data for AMR) + #------------------------------------------------------------------ + + clawdata = rundata.clawdata # initialized when rundata instantiated + + + # Set single grid parameters first. + # See below for AMR parameters. + + + # --------------- + # Spatial domain: + # --------------- + + # Number of space dimensions: + clawdata.num_dim = num_dim + + # Lower and upper edge of computational domain: + clawdata.lower[0] = {xlower:e} # xlower + clawdata.upper[0] = {xupper:e} # xupper + clawdata.lower[1] = {ylower:e} # ylower + clawdata.upper[1] = {yupper:e} # yupper + + # Number of grid cells: + clawdata.num_cells[0] = {mx:d} # mx + clawdata.num_cells[1] = {my:d} # my + + + # --------------- + # Size of system: + # --------------- + + # Number of equations in the system: + clawdata.num_eqn = {num_eqn:d} + + # Number of auxiliary variables in the aux array (initialized in setaux) + clawdata.num_aux = {num_aux:d} + + # Index of aux array corresponding to capacity function, if there is one: + clawdata.capa_index = {capa_index:d} + + + # ------------- + # Initial time: + # ------------- + + clawdata.t0 = {t0:f} + + + # Restart from checkpoint file of a previous run? + # Note: If restarting, you must also change the Makefile to set: + # RESTART = True + # If restarting, t0 above should be from original run, and the + # restart_file 'fort.chkNNNNN' specified below should be in + # the OUTDIR indicated in Makefile. + + clawdata.restart = False # True to restart from prior results + clawdata.restart_file = 'fort.chk00006' # File to use for restart data + + + # ------------- + # Output times: + #-------------- + + # Specify at what times the results should be written to fort.q files. + # Note that the time integration stops after the final output time. + + clawdata.output_style = 1 + + if clawdata.output_style==1: + # Output ntimes frames at equally spaced times up to tfinal: + # Can specify num_output_times = 0 for no output + clawdata.num_output_times = {num_output_times:d} + clawdata.tfinal = {tfinal:f} + clawdata.output_t0 = True # output at initial (or restart) time? + + elif clawdata.output_style == 2: + # Specify a list or numpy array of output times: + # Include t0 if you want output at the initial time. + clawdata.output_times = [0., 0.1] + + elif clawdata.output_style == 3: + # Output every step_interval timesteps over total_steps timesteps: + clawdata.output_step_interval = 2 + clawdata.total_steps = 4 + clawdata.output_t0 = True # output at initial (or restart) time? + + + clawdata.output_format == 'ascii' # 'ascii' or 'netcdf' + + clawdata.output_q_components = 'all' # could be list such as [True,True] + clawdata.output_aux_components = 'none' # could be list + clawdata.output_aux_onlyonce = True # output aux arrays only at t0 + + + # --------------------------------------------------- + # Verbosity of messages to screen during integration: + # --------------------------------------------------- + + # The current t, dt, and cfl will be printed every time step + # at AMR levels <= verbosity. Set verbosity = 0 for no printing. + # (E.g. verbosity == 2 means print only on levels 1 and 2.) + clawdata.verbosity = 0 + + + + # -------------- + # Time stepping: + # -------------- + + # if dt_variable==True: variable time steps used based on cfl_desired, + # if dt_variable==False: fixed time steps dt = dt_initial always used. + clawdata.dt_variable = {dt_variable:s} + + # Initial time step for variable dt. + # (If dt_variable==0 then dt=dt_initial for all steps) + clawdata.dt_initial = {dt_initial:e} + + # Max time step to be allowed if variable dt used: + clawdata.dt_max = {dt_max:e} + + # Desired Courant number if variable dt used + clawdata.cfl_desired = {cfl_desired:f} + # max Courant number to allow without retaking step with a smaller dt: + clawdata.cfl_max = {cfl_max:f} + + # Maximum number of time steps to allow between output times: + clawdata.steps_max = {steps_max:d} + + + # ------------------ + # Method to be used: + # ------------------ + + # Order of accuracy: 1 => Godunov, 2 => Lax-Wendroff plus limiters + clawdata.order = {order:d} + + # Use dimensional splitting? (not yet available for AMR) + clawdata.dimensional_split = 'unsplit' + + # For unsplit method, transverse_waves can be + # 0 or 'none' ==> donor cell (only normal solver used) + # 1 or 'increment' ==> corner transport of waves + # 2 or 'all' ==> corner transport of 2nd order corrections too + clawdata.transverse_waves = {transverse_waves:d} + + + # Number of waves in the Riemann solution: + clawdata.num_waves = {num_waves:d} + + # List of limiters to use for each wave family: + # Required: len(limiter) == num_waves + # Some options: + # 0 or 'none' ==> no limiter (Lax-Wendroff) + # 1 or 'minmod' ==> minmod + # 2 or 'superbee' ==> superbee + # 3 or 'mc' ==> MC limiter + # 4 or 'vanleer' ==> van Leer + clawdata.limiter = {limiter:s} + + clawdata.fwave = False # True ==> use f-wave version of algorithms + + # Source terms splitting: + # src_split == 0 or 'none' ==> no source term (src routine never called) + # src_split == 1 or 'godunov' ==> Godunov (1st order) splitting used, + # src_split == 2 or 'strang' ==> Strang (2nd order) splitting used, not recommended. + clawdata.source_split = {source_split:d} + + + # -------------------- + # Boundary conditions: + # -------------------- + + # Number of ghost cells (usually 2) + clawdata.num_ghost = {num_ghost:d} + + # Choice of BCs at xlower and xupper: + # 0 or 'user' => user specified (must modify bcNamr.f to use this option) + # 1 or 'extrap' => extrapolation (non-reflecting outflow) + # 2 or 'periodic' => periodic (must specify this at both boundaries) + # 3 or 'wall' => solid wall for systems where q(2) is normal velocity + + clawdata.bc_lower[0] = {mthbc_xlower:s} # at xlower + clawdata.bc_upper[0] = {mthbc_xupper:s} # at xupper + + clawdata.bc_lower[1] = {mthbc_ylower:s} # at ylower + clawdata.bc_upper[1] = {mthbc_yupper:s} # at yupper + + + + # --------------- + # AMR parameters: + # --------------- + + + # max number of refinement levels: + clawdata.amr_levels_max = {amr_levels_max:d} + + # List of refinement ratios at each level (length at least amr_level_max-1) + clawdata.refinement_ratios_x = {refinement_ratios_x:s} + clawdata.refinement_ratios_y = {refinement_ratios_y:s} + clawdata.refinement_ratios_t = {refinement_ratios_t:s} + + + # Specify type of each aux variable in clawdata.auxtype. + # This must be a list of length num_aux, each element of which is one of: + # 'center', 'capacity', 'xleft', or 'yleft' (see documentation). + clawdata.aux_type = {aux_type:s} + + + # Flag for refinement based on Richardson error estimater: + clawdata.flag_richardson = {flag_richardson:s} # use Richardson? + clawdata.flag_richardson_tol = {flag_richardson_tol:e} # Richardson tolerance + + # Flag for refinement using routine flag2refine: + clawdata.flag2refine = {flag2refine:s} # use this? + clawdata.flag2refine_tol = {flag2refine_tol:e} # tolerance used in this routine + # User can modify flag2refine to change the criterion for flagging. + # Default: check maximum absolute difference of first component of q + # between a cell and each of its neighbors. + + # steps to take on each level L between regriddings of level L+1: + clawdata.regrid_interval = {regrid_interval:d} + + # width of buffer zone around flagged points: + # (typically the same as regrid_interval so waves don't escape): + clawdata.regrid_buffer_width = {regrid_buffer_width:d} + + # clustering alg. cutoff for (# flagged pts) / (total # of cells refined) + # (closer to 1.0 => more small grids may be needed to cover flagged cells) + clawdata.clustering_cutoff = {clustering_cutoff:f} + + # print info about each regridding up to this level: + clawdata.verbosity_regrid = 0 + + # Specify when checkpoint files should be created that can be + # used to restart a computation. + + clawdata.checkpt_style = 1 + + if clawdata.checkpt_style == 0: + # Do not checkpoint at all + pass + + elif clawdata.checkpt_style == 1: + # Checkpoint only at tfinal. + pass + + elif clawdata.checkpt_style == 2: + # Specify a list of checkpoint times. + clawdata.checkpt_times = [0.1,0.15] + + elif clawdata.checkpt_style == 3: + # Checkpoint every checkpt_interval timesteps (on Level 1) + # and at the final time. + clawdata.checkpt_interval = 5 + + + # ----- For developers ----- + # Toggle debugging print statements: + clawdata.dprint = False # print domain flags + clawdata.eprint = False # print err est flags + clawdata.edebug = False # even more err est flags + clawdata.gprint = False # grid bisection/clustering + clawdata.nprint = False # proper nesting output + clawdata.pprint = False # proj. of tagged points + clawdata.rprint = False # print regridding summary + clawdata.sprint = False # space/memory output + clawdata.tprint = False # time step reporting each level + clawdata.uprint = False # update/upbnd reporting + + return rundata + + # end of function setrun + # ---------------------- + + +if __name__ == '__main__': + # Set up run-time parameters and write all data files. + import sys + rundata = setrun(*sys.argv[1:]) + rundata.write() + From f76a17a42d6dce91be844eae4ab74e5071079da6 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Fri, 5 Oct 2012 20:29:08 -0400 Subject: [PATCH 16/22] Added gauges. Also regions, but not yet implemented in Fortran. --- src/python/clawutil/clawdata.py | 2 +- .../conversion/convert_setrun_amrclaw_2d.py | 15 ++++++++++++++ .../conversion/setrun_template_amrclaw_2d.py | 20 +++++++++++++++++++ 3 files changed, 36 insertions(+), 1 deletion(-) diff --git a/src/python/clawutil/clawdata.py b/src/python/clawutil/clawdata.py index 6af9d5ac..fe74ec64 100644 --- a/src/python/clawutil/clawdata.py +++ b/src/python/clawutil/clawdata.py @@ -319,7 +319,7 @@ def __init__(self, num_dim): def write(self): print 'Creating data file amrclaw.data for use with xamr' make_amrclawdatafile(self) - #make_setgauges_datafile(self) + make_setgauges_datafile(self) diff --git a/src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py b/src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py index 4efec909..3cdb1bdb 100644 --- a/src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py +++ b/src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py @@ -31,6 +31,19 @@ def convert(setrun_file='setrun.py'): else: exec("mthbc_%s = '%s'" % (b,s)) + try: + gauges = c.gauges + except: + gauges = [] + + try: + regions = c.regions + except: + regions = [] + + + # ------------------------------------------------- + # Mapping from old setrun variables to new ones: mapping = { 'xlower': c.xlower, @@ -73,6 +86,8 @@ def convert(setrun_file='setrun.py'): 'regrid_interval': c.kcheck, 'regrid_buffer_width': c.ibuff, 'clustering_cutoff': c.cutoff, + 'gauges': gauges, + 'regions': regions, } newtext = template.format(**mapping) diff --git a/src/python/clawutil/conversion/setrun_template_amrclaw_2d.py b/src/python/clawutil/conversion/setrun_template_amrclaw_2d.py index 94226805..c7cb4d9e 100644 --- a/src/python/clawutil/conversion/setrun_template_amrclaw_2d.py +++ b/src/python/clawutil/conversion/setrun_template_amrclaw_2d.py @@ -229,6 +229,13 @@ def setrun(claw_pkg='amrclaw'): clawdata.bc_lower[1] = {mthbc_ylower:s} # at ylower clawdata.bc_upper[1] = {mthbc_yupper:s} # at yupper + + # --------------- + # Gauges: + # --------------- + clawdata.gauges = {gauges:s} + # for gauges append lines of the form [gaugeno, x, y, t1, t2] + # --------------- @@ -276,6 +283,19 @@ def setrun(claw_pkg='amrclaw'): # print info about each regridding up to this level: clawdata.verbosity_regrid = 0 + + # --------------- + # Regions: + # --------------- + clawdata.regions = {regions:s} + # to specify regions of refinement append lines of the form + # [minlevel,maxlevel,t1,t2,x1,x2,y1,y2] + + + # -------------- + # Checkpointing: + # -------------- + # Specify when checkpoint files should be created that can be # used to restart a computation. From 6f9d93b750bad8764100d8544a9470c14cdbb161 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Sun, 7 Oct 2012 15:30:51 -0400 Subject: [PATCH 17/22] improved conversion tool - added Makefile, use claw_pkg --- src/python/clawutil/clawdata.py | 2 + .../clawutil/conversion/Makefile_amrclaw_2d | 134 ++ .../conversion/convert_setrun_amrclaw_2d.py | 56 +- .../clawutil/conversion/pyclaw/__init__.py | 3 + src/python/clawutil/conversion/pyclaw/data.py | 1429 +++++++++++++++++ 5 files changed, 1618 insertions(+), 6 deletions(-) create mode 100644 src/python/clawutil/conversion/Makefile_amrclaw_2d create mode 100644 src/python/clawutil/conversion/pyclaw/__init__.py create mode 100644 src/python/clawutil/conversion/pyclaw/data.py diff --git a/src/python/clawutil/clawdata.py b/src/python/clawutil/clawdata.py index fe74ec64..f7801115 100644 --- a/src/python/clawutil/clawdata.py +++ b/src/python/clawutil/clawdata.py @@ -320,6 +320,8 @@ def write(self): print 'Creating data file amrclaw.data for use with xamr' make_amrclawdatafile(self) make_setgauges_datafile(self) + if len(self.regions) > 0: + print "*** Warning: regions not yet implemented!" diff --git a/src/python/clawutil/conversion/Makefile_amrclaw_2d b/src/python/clawutil/conversion/Makefile_amrclaw_2d new file mode 100644 index 00000000..c546adf4 --- /dev/null +++ b/src/python/clawutil/conversion/Makefile_amrclaw_2d @@ -0,0 +1,134 @@ + +# Makefile for Clawpack code in this directory. +# This version only sets the local files and frequently changed +# options, and then includes the standard makefile pointed to by CLAWMAKE. +CLAWMAKE = $(CLAWUTIL)/src/Makefile.common + +# See the above file for details and a list of make options, or type +# make .help +# at the unix prompt. + + +# Adjust these variables if desired: +# ---------------------------------- + +CLAW_PKG = amrclaw # Clawpack package to use +EXE = xamr # Executable to create +SETRUN_FILE = setrun.py # File containing function to make data +OUTDIR = _output # Directory for output +SETPLOT_FILE = setplot.py # File containing function to set plots +PLOTDIR = _plots # Directory for plots + +OVERWRITE ?= True # False ==> make a copy of OUTDIR first +RESTART ?= False # Should = clawdata.restart in setrun + +# Environment variable FC should be set to fortran compiler, e.g. gfortran +FC ?= gfortran # default if not set as environment variable +# Add any desired compiler flags such as -g here: +FFLAGS ?= -O2 +#FFLAGS = -W -Wall -fbounds-check -Wunderflow -O -ffpe-trap=zero,overflow,underflow -g + +# --------------------------------- +# List of sources for this program: +# --------------------------------- +MODULES = \ + $(AMRCLAW)/src/2d/amr_module.f90 \ + +SOURCES = \ + qinit.f \ + setprob.f \ + $(RIEMANN)/src/rpn2_advection.f \ + $(RIEMANN)/src/rpt2_advection.f \ + $(AMRCLAW)/src/2d/amr2.f \ + $(AMRCLAW)/src/2d/setaux.f \ + $(AMRCLAW)/src/2d/bc2amr.f \ + $(AMRCLAW)/src/2d/b4step2.f \ + $(AMRCLAW)/src/2d/qad.f \ + $(AMRCLAW)/src/2d/src2.f \ + $(AMRCLAW)/src/2d/src1d.f \ + $(AMRCLAW)/src/2d/advanc.f \ + $(AMRCLAW)/src/2d/bound.f \ + $(AMRCLAW)/src/2d/stepgrid.f \ + $(AMRCLAW)/src/2d/auxcoarsen.f \ + $(AMRCLAW)/src/2d/fixcapaq.f \ + $(AMRCLAW)/src/2d/estdt.f \ + $(AMRCLAW)/src/2d/igetsp.f \ + $(AMRCLAW)/src/2d/reclam.f \ + $(AMRCLAW)/src/2d/birect.f \ + $(AMRCLAW)/src/2d/cleanup.f \ + $(AMRCLAW)/src/2d/colate.f \ + $(AMRCLAW)/src/2d/bufnst.f \ + $(AMRCLAW)/src/2d/spest.f \ + $(AMRCLAW)/src/2d/flag2refine.f \ + $(AMRCLAW)/src/2d/allowflag.f \ + $(AMRCLAW)/src/2d/errest.f \ + $(AMRCLAW)/src/2d/errf1.f \ + $(AMRCLAW)/src/2d/gfixup.f \ + $(AMRCLAW)/src/2d/filval.f \ + $(AMRCLAW)/src/2d/filpatch.f \ + $(AMRCLAW)/src/2d/prefilp.f \ + $(AMRCLAW)/src/2d/flglvl.f \ + $(AMRCLAW)/src/2d/fluxad.f \ + $(AMRCLAW)/src/2d/fluxsv.f \ + $(AMRCLAW)/src/2d/ginit.f \ + $(AMRCLAW)/src/2d/grdfit.f \ + $(AMRCLAW)/src/2d/intfil.f \ + $(AMRCLAW)/src/2d/moment.f \ + $(AMRCLAW)/src/2d/nestck.f \ + $(AMRCLAW)/src/2d/prepf.f \ + $(AMRCLAW)/src/2d/prepc.f \ + $(AMRCLAW)/src/2d/projec.f \ + $(AMRCLAW)/src/2d/signs.f \ + $(AMRCLAW)/src/2d/findcut.f \ + $(AMRCLAW)/src/2d/smartbis.f \ + $(AMRCLAW)/src/2d/putnod.f \ + $(AMRCLAW)/src/2d/putsp.f \ + $(AMRCLAW)/src/2d/regrid.f \ + $(AMRCLAW)/src/2d/setgrd.f \ + $(AMRCLAW)/src/2d/setuse.f \ + $(AMRCLAW)/src/2d/stst1.f \ + $(AMRCLAW)/src/2d/tick.f \ + $(AMRCLAW)/src/2d/trimbd.f \ + $(AMRCLAW)/src/2d/update.f \ + $(AMRCLAW)/src/2d/nodget.f \ + $(AMRCLAW)/src/2d/upbnd.f \ + $(AMRCLAW)/src/2d/basic.f \ + $(AMRCLAW)/src/2d/outval.f \ + $(AMRCLAW)/src/2d/copysol.f \ + $(AMRCLAW)/src/2d/outvar.f \ + $(AMRCLAW)/src/2d/outmsh.f \ + $(AMRCLAW)/src/2d/outtre.f \ + $(AMRCLAW)/src/2d/domain.f \ + $(AMRCLAW)/src/2d/setflags.f \ + $(AMRCLAW)/src/2d/shiftset.f \ + $(AMRCLAW)/src/2d/conck.f \ + $(AMRCLAW)/src/2d/domshrink.f \ + $(AMRCLAW)/src/2d/domprep.f \ + $(AMRCLAW)/src/2d/domup.f \ + $(AMRCLAW)/src/2d/domcopy.f \ + $(AMRCLAW)/src/2d/coarsen.f \ + $(AMRCLAW)/src/2d/intcopy.f \ + $(AMRCLAW)/src/2d/preintcopy.f \ + $(AMRCLAW)/src/2d/icall.f \ + $(AMRCLAW)/src/2d/preicall.f \ + $(AMRCLAW)/src/2d/step2.f90 \ + $(AMRCLAW)/src/2d/flux2.f \ + $(AMRCLAW)/src/2d/inlinelimiter.f \ + $(AMRCLAW)/src/2d/cstore.f \ + $(AMRCLAW)/src/2d/saveqc.f \ + $(AMRCLAW)/src/2d/valout.f \ + $(AMRCLAW)/src/2d/check.f \ + $(AMRCLAW)/src/2d/restrt.f \ + $(AMRCLAW)/src/2d/setgauges.f \ + $(AMRCLAW)/src/2d/dumpgauge.f \ + $(AMRCLAW)/src/2d/quick_sort1.f \ + $(AMRCLAW)/src/2d/opendatafile.f \ + $(AMRCLAW)/src/2d/init_alloc.f90 \ + $(AMRCLAW)/src/2d/restrt_alloc.f90 \ + $(AMRCLAW)/src/2d/resize_alloc.f90 \ +# $(AMRCLAW)/src/2d/resize_alloc_static.f90 \ + +#------------------------------------------------------------------- +# Include Makefile containing standard definitions and make options: +include $(CLAWMAKE) + diff --git a/src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py b/src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py index 3cdb1bdb..9cde34aa 100644 --- a/src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py +++ b/src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py @@ -6,11 +6,29 @@ import os,sys clawutil = os.environ['CLAWUTIL'] + '/src/python/clawutil' -template = open(clawutil + '/conversion/setrun_template_amrclaw_2d.py').read() +template_amrclaw_2d = open(clawutil \ + + '/conversion/setrun_template_amrclaw_2d.py').read() sys.path.insert(0,os.getcwd()) +sys.path.append(os.getcwd() + '/pyclaw') -def convert(setrun_file='setrun.py'): +def convert(setrun_file='setrun.py', claw_pkg=None): + + setrun_text = open(setrun_file).readlines() + if claw_pkg is None: + for line in setrun_text: + if 'claw_pkg' in line: + if 'classic' in line: + claw_pkg = 'classic' + elif 'amrclaw' in line: + claw_pkg = 'amrclaw' + elif 'geoclaw' in line: + claw_pkg = 'geoclaw' + + if claw_pkg is None: + raise ValueError("*** Could not determine claw_pkg from %s" \ + % setrun_file) + setrun_module = os.path.splitext(setrun_file)[0] exec('from %s import setrun' % setrun_module) @@ -90,8 +108,11 @@ def convert(setrun_file='setrun.py'): 'regions': regions, } - newtext = template.format(**mapping) - new_setrun_file = 'new_' + setrun_file + if claw_pkg == 'amrclaw': + newtext = template_amrclaw_2d.format(**mapping) + else: + raise ValueError("*** convert not yet implemented for %s" \ + % claw_pkg) setrun_text = open(setrun_file).readlines() for line in setrun_text: @@ -103,8 +124,31 @@ def convert(setrun_file='setrun.py'): % (setrun_file, new_setrun_file) - open(new_setrun_file,'w').write(newtext) - print 'Created ', new_setrun_file + os.system("mv %s original_%s" % (setrun_file,setrun_file)) + print 'Moved %s to original_%s ' % (setrun_file,setrun_file) + open(setrun_file,'w').write(newtext) + print 'Created ', setrun_file + + copy_Makefile(claw_pkg) + + +def copy_Makefile(claw_pkg): + import pdb; pdb.set_trace() + if claw_pkg == 'amrclaw': + try: + os.system("mv Makefile original_Makefile") + os.system("cp %s/conversion/Makefile_amrclaw_2d Makefile" \ + % clawutil) + except: + raise Exception("*** Error copying Makefile") + else: + raise ValueError("*** convert not yet implemented for %s" \ + % claw_pkg) + + print "Moved Makefile to original_Makefile" + print "Created new Makefile template -- must be customized!" + print "*** Edit Makefile based on original_Makefile, e.g. point to" + print "*** any local files, correct Riemann solver, etc." if __name__ == "__main__": convert(*sys.argv[1:]) diff --git a/src/python/clawutil/conversion/pyclaw/__init__.py b/src/python/clawutil/conversion/pyclaw/__init__.py new file mode 100644 index 00000000..8611613a --- /dev/null +++ b/src/python/clawutil/conversion/pyclaw/__init__.py @@ -0,0 +1,3 @@ + +__all__ = ['data'] + diff --git a/src/python/clawutil/conversion/pyclaw/data.py b/src/python/clawutil/conversion/pyclaw/data.py new file mode 100644 index 00000000..acda3564 --- /dev/null +++ b/src/python/clawutil/conversion/pyclaw/data.py @@ -0,0 +1,1429 @@ +#!/usr/bin/env python +# encoding: utf-8 +r""" +Data Module + +Contains the general class definition and the subclasses of the Clawpack data +objects. + +:Authors: + Kyle T. Mandli and Randall J. LeVeque (2008-08-07) Initial version + + Randall J. LeVeque (2008-08-07) Plotting data objects + + Alan McIntyre (2009-01-01) Speed ups and rebuilding of Data + + Kyle T. Mandli (2009-04-01) Stripped down and improved version +""" +# ============================================================================ +# Copyright (C) 2008 Kyle T. Mandli +# Copyright (C) 2008 Randall J. LeVeque +# Copyright (C) 2009 Alan McIntyre +# +# Distributed under the terms of the Berkeley Software Distribution (BSD) +# license +# http://www.opensource.org/licenses/ +# ============================================================================ + +import shutil +import os +import copy +import re +import logging + +# ========== Parse Value Utility Function ==================================== +def _parse_value(value): + r""" + Attempt to make sense of a value string from a config file. If the + value is not obviously an integer, float, or boolean, it is returned as + a string stripped of leading and trailing whitespace. + + :Input: + - *value* - (string) Value string to be parsed + + :Output: + - (id) - Appropriate object based on *value* + """ + value = value.strip() + if not value: + return None + + # assume that values containing spaces are lists of values + if len(value.split()) > 1: + return [_parse_value(vv) for vv in value.split()] + + try: + # see if it's an integer + value = int(value) + except ValueError: + try: + # see if it's a float + value = float(value) + except ValueError: + # see if it's a bool + if value[0] == 'T': + value = True + elif value[0] == 'F': + value = False + + return value + + +# ============================================================================ +# General Data Class +# ============================================================================ +class Data(object): + r""" + Generalized clawpack data object + + Generalized class for Clawpack data. Contains generic methods for reading + and writing data to and from a data file. + + :Initialization: + Input: + - *data_files* - (List of strings) Paths to data files to be read in, + an empty data object can be created by providing no data files. + - *attributes* - (List of strings) List of required attribute names + which will be initialized to None. + + :Version: 1.2 (2009-04-01) + """ + + __name__ = 'Data' + + def __init__(self, data_files=[], attributes=None): + """ + Initialize a Data object + + See :class:`Data` for more info. + """ + + # Internal bookkeeping variables + self.__attributes = [] + self.__owners = {} + + # Setup data logger + self.logger = logging.getLogger('data') + + # Initialize from attribute list provided + if attributes: + for attr in attributes: + self.add_attribute(attr,None,None) + + # Read data files from data_files list + if isinstance(data_files, basestring): + data_files = [data_files] + elif not isinstance(data_files, list): + raise Exception("data_files must be a list of strings") + + if len(data_files) > 0: + self.read(data_files) + + # ========== Return string representation of this Data Object ======== + def __str__(self): + output = "%s%s%s\n" % ("Name".ljust(25),"Value".ljust(12), + "Owner".ljust(12)) + for (k,v) in self.iteritems(): + output += "%s%s%s\n" % (str(k).ljust(25), + str(v).ljust(12), + str(self.__owners[k]).ljust(12)) + return output + + # ========== Access Methods ============================================== + def add_attribute(self, name, value=None, owner=None): + r""" + Adds an attribute called name to the data object + + If an attribute needs to be added to the object, this routine must be + called or the attribute will not be written out. + + :Input: + - *name* - (string) Name of the data attribute + - *value* - (id) Value to set *name* to, defaults to None + - *owner* - (id) Owner of this particular attribute + """ + setattr(self,name,value) + self.__owners[name] = owner + if name not in self.__attributes: + self.__attributes.append(name) + + def remove_attributes(self, arg_list): + r""" + Remove the listed attributes. + """ + + # Convert to list if args is not already a list + if not isinstance(arg_list,list): + arg_list = [arg_list] + + for arg in arg_list: + self.__owners.pop(arg) + self.__attributes.remove(arg) + delattr(self,arg) + + def attributes(): + def fget(self): return self.__attributes + return locals() + attributes = property(**attributes()) + + def has_attribute(self,name): + r""" + Check if this data object has the given attributes + + :Input: + - *name* - (string) Name of attribute + + :Output: + - (bool) - True if data object contains a data attribute name + """ + return name in self.__attributes + + def set_owner(self,name,owner): + r""" + Sets the owner of the given data + + :Input: + - *name* - (string) Name of attribute + - *owner* - (id) Owner of the attribute + """ + if name not in self.__attributes: + raise KeyError("No attribute named %s" % name) + self.__owners[name] = owner + + def get_owner(self,name): + r""" + Returns the owner of the data attribute name + + :Input: + - *name* - (string) Name of attribute + + :Output: + - (id) - Owner of attribute + """ + return self.__owners[name] + + def get_owners(self,supplementary_file=None): + r""" + Returns a list of owners excluding the owner None + + If supplementary_file is provided, None is replace by that owner. + + :Input: + - *supplementary_file* - (string) Supplementary file, defaults to + None. + + :Output: + - (list) - Returns a list of owners + """ + owners = [] + for (key,owner) in self.__owners.iteritems(): + if owner is None: + self.__owners[key] = supplementary_file + # This simultaneously finds one instance of an owner and tests + # to see if the supplementary_file is not None + owner = self.__owners[key] + if owner not in owners and owner is not None: + owners.append(owner) + return owners + + def iteritems(self): + r""" + Returns an iterator of keys and values from this object + + :Output: + - (Iterator) Iterator over keys and values + """ + return [(k,getattr(self,k)) for k in self.__attributes] + + # ========== Read in a collection of data files ========================== + def read(self,data_paths): + r""" + Read data in from a clawpack style data file. + + Any lines of the form:: + + values =: name + + is used to set an attribute of self. + + INPUT + + data_paths : Path to a data file to be read in, can also be a list + of files to be read in. + """ + if isinstance(data_paths, basestring): + data_paths = [data_paths] + + for filename in data_paths: + filename = os.path.abspath(filename) + if not os.path.exists(filename): + raise Exception("No such data file: %s" % filename) + + # self.logger.info("Reading from %s" % filename) + + for lineno, line in enumerate(file(filename)): + if '=:' not in line: + continue + + value, tail = line.split('=:') + varname = tail.split()[0] + + oldval = getattr(self, varname, None) + newval = _parse_value(value) + if oldval is not None: + vals = "(old=%r,new=%r)" % (oldval, newval) + # self.logger.debug("Overwriting %s %s" % (varname, vals)) + + # if newval is None: + # self.logger.warning("Empty value for %s" % varname) + + self.add_attribute(varname, newval, filename) + + # ========== Write out the data from this object ========================= + def write(self,data_files=None,supplementary_file=None): + r""" + Write out the contents of the data object + + This method writes out the current required attributes of the data + object to a file or list of files. The format for the output will be + in the form:: + + values =: name + + The order is either retained from the files in the data list or + written in the order they are in the list of attributes + + The behavior is determined by the arguments passed into the routine: + + No arguments: + + The contents of the object will be written out to the files listed + in data_files only if each attribute is contained in the file. + This implies that if an attribute is not located in any of the + files in data_files then it will not be written out to file. + + If data_files is provided and data_files is a valid owner: + + Write out the attributes appropriate to that file + + If data_files is provided and not(data_files in owner): + + Write all attributes to the data_file given + + If supplementary_file is provided: + + Write out any attributes without an owner to this file, all owned + attributes will be written out to the approriate files + """ + + # Expand supplementary_file if it is not None + if supplementary_file is not None: + supplementary_file = os.path.abspath(supplementary_file) + + # Create list of owners + owners = self.get_owners(supplementary_file=supplementary_file) + + #print 'in write: data_files = ',data_files + # Write to the entire owner list + if data_files is None: + file_list = owners + elif isinstance(data_files,str): + #print '

in write'; import sys; sys.exit(0) + path = os.path.abspath(data_files) + if path not in owners: + # Create temporary data file to store all data in the object + try: + temp_file = open(path,'w') + for key in self.__attributes: + temp_file.write("1 =: %s\n" % key) + temp_file.close() + except IOError, (errno, strerror): + print "I/O error(%s): %s" % (errno, strerror) + raise + except: + raise + # Add the path to the file_list + file_list = [path] + # Check to make sure all the paths are in the owner list + elif isinstance(data_files,list): + for path in data_files: + path = os.path.abspath(path) + if not(path in owners): + print "%s is not a registered owner!" + return + file_list = data_files + else: + raise Exception("Invalid argument list given to write().") + + # Create temporary supplementary file if requested + if supplementary_file is not None: + try: + sup_file = open(supplementary_file,'w') + for attr in self.__attributes: + if self.__owners[attr] is supplementary_file: + sup_file.write("-1 =: %s\n" % attr) + self.__owners[attr] = supplementary_file + sup_file.close() + except: + raise + + + # Regular expression for searching each file + regexp = re.compile(r"(?P.*)=:(?P.*)") + # Loop over each file + for data_path in file_list: + # Open the data file and temporary file + try: + data_file = open(data_path,'r') + except(IOError): + raise + try: + temp_path = os.path.join(os.path.dirname(data_path), \ + 'temp.' + os.path.basename(data_path)) + temp_file = open(temp_path,'w') + except(IOError): + print "IOERROR" + raise + + try: + for line in data_file: + result = regexp.search(line) + if result: + name = re.split(r'\s+', result.group('name').strip())[0] + values = re.split(r'\s+', result.group('values').strip()) + + if len(values) == 0: + line = '' + elif self.__owners[name] == data_path or \ + data_path not in self.__owners: + newvalues = getattr(self,name) + + # Convert newvalues to an appropriate string repr + if isinstance(newvalues,tuple) \ + | isinstance(newvalues,list): + # Remove [], (), and ',' + newstring = repr(newvalues)[1:-1] + newstring = newstring.replace(',','') + elif isinstance(newvalues,bool): + if newvalues: + newstring = 'T' + else: + newstring = 'F' + else: + newstring = repr(newvalues) + + newstart = str.ljust(newstring,25) + line = line.replace(result.group('values') + "=:", \ + newstart + " =:") + else: + print "Error writing out %s" % name + raise AttributeError, name + + # Write the new line + temp_file.write(line) + except: + raise + + # Close files + data_file.close() + temp_file.close() + + # Rename the temporary file to the data_path name + try: + shutil.move(temp_path,data_path) + except: + raise + + +#----------------------------------------------------------------------- + +# New classes and functions for dealing with data in setrun function. + +class ClawInputData(Data): + r""" + Object that will be written out to claw.data. + """ + def __init__(self, ndim): + super(ClawInputData,self).__init__() + self.add_attribute('ndim',ndim) + + # Set default values: + if ndim == 1: + self.add_attribute('mx',100) + self.add_attribute('nout',5) + self.add_attribute('outstyle',1) + self.add_attribute('tfinal',1.0) + self.add_attribute('dt_initial',1.e-5) + self.add_attribute('dt_max',1.e99) + self.add_attribute('cfl_desired',0.9) + self.add_attribute('cfl_max',1.0) + self.add_attribute('max_steps',5000) + self.add_attribute('dt_variable',1) + self.add_attribute('order',2) + self.add_attribute('order_trans',0) + self.add_attribute('verbosity',0) + self.add_attribute('src_split',0) + self.add_attribute('mcapa',0) + self.add_attribute('maux',0) + self.add_attribute('meqn',1) + self.add_attribute('mwaves',1) + self.add_attribute('mthlim',[4]) + self.add_attribute('t0',0.) + self.add_attribute('xlower',0.) + self.add_attribute('xupper',1.) + self.add_attribute('mbc',2) + self.add_attribute('mthbc_xlower',1) + self.add_attribute('mthbc_xupper',1) + self.add_attribute('restart',0) + self.add_attribute('N_restart',0) + + + elif ndim == 2: + self.add_attribute('mx',100) + self.add_attribute('my',100) + self.add_attribute('nout',5) + self.add_attribute('outstyle',1) + self.add_attribute('tfinal',1.0) + self.add_attribute('dt_initial',1.e-5) + self.add_attribute('dt_max',1.e99) + self.add_attribute('cfl_desired',0.9) + self.add_attribute('cfl_max',1.0) + self.add_attribute('max_steps',5000) + self.add_attribute('dt_variable',1) + self.add_attribute('order',2) + self.add_attribute('order_trans',2) + self.add_attribute('verbosity',0) + self.add_attribute('src_split',0) + self.add_attribute('mcapa',0) + self.add_attribute('maux',0) + self.add_attribute('meqn',1) + self.add_attribute('mwaves',1) + self.add_attribute('mthlim',[4]) + self.add_attribute('t0',0.) + self.add_attribute('xlower',0.) + self.add_attribute('xupper',1.) + self.add_attribute('ylower',0.) + self.add_attribute('yupper',1.) + self.add_attribute('mbc',2) + self.add_attribute('mthbc_xlower',1) + self.add_attribute('mthbc_xupper',1) + self.add_attribute('mthbc_ylower',1) + self.add_attribute('mthbc_yupper',1) + self.add_attribute('restart',0) + self.add_attribute('N_restart',0) + + else: + raise AttributeError("Only ndim=1 or 2 supported so far") + + def write(self): + print 'Creating data file claw.data for use with xclaw' + make_clawdatafile(self) + + + +class AmrclawInputData(Data): + r""" + Object that will be written out to amr2ez.data. + """ + def __init__(self, ndim): + super(AmrclawInputData,self).__init__() + self.add_attribute('ndim',ndim) + + # Set default values: + if ndim == 1: + self.add_attribute('mx',100) + self.add_attribute('nout',5) + self.add_attribute('outstyle',1) + self.add_attribute('tfinal',1.0) + self.add_attribute('dt_initial',1.e-5) + self.add_attribute('dt_max',1.e99) + self.add_attribute('cfl_desired',0.9) + self.add_attribute('cfl_max',1.0) + self.add_attribute('max_steps',5000) + self.add_attribute('dt_variable',1) + self.add_attribute('order',2) + self.add_attribute('order_trans',0) + self.add_attribute('verbosity',0) + self.add_attribute('src_split',0) + self.add_attribute('mcapa',0) + self.add_attribute('maux',0) + self.add_attribute('meqn',1) + self.add_attribute('mwaves',1) + self.add_attribute('mthlim',[4]) + self.add_attribute('t0',0.) + self.add_attribute('xlower',0.) + self.add_attribute('xupper',1.) + self.add_attribute('mbc',2) + self.add_attribute('mthbc_xlower',1) + self.add_attribute('mthbc_xupper',1) + self.add_attribute('restart',0) + self.add_attribute('N_restart',0) + + # attributes need only since AMR is done using 2d amrclaw: + self.add_attribute('my',1) + self.add_attribute('ylower',0.) + self.add_attribute('yupper',1.) + self.add_attribute('mthbc_ylower',1) + self.add_attribute('mthbc_yupper',1) + self.add_attribute('inraty',[1,1,1,1,1,1]) + + elif ndim == 2: + self.add_attribute('mx',100) + self.add_attribute('my',100) + self.add_attribute('nout',5) + self.add_attribute('outstyle',1) + self.add_attribute('tfinal',1.0) + self.add_attribute('dt_initial',1.e-5) + self.add_attribute('dt_max',1.e99) + self.add_attribute('cfl_desired',0.9) + self.add_attribute('cfl_max',1.0) + self.add_attribute('max_steps',5000) + self.add_attribute('dt_variable',1) + self.add_attribute('order',2) + self.add_attribute('order_trans',2) + self.add_attribute('verbosity',0) + self.add_attribute('src_split',0) + self.add_attribute('mcapa',0) + self.add_attribute('maux',0) + self.add_attribute('meqn',1) + self.add_attribute('mwaves',1) + self.add_attribute('mthlim',[4]) + self.add_attribute('t0',0.) + self.add_attribute('xlower',0.) + self.add_attribute('xupper',1.) + self.add_attribute('ylower',0.) + self.add_attribute('yupper',1.) + self.add_attribute('mbc',2) + self.add_attribute('mthbc_xlower',1) + self.add_attribute('mthbc_xupper',1) + self.add_attribute('mthbc_ylower',1) + self.add_attribute('mthbc_yupper',1) + self.add_attribute('restart',0) + self.add_attribute('N_restart',0) + self.add_attribute('inraty',[1]) + + if ndim <= 2: + # AMR parameters: + self.add_attribute('mxnest',-1) + self.add_attribute('inratx',[1]) + self.add_attribute('inratt',[1]) + self.add_attribute('auxtype',[]) + self.add_attribute('restart',False) + self.add_attribute('checkpt_iousr',1000) + self.add_attribute('tchk',[]) + self.add_attribute('tol',-1.0) + self.add_attribute('tolsp',0.05) + self.add_attribute('kcheck',2) + self.add_attribute('ibuff',3) + self.add_attribute('cutoff',0.7) + self.add_attribute('PRINT',False) + self.add_attribute('NCAR',False) + self.add_attribute('fortq',True) + self.add_attribute('dprint',False) + self.add_attribute('eprint',False) + self.add_attribute('edebug',False) + self.add_attribute('gprint',False) + self.add_attribute('nprint',False) + self.add_attribute('pprint',False) + self.add_attribute('rprint',False) + self.add_attribute('sprint',False) + self.add_attribute('tprint',False) + self.add_attribute('uprint',False) + else: + print '*** Error: only ndim=1 or 2 supported so far ***' + raise AttributeError("Only ndim=1 or 2 supported so far") + + def write(self): + print 'Creating data file amr2ez.data for use with xamr' + make_amrclawdatafile(self) + make_setgauges_datafile(self) + + +class SharpclawInputData(Data): + r""" + Object that will be written out to claw.data. + """ + def __init__(self, ndim): + super(SharpclawInputData,self).__init__() + self.add_attribute('ndim',ndim) + + # Set default values: + if ndim == 1: + self.add_attribute('mx',100) + self.add_attribute('nout',5) + self.add_attribute('outstyle',1) + self.add_attribute('tfinal',1.0) + self.add_attribute('dt_initial',1.e-5) + self.add_attribute('dt_max',1.e99) + self.add_attribute('cfl_desired',0.9) + self.add_attribute('cfl_max',1.0) + self.add_attribute('max_steps',5000) + self.add_attribute('dt_variable',1) + self.add_attribute('verbosity',0) + self.add_attribute('mcapa',0) + self.add_attribute('maux',0) + self.add_attribute('meqn',1) + self.add_attribute('mwaves',1) + self.add_attribute('mthlim',[5]) + self.add_attribute('t0',0.) + self.add_attribute('xlower',0.) + self.add_attribute('xupper',1.) + self.add_attribute('mbc',3) + self.add_attribute('mthbc_xlower',1) + self.add_attribute('mthbc_xupper',1) + self.add_attribute('restart',0) + self.add_attribute('N_restart',0) + self.add_attribute('time_integrator',2) + self.add_attribute('tfluct_solver',0) + self.add_attribute('char_decomp',0) + self.add_attribute('lim_type',2) + self.add_attribute('src_term',0) + + + elif ndim == 2: + self.add_attribute('mx',100) + self.add_attribute('my',100) + self.add_attribute('nout',5) + self.add_attribute('outstyle',1) + self.add_attribute('tfinal',1.0) + self.add_attribute('dt_initial',1.e-5) + self.add_attribute('dt_max',1.e99) + self.add_attribute('cfl_desired',0.9) + self.add_attribute('cfl_max',1.0) + self.add_attribute('max_steps',5000) + self.add_attribute('dt_variable',1) + self.add_attribute('verbosity',0) + self.add_attribute('mcapa',0) + self.add_attribute('maux',0) + self.add_attribute('meqn',1) + self.add_attribute('mwaves',1) + self.add_attribute('mthlim',[5]) + self.add_attribute('t0',0.) + self.add_attribute('xlower',0.) + self.add_attribute('xupper',1.) + self.add_attribute('ylower',0.) + self.add_attribute('yupper',1.) + self.add_attribute('mbc',3) + self.add_attribute('mthbc_xlower',1) + self.add_attribute('mthbc_xupper',1) + self.add_attribute('mthbc_ylower',1) + self.add_attribute('mthbc_yupper',1) + self.add_attribute('restart',0) + self.add_attribute('N_restart',0) + self.add_attribute('time_integrator',2) + self.add_attribute('tfluct_solver',0) + self.add_attribute('char_decomp',0) + self.add_attribute('lim_type',2) + self.add_attribute('src_term',0) + + else: + raise AttributeError("Only ndim=1 or 2 supported so far") + + def write(self): + print 'Creating data file sharpclaw.data for use with xsclaw' + make_sharpclawdatafile(self) + + + + +def open_datafile(name, datasource='setrun.py'): + """ + Open a data file and write a warning header. + Warning header starts with '#' character. These lines are skipped if + data file is opened using the library routine opendatafile. + + :Input: + - *name* - (string) Name of data file + - *datasource* - (string) Source for the data + + :Output: + - (file) - file object + """ + + import string + + source = string.ljust(datasource,25) + file = open(name, 'w') + file.write('########################################################\n') + file.write('### DO NOT EDIT THIS FILE: GENERATED AUTOMATICALLY ####\n') + file.write('### To modify data, edit %s ####\n' % source) + file.write('### and then "make .data" ####\n') + file.write('########################################################\n\n') + + return file + + +def data_write(file, dataobj, name=None, descr=''): + r""" + Write out value to data file, in the form :: + + value =: name descr + + Remove brackets and commas from lists, and replace booleans by T/F. + Also convert numpy array to a list first. + + :Input: + - *name* - (string) normally a string defining the variable, + ``if name==None``, write a blank line. + - *descr* - (string) A short description to appear on the line + """ + + import string + if name is None: + file.write('\n') + else: + try: + value = getattr(dataobj, name) + except: + print "Variable missing: ",name + print " from dataobj = ", dataobj + raise + # Convert value to an appropriate string repr + import numpy + if isinstance(value,numpy.ndarray): + value = list(value) + if isinstance(value,tuple) | isinstance(value,list): + # Remove [], (), and ',' + string_value = repr(value)[1:-1] + string_value = string_value.replace(',','') + elif isinstance(value,bool): + if value: + string_value = 'T' + else: + string_value = 'F' + else: + string_value = repr(value) + padded_value = string.ljust(string_value, 25) + padded_name = string.ljust(name, 12) + file.write('%s =: %s %s\n' % (padded_value, padded_name, descr)) + + +def make_clawdatafile(clawdata): + r""" + Take the data specified in clawdata and write it to claw.data in the + form required by the Fortran code lib/main.f95. + """ + + + # open file and write a warning header: + file = open_datafile('claw.data') + + ndim = clawdata.ndim + data_write(file, clawdata, 'ndim', '(number of dimensions)') + data_write(file, clawdata, 'mx', '(cells in x direction)') + if ndim > 1: + data_write(file, clawdata, 'my', '(cells in y direction)') + if ndim == 3: + data_write(file, clawdata, 'mz', '(cells in z direction)') + data_write(file, clawdata, None) # writes blank line + + data_write(file, clawdata, 'nout', '(number of output times)') + data_write(file, clawdata, 'outstyle', '(style of specifying output times)') + if clawdata.outstyle == 1: + data_write(file, clawdata, 'tfinal', '(final time)') + elif clawdata.outstyle == 2: + data_write(file, clawdata, 'tout', '(output times)') + elif clawdata.outstyle == 3: + data_write(file, clawdata, 'iout', '(output every iout steps)') + elif clawdata.outstyle == 4: + data_write(file, clawdata, 'output_time_interval', '(between outputs)') + data_write(file, clawdata, 'tfinal', '(final time)') + + else: + print '*** Error: unrecognized outstyle' + raise + return + + data_write(file, clawdata, None) + data_write(file, clawdata, 'dt_initial', '(initial time step dt)') + data_write(file, clawdata, 'dt_max', '(max allowable dt)') + data_write(file, clawdata, 'cfl_max', '(max allowable Courant number)') + data_write(file, clawdata, 'cfl_desired', '(desired Courant number)') + data_write(file, clawdata, 'max_steps', '(max time steps per call to claw)') + data_write(file, clawdata, None) + data_write(file, clawdata, 'dt_variable', '(1 for variable dt, 0 for fixed)') + data_write(file, clawdata, 'order', '(1 or 2)') + if ndim == 1: + data_write(file, clawdata, 'order_trans', '(not used in 1d)') + else: + data_write(file, clawdata, 'order_trans', '(transverse order)') + data_write(file, clawdata, 'verbosity', '(verbosity of output)') + data_write(file, clawdata, 'src_split', '(source term splitting)') + data_write(file, clawdata, 'mcapa', '(aux index for capacity fcn)') + data_write(file, clawdata, 'maux', '(number of aux variables)') + data_write(file, clawdata, None) + + data_write(file, clawdata, 'meqn', '(number of equations)') + data_write(file, clawdata, 'mwaves', '(number of waves)') + data_write(file, clawdata, 'mthlim', '(limiter choice for each wave)') + data_write(file, clawdata, None) + + data_write(file, clawdata, 't0', '(initial time)') + data_write(file, clawdata, 'xlower', '(xlower)') + data_write(file, clawdata, 'xupper', '(xupper)') + if ndim > 1: + data_write(file, clawdata, 'ylower', '(ylower)') + data_write(file, clawdata, 'yupper', '(yupper)') + if ndim == 3: + data_write(file, clawdata, 'zlower', '(zlower)') + data_write(file, clawdata, 'zupper', '(zupper)') + data_write(file, clawdata, None) + + data_write(file, clawdata, 'mbc', '(number of ghost cells)') + data_write(file, clawdata, 'mthbc_xlower', '(type of BC at xlower)') + data_write(file, clawdata, 'mthbc_xupper', '(type of BC at xupper)') + if ndim > 1: + data_write(file, clawdata, 'mthbc_ylower', '(type of BC at ylower)') + data_write(file, clawdata, 'mthbc_yupper', '(type of BC at yupper)') + if ndim == 3: + data_write(file, clawdata, 'mthbc_zlower', '(type of BC at zlower)') + data_write(file, clawdata, 'mthbc_zupper', '(type of BC at zupper)') + + data_write(file, clawdata, 'restart', '(1 to restart from a past run)') + data_write(file, clawdata, 'N_restart', '(which frame to restart from)') + data_write(file, clawdata, None) + + file.close() + +def make_amrclawdatafile(clawdata): + r""" + Take the data specified in clawdata and write it to claw.data in the + form required by the Fortran code lib/main.f95. + """ + + + # open file and write a warning header: + file = open_datafile('amr2ez.data') + + ndim = clawdata.ndim + #data_write(file, clawdata, 'ndim', '(number of dimensions)') + data_write(file, clawdata, 'mx', '(cells in x direction)') + data_write(file, clawdata, 'my', '(cells in y direction)') + if ndim == 3: + data_write(file, clawdata, 'mz', '(cells in z direction)') + + data_write(file, clawdata, 'mxnest', '(max number of grid levels)') + if len(clawdata.inratx) < max(abs(clawdata.mxnest)-1, 1): + raise ValueError("*** Error in data parameter: " + \ + "require len(inratx) >= %s " % max(abs(clawdata.mxnest) - 1, 1)) + data_write(file, clawdata, 'inratx', '(refinement ratios)') + if clawdata.mxnest < 0: + # negative mxnest indicates anisotropic refinement + if len(clawdata.inraty) < max(abs(clawdata.mxnest)-1, 1): + raise ValueError("*** Error in data parameter: " + \ + "require len(inraty) >= %s " % max(abs(clawdata.mxnest) - 1, 1)) + data_write(file, clawdata, 'inraty', '(refinement ratios)') + if ndim == 3: + if len(clawdata.inratz) < max(abs(clawdata.mxnest)-1, 1): + raise ValueError("*** Error in data parameter: " + \ + "require len(inratz) >= %s " % max(abs(clawdata.mxnest) - 1, 1)) + data_write(file, clawdata, 'inratz', '(refinement ratios)') + if len(clawdata.inratt) < max(abs(clawdata.mxnest)-1, 1): + raise ValueError("*** Error in data parameter: " + \ + "require len(inratt) >= %s " % max(abs(clawdata.mxnest) - 1, 1)) + data_write(file, clawdata, 'inratt', '(refinement ratios)') + + data_write(file, clawdata, None) # writes blank line + + data_write(file, clawdata, 'nout', '(number of output times)') + data_write(file, clawdata, 'outstyle', '(style of specifying output times)') + if clawdata.outstyle == 1: + data_write(file, clawdata, 'tfinal', '(final time)') + elif clawdata.outstyle == 2: + data_write(file, clawdata, 'tout', '(output times)') + elif clawdata.outstyle == 3: + data_write(file, clawdata, 'iout', '(output every iout steps)') + elif clawdata.outstyle == 4: + data_write(file, clawdata, 'output_time_interval', '(between outputs)') + data_write(file, clawdata, 'tfinal', '(final time)') + else: + print '*** Error: unrecognized outstyle' + raise + return + + data_write(file, clawdata, None) + data_write(file, clawdata, 'dt_initial', '(initial time step dt)') + data_write(file, clawdata, 'dt_max', '(max allowable dt)') + data_write(file, clawdata, 'cfl_max', '(max allowable Courant number)') + data_write(file, clawdata, 'cfl_desired', '(desired Courant number)') + data_write(file, clawdata, 'max_steps', '(max time steps per call to claw)') + data_write(file, clawdata, None) + data_write(file, clawdata, 'dt_variable', '(1 for variable dt, 0 for fixed)') + data_write(file, clawdata, 'order', '(1 or 2)') + if ndim == 1: + data_write(file, clawdata, 'order_trans', '(not used in 1d)') + else: + data_write(file, clawdata, 'order_trans', '(transverse order)') + data_write(file, clawdata, 'verbosity', '(verbosity of output)') + data_write(file, clawdata, 'src_split', '(source term splitting)') + data_write(file, clawdata, 'mcapa', '(aux index for capacity fcn)') + data_write(file, clawdata, 'maux', '(number of aux variables)') + if len(clawdata.auxtype) != clawdata.maux: + file.close() + print "*** Error: An auxtype array must be specified of length maux" + raise AttributeError, "require len(clawdata.auxtype) == clawdata.maux" + for i in range(clawdata.maux): + file.write("'%s'\n" % clawdata.auxtype[i]) + data_write(file, clawdata, None) + + data_write(file, clawdata, 'meqn', '(number of equations)') + data_write(file, clawdata, 'mwaves', '(number of waves)') + data_write(file, clawdata, 'mthlim', '(limiter choice for each wave)') + data_write(file, clawdata, None) + + data_write(file, clawdata, 't0', '(initial time)') + data_write(file, clawdata, 'xlower', '(xlower)') + data_write(file, clawdata, 'xupper', '(xupper)') + data_write(file, clawdata, 'ylower', '(ylower)') + data_write(file, clawdata, 'yupper', '(yupper)') + if ndim == 3: + data_write(file, clawdata, 'zlower', '(zlower)') + data_write(file, clawdata, 'zupper', '(zupper)') + data_write(file, clawdata, None) + + data_write(file, clawdata, 'mbc', '(number of ghost cells)') + data_write(file, clawdata, 'mthbc_xlower', '(type of BC at xlower)') + data_write(file, clawdata, 'mthbc_xupper', '(type of BC at xupper)') + data_write(file, clawdata, 'mthbc_ylower', '(type of BC at ylower)') + data_write(file, clawdata, 'mthbc_yupper', '(type of BC at yupper)') + if ndim == 3: + data_write(file, clawdata, 'mthbc_zlower', '(type of BC at zlower)') + data_write(file, clawdata, 'mthbc_zupper', '(type of BC at zupper)') + data_write(file, clawdata, None) + + data_write(file, clawdata, 'restart', '(1 to restart from a past run)') + data_write(file, clawdata, 'checkpt_iousr', '(how often to checkpoint)') + if clawdata.checkpt_iousr < 0: + data_write(file, clawdata, 'tchk', '(checkpoint times)') + data_write(file, clawdata, None) + + data_write(file, clawdata, 'tol', '(tolerance for Richardson extrap)') + data_write(file, clawdata, 'tolsp', '(tolerance used in flag2refine)') + data_write(file, clawdata, 'kcheck', '(how often to regrid)') + data_write(file, clawdata, 'ibuff', '(buffer zone around flagged pts)') + data_write(file, clawdata, 'cutoff', '(efficiency cutoff for grid gen.)') + data_write(file, clawdata, None) + + data_write(file, clawdata, 'PRINT', '(print to fort.amr)') + data_write(file, clawdata, 'NCAR', '(obsolete!)') + data_write(file, clawdata, 'fortq', '(Output to fort.q* files)') + data_write(file, clawdata, None) + + data_write(file, clawdata, 'dprint', '(print domain flags)') + data_write(file, clawdata, 'eprint', '(print err est flags)') + data_write(file, clawdata, 'edebug', '(even more err est flags)') + data_write(file, clawdata, 'gprint', '(grid bisection/clustering)') + data_write(file, clawdata, 'nprint', '(proper nesting output)') + data_write(file, clawdata, 'pprint', '(proj. of tagged points)') + data_write(file, clawdata, 'rprint', '(print regridding summary)') + data_write(file, clawdata, 'sprint', '(space/memory output)') + data_write(file, clawdata, 'tprint', '(time step reporting each level)') + data_write(file, clawdata, 'uprint', '(update/upbnd reporting)') + + file.close() + + +def make_sharpclawdatafile(clawdata): + r""" + Take the data specified in clawdata and write it to sharpclaw.data in the + form required by the Fortran code lib/main.f95. + """ + + + # open file and write a warning header: + file = open_datafile('sharpclaw.data') + + ndim = clawdata.ndim + data_write(file, clawdata, 'ndim', '(number of dimensions)') + data_write(file, clawdata, 'mx', '(cells in x direction)') + if ndim > 1: + data_write(file, clawdata, 'my', '(cells in y direction)') + if ndim == 3: + data_write(file, clawdata, 'mz', '(cells in z direction)') + data_write(file, clawdata, None) # writes blank line + + data_write(file, clawdata, 'nout', '(number of output times)') + data_write(file, clawdata, 'outstyle', '(style of specifying output times)') + if clawdata.outstyle == 1: + data_write(file, clawdata, 'tfinal', '(final time)') + elif clawdata.outstyle == 2: + data_write(file, clawdata, 'tout', '(output times)') + elif clawdata.outstyle == 3: + data_write(file, clawdata, 'iout', '(output every iout steps)') + else: + print '*** Error: unrecognized outstyle' + raise + return + + data_write(file, clawdata, None) + data_write(file, clawdata, 'dt_initial', '(initial time step dt)') + data_write(file, clawdata, 'dt_max', '(max allowable dt)') + data_write(file, clawdata, 'cfl_max', '(max allowable Courant number)') + data_write(file, clawdata, 'cfl_desired', '(desired Courant number)') + data_write(file, clawdata, 'max_steps', '(max time steps per call to claw)') + data_write(file, clawdata, None) + data_write(file, clawdata, 'dt_variable', '(1 for variable dt, 0 for fixed)') + data_write(file, clawdata, 'time_integrator', '(time stepping scheme)') + data_write(file, clawdata, 'verbosity', '(verbosity of output)') + data_write(file, clawdata, 'src_term', '(source term present)') + data_write(file, clawdata, 'mcapa', '(aux index for capacity fcn)') + data_write(file, clawdata, 'maux', '(number of aux variables)') + data_write(file, clawdata, 'tfluct_solver', '(total fluctuation solver)') + data_write(file, clawdata, 'char_decomp', '(characteristic decomposition)') + data_write(file, clawdata, None) + + data_write(file, clawdata, 'meqn', '(number of equations)') + data_write(file, clawdata, 'mwaves', '(number of waves)') + data_write(file, clawdata, 'lim_type', '(0=None, 1=TVD, 2=WENO)') + data_write(file, clawdata, 'mthlim', '(limiter choice for each wave)') + data_write(file, clawdata, None) + + data_write(file, clawdata, 't0', '(initial time)') + data_write(file, clawdata, 'xlower', '(xlower)') + data_write(file, clawdata, 'xupper', '(xupper)') + if ndim > 1: + data_write(file, clawdata, 'ylower', '(ylower)') + data_write(file, clawdata, 'yupper', '(yupper)') + if ndim == 3: + data_write(file, clawdata, 'zlower', '(zlower)') + data_write(file, clawdata, 'zupper', '(zupper)') + data_write(file, clawdata, None) + + data_write(file, clawdata, 'mbc', '(number of ghost cells)') + data_write(file, clawdata, 'mthbc_xlower', '(type of BC at xlower)') + data_write(file, clawdata, 'mthbc_xupper', '(type of BC at xupper)') + if ndim > 1: + data_write(file, clawdata, 'mthbc_ylower', '(type of BC at ylower)') + data_write(file, clawdata, 'mthbc_yupper', '(type of BC at yupper)') + if ndim == 3: + data_write(file, clawdata, 'mthbc_zlower', '(type of BC at zlower)') + data_write(file, clawdata, 'mthbc_zupper', '(type of BC at zupper)') + + data_write(file, clawdata, 'restart', '(1 to restart from a past run)') + data_write(file, clawdata, 'N_restart', '(which frame to restart from)') + data_write(file, clawdata, None) + + file.close() + + +def make_userdatafile(userdata): + r""" + Create the data file using the parameters in userdata. + The parameters will be written to this file in the same order they were + specified using userdata.add_attribute. + Presumably the user will read these in using a Fortran routine, such as + setprob.f95, and the order is important. + """ + + # open file and write a warning header: + file = open_datafile(userdata._UserData__fname) + + # write all the parameters: + for param in userdata.attributes: + data_write(file, userdata, param, \ + userdata._UserData__descr[param]) + + file.close() + +def make_setgauges_datafile(clawdata): + """ + Create setgauges.data using gauges attribute of clawdata. + """ + gauges = getattr(clawdata,'gauges',[]) + ngauges = len(gauges) + + print 'Creating data file setgauges.data' + # open file and write a warning header: + file = open_datafile('setgauges.data') + file.write("%4i =: ngauges\n" % ngauges) + gaugeno_used = [] + for gauge in gauges: + gaugeno = gauge[0] + if gaugeno in gaugeno_used: + print "*** Gauge number %s used more than once! " % gaugeno + raise Exception("Repeated gauge number") + else: + gaugeno_used.append(gauge[0]) + file.write("%4i %19.10e %17.10e %13.6e %13.6e\n" % tuple(gauge)) + # or use this variant with =: + #gauge.append(gaugeno) + #file.write("%4i %19.10e %17.10e %13.6e %13.6e =: gauge%s\n" % tuple(gauge)) + file.close() + + +#----------------------------------------------------- +# New version 6/30/09 + +class ClawRunData(Data): + r""" + Object that will be written out to claw.data. + """ + def __init__(self, pkg, ndim): + super(ClawRunData,self).__init__() + self.add_attribute('pkg',pkg) + self.add_attribute('ndim',ndim) + self.add_attribute('datalist',[]) + + + if pkg.lower() in ['classic', 'classicclaw']: + self.add_attribute('xclawcmd', 'xclaw') + + # Required data set for basic run parameters: + clawdata = ClawInputData(ndim) + self.add_attribute('clawdata', clawdata) + self.datalist.append(clawdata) + + elif pkg.lower() in ['amrclaw', 'amr']: + self.add_attribute('xclawcmd', 'xamr') + + # Required data set for basic run parameters: + clawdata = AmrclawInputData(ndim) + self.add_attribute('clawdata', clawdata) + self.datalist.append(clawdata) + + elif pkg.lower() in ['geoclaw']: + self.add_attribute('xclawcmd', 'xgeoclaw') + + # Required data set for basic run parameters: + clawdata = AmrclawInputData(ndim) + self.add_attribute('clawdata', clawdata) + self.datalist.append(clawdata) + geodata = GeoclawInputData(ndim) + self.add_attribute('geodata', geodata) + self.datalist.append(geodata) + + elif pkg.lower() in ['sharpclaw']: + self.add_attribute('xclawcmd', 'xsclaw') + + # Required data set for basic run parameters: + clawdata = SharpclawInputData(ndim) + self.add_attribute('clawdata', clawdata) + self.datalist.append(clawdata) + + else: + raise AttributeError("Unrecognized Clawpack pkg = %s" % pkg) + + def new_UserData(self,name,fname): + r""" + Create a new attribute called name + for application specific data to be written + to the data file fname. + """ + userdata = UserData(fname) + self.datalist.append(userdata) + exec('self.%s = userdata' % name) + return userdata + + def add_GaugeData(self): + r""" + Create a gaugedata attribute for writing to gauges.data. + """ + gaugedata = GaugeData(self.ndim) + self.datalist.append(gaugedata) + self.gaugedata = gaugedata + return gaugedata + + def write(self): + for d in self.datalist: + d.write() + +class UserData(Data): + r""" + Object that will be written out to user file such as setprob.data, as + determined by the fname attribute. + """ + def __init__(self, fname): + super(UserData,self).__init__() + self.__fname = fname # file to be read by Fortran for this data + self.__descr = {} # dictionary to hold descriptions + + def add_param(self,name,value,descr=''): + self.add_attribute(name,value) + self.__descr[name] = descr + + def write(self): + print 'Creating data file %s' % self.__fname + make_userdatafile(self) + +class GaugeData(Data): + r""" + Data to be written out to gauge.data specifying gauges. + DEPRECATED: Use GeoclawInputData instead. + """ + def __init__(self, ndim): + super(GaugeData,self).__init__() + self.add_attribute('ndim',ndim) + self.add_attribute('ngauges',0) + self.__gauge_dict = {} + + def add_gauge(self,gaugeno,location,time_interval): + self.__gauge_dict[gaugeno] = (gaugeno, location, time_interval) + self.ngauges = len(self.__gauge_dict) + + def write(self): + print 'Creating data file gauges.data' + + # open file and write a warning header: + file = open_datafile('gauges.data') + + data_write(file, self, 'ngauges', 'Number of gauges') + data_write(file, self, None) + + ndim = self.ndim + + # write a line for each gauge: + for (gaugeno, gdata) in self.__gauge_dict.iteritems(): + tmin = gdata[2][0] + tmax = gdata[2][1] + if isinstance(gdata[1],(list,tuple)): + xyz = gdata[1] + x = xyz[0] + if ndim>1: + y = xyz[1] + if ndim>2: + z = xyz[2] + else: + x = gdata[1] + + if ndim==1: + file.write('%i %e %e %e' % (gdata[0],x,tmin,tmax)) + elif ndim==2: + file.write('%i %e %e %e %e' % (gdata[0],x,y,tmin,tmax)) + elif ndim==3: + file.write('%i %e %e %e %e %e' % (gdata[0],x,y,z,tmin,tmax)) + + printxyz = {1: 'x ', 2: 'x y ', 3: 'x y z'} + file.write('\n\n# Format of each line: \n# gaugeno %s tmin tmax'\ + % printxyz[ndim]) + file.close() + +class GeoclawInputData(Data): + r""" + Object that will be written out to the various GeoClaw data files. + """ + def __init__(self, ndim): + super(GeoclawInputData,self).__init__() + + # Set default values: + self.add_attribute('igravity',1) + self.add_attribute('iqinit',0) + self.add_attribute('icoriolis',1) + self.add_attribute('Rearth',6367500.0) + self.add_attribute('variable_dt_refinement_ratios',False) + # NEED TO CONTINUE! + + def write(self): + + print 'Creating data file setgeo.data' + # open file and write a warning header: + file = open_datafile('setgeo.data') + data_write(file, self, 'igravity') + data_write(file, self, 'gravity') + data_write(file, self, 'icoordsys') + data_write(file, self, 'icoriolis') + data_write(file, self, 'Rearth') + data_write(file, self, 'variable_dt_refinement_ratios') + file.close() + + print 'Creating data file settsunami.data' + # open file and write a warning header: + file = open_datafile('settsunami.data') + data_write(file, self, 'sealevel') + data_write(file, self, 'drytolerance') + data_write(file, self, 'wavetolerance') + data_write(file, self, 'depthdeep') + data_write(file, self, 'maxleveldeep') + data_write(file, self, 'ifriction') + data_write(file, self, 'coeffmanning') + data_write(file, self, 'frictiondepth') + file.close() + + print 'Creating data file settopo.data' + # open file and write a warning header: + file = open_datafile('settopo.data') + self.ntopofiles = len(self.topofiles) + data_write(file, self, 'ntopofiles') + for tfile in self.topofiles: + try: + fname = os.path.abspath(tfile[-1]) + except: + print "*** Error: file not found: ",tfile[-1] + raise MissingFile("file not found") + file.write("\n'%s' \n " % fname) + file.write("%3i %3i %3i %20.10e %20.10e \n" % tuple(tfile[:-1])) + file.close() + + print 'Creating data file setdtopo.data' + # open file and write a warning header: + file = open_datafile('setdtopo.data') + self.mdtopofiles = len(self.dtopofiles) + data_write(file, self, 'mdtopofiles') + data_write(file, self, None) + for tfile in self.dtopofiles: + try: + fname = "'%s'" % os.path.abspath(tfile[-1]) + except: + print "*** Error: file not found: ",tfile[-1] + raise MissingFile("file not found") + file.write("\n%s \n" % fname) + file.write("%3i %3i %3i\n" % tuple(tfile[:-1])) + file.close() + + print 'Creating data file setqinit.data' + # open file and write a warning header: + file = open_datafile('setqinit.data') + # self.iqinit tells which component of q is perturbed! + data_write(file, self, 'iqinit') + data_write(file, self, None) + for tfile in self.qinitfiles: + try: + fname = "'%s'" % os.path.abspath(tfile[-1]) + except: + print "*** Error: file not found: ",tfile[-1] + raise MissingFile("file not found") + file.write("\n%s \n" % fname) + file.write("%3i %3i \n" % tuple(tfile[:-1])) + file.close() + + make_setgauges_datafile(self) + +# print 'Creating data file setgauges.data' +# # open file and write a warning header: +# file = open_datafile('setgauges.data') +# self.ngauges = len(self.gauges) +# data_write(file, self, 'ngauges') +# data_write(file, self, None) +# gaugeno_used = [] +# for gauge in self.gauges: +# gaugeno = gauge[0] +# if gaugeno in gaugeno_used: +# print "*** Gauge number %s used more than once! " % gaugeno +# raise Exception("Repeated gauge number") +# else: +# gaugeno_used.append(gauge[0]) +# gauge.append(gaugeno) +# file.write("%3i %19.10e %19.10e %15.6e %15.6e =: gauge%s\n" % tuple(gauge)) +# file.close() + + + print 'Creating data file setfixedgrids.data' + # open file and write a warning header: + file = open_datafile('setfixedgrids.data') + self.nfixedgrids = len(self.fixedgrids) + data_write(file, self, 'nfixedgrids') + data_write(file, self, None) + for fixedgrid in self.fixedgrids: + file.write(11*"%g " % tuple(fixedgrid) +"\n") + file.close() + + + print 'Creating data file setregions.data' + # open file and write a warning header: + file = open_datafile('setregions.data') + self.nregions = len(self.regions) + data_write(file, self, 'nregions') + data_write(file, self, None) + for regions in self.regions: + file.write(8*"%g " % tuple(regions) +"\n") + file.close() + From 2e9f076b54287c1788d1379055ba3ed16d121104 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Sun, 7 Oct 2012 15:32:28 -0400 Subject: [PATCH 18/22] Changed name to convert.py: now more general --- .../conversion/{convert_setrun_amrclaw_2d.py => convert.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename src/python/clawutil/conversion/{convert_setrun_amrclaw_2d.py => convert.py} (100%) diff --git a/src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py b/src/python/clawutil/conversion/convert.py similarity index 100% rename from src/python/clawutil/conversion/convert_setrun_amrclaw_2d.py rename to src/python/clawutil/conversion/convert.py From 593f4419c703dd3ae6e0aea80eacb5317e063f72 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Sun, 7 Oct 2012 16:15:51 -0400 Subject: [PATCH 19/22] Fixed minor bugs in convert.py --- src/python/clawutil/conversion/convert.py | 30 +++++++++++++++++------ 1 file changed, 22 insertions(+), 8 deletions(-) diff --git a/src/python/clawutil/conversion/convert.py b/src/python/clawutil/conversion/convert.py index 9cde34aa..0098938b 100644 --- a/src/python/clawutil/conversion/convert.py +++ b/src/python/clawutil/conversion/convert.py @@ -12,7 +12,7 @@ sys.path.insert(0,os.getcwd()) sys.path.append(os.getcwd() + '/pyclaw') -def convert(setrun_file='setrun.py', claw_pkg=None): +def convert_setrun(setrun_file='setrun.py', claw_pkg=None): setrun_text = open(setrun_file).readlines() if claw_pkg is None: @@ -38,7 +38,6 @@ def convert(setrun_file='setrun.py', claw_pkg=None): limiter_map = {0:'none',1:'minmod',2:'superbee',3:'mc',4:'vanleer'} limiter = [limiter_map.get(i,i) for i in c.mthlim] - print "limiter: ", c.mthlim, limiter bc_map = {0:'user', 1:'extrap', 2:'periodic', 3:'wall'} @@ -111,7 +110,7 @@ def convert(setrun_file='setrun.py', claw_pkg=None): if claw_pkg == 'amrclaw': newtext = template_amrclaw_2d.format(**mapping) else: - raise ValueError("*** convert not yet implemented for %s" \ + raise ValueError("*** convert not yet implemented for claw_pkg = %s" \ % claw_pkg) setrun_text = open(setrun_file).readlines() @@ -128,12 +127,10 @@ def convert(setrun_file='setrun.py', claw_pkg=None): print 'Moved %s to original_%s ' % (setrun_file,setrun_file) open(setrun_file,'w').write(newtext) print 'Created ', setrun_file - - copy_Makefile(claw_pkg) + return claw_pkg def copy_Makefile(claw_pkg): - import pdb; pdb.set_trace() if claw_pkg == 'amrclaw': try: os.system("mv Makefile original_Makefile") @@ -142,7 +139,7 @@ def copy_Makefile(claw_pkg): except: raise Exception("*** Error copying Makefile") else: - raise ValueError("*** convert not yet implemented for %s" \ + raise ValueError("*** convert not yet implemented for claw_pkg = %s" \ % claw_pkg) print "Moved Makefile to original_Makefile" @@ -150,5 +147,22 @@ def copy_Makefile(claw_pkg): print "*** Edit Makefile based on original_Makefile, e.g. point to" print "*** any local files, correct Riemann solver, etc." + +def convert_setplot(setplot_file='setplot.py'): + + setplot_text = open(setplot_file).read() + setplot_text = setplot_text.replace('pyclaw.plotters','clawpack.visclaw') + setplot_text = setplot_text.replace('2d_grid','2d_patch') + setplot_text = setplot_text.replace('gridedges','patchedges') + setplot_text = setplot_text.replace('gridlines','celledges') + + os.system("mv %s original_%s" % (setplot_file,setplot_file)) + print 'Moved %s to original_%s ' % (setplot_file,setplot_file) + open(setplot_file,'w').write(setplot_text) + print 'Created ', setplot_file + + if __name__ == "__main__": - convert(*sys.argv[1:]) + claw_pkg = convert_setrun() + copy_Makefile(claw_pkg) + convert_setplot() From 39e144add684b078ed49f6c1abaf829791bb1aa0 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Sun, 7 Oct 2012 19:48:05 -0400 Subject: [PATCH 20/22] added messages about other changes needed. --- src/python/clawutil/conversion/convert.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/python/clawutil/conversion/convert.py b/src/python/clawutil/conversion/convert.py index 0098938b..1072ecce 100644 --- a/src/python/clawutil/conversion/convert.py +++ b/src/python/clawutil/conversion/convert.py @@ -146,6 +146,8 @@ def copy_Makefile(claw_pkg): print "Created new Makefile template -- must be customized!" print "*** Edit Makefile based on original_Makefile, e.g. point to" print "*** any local files, correct Riemann solver, etc." + print "*** You might have to make other modifications to local fortran" + print "*** files -- in particular indices have been reordered!" def convert_setplot(setplot_file='setplot.py'): From ec4567749062ce48783330b234a29fb4956667fc Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Sun, 7 Oct 2012 23:15:16 -0400 Subject: [PATCH 21/22] added init_iflags.f to Makefile template --- src/python/clawutil/conversion/Makefile_amrclaw_2d | 1 + 1 file changed, 1 insertion(+) diff --git a/src/python/clawutil/conversion/Makefile_amrclaw_2d b/src/python/clawutil/conversion/Makefile_amrclaw_2d index c546adf4..66608769 100644 --- a/src/python/clawutil/conversion/Makefile_amrclaw_2d +++ b/src/python/clawutil/conversion/Makefile_amrclaw_2d @@ -52,6 +52,7 @@ SOURCES = \ $(AMRCLAW)/src/2d/auxcoarsen.f \ $(AMRCLAW)/src/2d/fixcapaq.f \ $(AMRCLAW)/src/2d/estdt.f \ + $(AMRCLAW)/src/2d/init_iflags.f \ $(AMRCLAW)/src/2d/igetsp.f \ $(AMRCLAW)/src/2d/reclam.f \ $(AMRCLAW)/src/2d/birect.f \ From 453ac139c2d21f7b184e4f3a2c3a2ec699aa5de3 Mon Sep 17 00:00:00 2001 From: Randy LeVeque Date: Wed, 10 Oct 2012 15:49:26 -0400 Subject: [PATCH 22/22] Fixed Makefile.commont to change CLAW/util to CLAWUTIL Also added clawcode2html.py to clawutil and fixed Makefile.common to point to this. Need to add other required files for html, e.g. doc.css and jsMath somewhere. Or MathJax? Or reconsider using this system at all? --- src/Makefile.common | 4 +- src/python/clawutil/clawcode2html.py | 586 +++++++++++++++++++++++++++ 2 files changed, 588 insertions(+), 2 deletions(-) create mode 100644 src/python/clawutil/clawcode2html.py diff --git a/src/Makefile.common b/src/Makefile.common index 1e1137f9..b55618f8 100644 --- a/src/Makefile.common +++ b/src/Makefile.common @@ -131,7 +131,7 @@ debug: #---------------------------------------------------------------------------- # Command to create *.html files from *.f etc: -CC2HTML = $(CLAW_PYTHON) $(CLAW)/doc/clawcode2html.py --force +CC2HTML = $(CLAW_PYTHON) $(CLAWUTIL)/src/python/clawutil/clawcode2html.py --force # make list of html files to be created by 'make .htmls': HTML = \ @@ -182,7 +182,7 @@ data: $(MAKEFILE_LIST); # Run the code without checking dependencies: output: $(MAKEFILE_LIST); -rm -f .output - $(CLAW_PYTHON) $(CLAW)/clawutil/src/python/clawutil/runclaw.py $(EXE) $(OUTDIR) \ + $(CLAW_PYTHON) $(CLAWUTIL)/src/python/clawutil/runclaw.py $(EXE) $(OUTDIR) \ $(OVERWRITE) $(RESTART) @echo $(OUTDIR) > .output diff --git a/src/python/clawutil/clawcode2html.py b/src/python/clawutil/clawcode2html.py new file mode 100644 index 00000000..69763797 --- /dev/null +++ b/src/python/clawutil/clawcode2html.py @@ -0,0 +1,586 @@ +#!/usr/bin/env python + +# convert CLAWPACK source code, data files, READMEs, etc. into html. +# for example, +# clawcode2html filename.f +# generates +# filename.f.html +# If filename.f.html already exists, you will be prompted before +# overwriting unless the -f or --force flag is used, e.g. +# clawcode2html --force filename.f +# +# Based on mathcode2html.py from +# http://www.amath.washington.edu/~rjl/mathcode2html +# with some modifications for CLAWPACK. +# +# The environment variable CLAW must be properly set to the root +# of the claw directory before using this script. +# +# Most of code is put into 

 environment.
+# Any comments enclosed by begin_html and end_html are taken out 
+# of the 
 environment and indented properly (using a table) 
+# to match the surrounding code.
+
+# By default, the html comments are offset in blue font, except if the 
+# input file has extension .txt or no extension, in which case it's 
+# left as black.  The default_color can be changed below.
+# Also, the begin_html line may contain [color: red] for example,
+# to determine the color of this comment.
+
+# You may modify the recognized extensions and comment characters below.
+
+# Allows many latex commands in comments if jsMath is used on webpage.
+# In this case make sure the variable jsMathScript is properly set below.
+# If you don't want to include a call to the jsMath script on the html
+# page, invoke mathcode2html with the --nojsmath option.
+
+
+#---------------------------------------------------------------------------
+# Copyright (C) 2008   Randall J. LeVeque 
+#
+# Distributed as part of Clawpack, under the BSD license
+# See www.clawpack.org
+#---------------------------------------------------------------------------
+
+
+import sys,os,glob
+import string,re
+import time
+try:
+    from optparse import OptionParser
+except:
+    print 'You must use a more recent version of Python'
+    sys.exit(1)
+
+# parse command line arguments:
+parser = OptionParser()
+parser.add_option("-f", "--force",
+                  action="store_true", dest="forced", default=False,
+                  help="force action even if it overwrites html file")
+parser.add_option("--nojsmath",
+                  action="store_false", dest="nojsMath", default=False,
+                  help="don't include call to jsMath script in html")
+parser.add_option("-q", "--quiet",
+                  action="store_false", dest="verbose", default=True,
+                  help="don't print status messages to stdout")
+parser.add_option("--noheader",
+                  action="store_false", dest="header", default=True,
+                  help="suppress printing header at top of html page")
+parser.add_option("--dropext",
+                  action="store_true", dest="dropext", default=False,
+                  help="drop the file extension before adding .html for output")
+parser.add_option("--eagle",
+                  action="store_true", dest="eagle", default=False,
+                  help="load the eagleclaw.css style")
+
+(options, infiles) = parser.parse_args()
+
+forced = options.forced
+nojsMath = options.nojsMath
+verbose = options.verbose
+header = options.header
+dropext = options.dropext 
+eagle = options.eagle 
+
+
+
+# CLAWPACK environment variables:
+
+try:
+    clawdir = os.getenv('CLAW')  # assumes environment variable set properly
+except:
+    print "CLAW environment variable not set"
+    print "You need to run setenv.py before setup.py"
+    sys.exit(1)
+
+if clawdir == None:
+    print "CLAW environment variable not set"
+    print "You need to run setenv.py before setup.py"
+    sys.exit(1)
+
+
+# Create addresses for links on html pages.
+# change the lines below if you want to point to a webpage home instead
+# of the local file system  (e.g.  clawaddr = "http://www.mywebpage/claw")
+
+clawaddr = 'http://localhost:50005'
+#clawaddr = 'http://kingkong.amath.washington.edu/claw4'
+
+
+# Set comment characters for different programming languages:
+# Augment or modify as desired.
+commentchar = { '.f'  : ['!', '#'], \
+                '.f95'  : ['!','#'], \
+                '.f90'  : ['!','#'], \
+                '.m'  : '%', \
+                '.py' : '#', \
+                '.sh' : '#', \
+                '.data' : ['#','=:'], \
+                '.txt': None, \
+                'Makefile': '#', \
+                ''    : None}
+
+firstfort = ['c','*','C','!']   # valid fortran .f comment char's in col. 1
+firstfort95 = ['!']   # valid fortran .f95 comment char's in col. 1
+
+leadingindent = ''    # additional indentation for webpage, if desired
+
+default_color = 'blue'
+
+
+try:
+    infiles.remove('clawcode2html.py')  # can't apply this code to itself!
+except:
+    pass
+
+
+for infilename in infiles:
+
+    # check if this is a code file of a recognized language.
+    ext = os.path.splitext(infilename)[1]
+    if infilename == 'Makefile':
+        ext = 'Makefile'  # special case
+    
+    if not commentchar.has_key(ext):
+        print "  "
+        print "  Warning: Unrecognized extension, will proceed"
+        print "           with no replacement of comment characters"
+        commentchar[ext] = None 
+    
+    
+    # open input and output files:
+    #-----------------------------
+    
+    try:
+        ifile = open(infilename,'r')
+    except:
+        print "File not found:", infilename
+        sys.exit(1)
+
+    # Search for [use: ...] statements in file:
+    all_lines = ifile.read()
+    regexp = re.compile(r"\[use:[^\]]*jsMath")
+    result = regexp.search(all_lines)
+
+    # use jsMath if [use:jsMath] found and option --nojsmath was
+    # not used in call:
+    usejsMath = (result is not None) & (not nojsMath)
+
+    regexp = re.compile(r"\[use:(?P[^\]]*).css\]")
+    result = regexp.search(all_lines)
+    if result is not None:
+        cssfile = result.group('cssfile').strip() + '.css'
+    else:
+        cssfile = None
+
+    
+    ifile.seek(0)  # return to start of file
+    lines = ifile.readlines()
+    
+    if dropext:
+        infileroot = os.path.splitext(infilename)[0]
+        outfilename = infileroot + '.html'
+    else:
+        outfilename = infilename + '.html'
+
+    if (glob.glob(outfilename) != []) & (not forced):
+        sys.stdout.write('  OK to overwrite %s?  '  %  outfilename)
+        answer = raw_input()
+        if answer not in ['y','Y','yes']:
+            print '  Aborting!'
+            sys.exit(1)
+    
+    ofile = open(outfilename,'w')
+    
+    
+    # start creating html file:
+    #--------------------------
+    
+    if verbose:
+        print '  Converting ', infilename, ' to ', outfilename
+
+    
+    ofile.write("""""" % infilename)
+
+    ofile.write('\n\n\n %s \n\n'  % outfilename)
+    if eagle:
+        ofile.write("""
+          
+          
+          
+           
+          
+        """ % (clawaddr,clawaddr))
+    elif cssfile:
+        ofile.write("""
+          
+          
+          
+           
+          
+        """ % (clawaddr, cssfile, clawaddr))
+    else:
+        ofile.write(
+           """
+          
+           
+           
+           
+           
+           """ % clawaddr)
+
+    
+    # determine time and reformat:
+    time1 = time.asctime()
+    year = time1[-5:]
+    day = time1[:-14]
+    hour = time1[-13:-5]
+    creationtime = day + year + ' at ' + hour
+
+    # put full file name with path into a comment for future reference:
+    fullinfilename = os.path.join(os.getcwd(),infilename)
+    ofile.write('\n\n'  % fullinfilename)
+    ofile.write('\n\n'  % creationtime)
+    
+    
+    if header:
+        #ofile.write('
 
 \n')
+        ofile.write('\n' % outfilename)
+    
+        ofile.write("""
+            
 
 \n')
+        ofile.write('  %s  CLAWPACK""" % clawaddr)
+
+        ofile.write('    
 
 \n')
+    
+        ofile.write(' Source file:   %s \n' \
+                     % (infilename,infilename))
+        ofile.write('
\n')
+        ofile.write(' Directory:    %s \n' %  os.getcwd())
+        ofile.write('
\n')
+        ofile.write(' Converted:    %s \n' % creationtime)
+        ofile.write('  using clawcode2html\n'\
+                    % clawaddr)
+        ofile.write('
\n')
+        ofile.write('  This documentation file will \n')
+        ofile.write('not reflect any later changes in the source file. \n')
+        ofile.write('
\n')
+        ofile.write('
\n')
+    
+    
+    if usejsMath:
+        
+        # Set jsMathScript to the file or URL of the java script load.js.
+
+        # proper location for using webserver started by executing
+        # "python startserver.py" in the $CLAW directory:
+        jsMathScript = "%s/doc/load.js"  % clawaddr
+
+        # script location for posting on kingkong server:
+        # jsMathScript = "http://kingkong.amath.washington.edu/claw/doc/load.js"
+    
+        # script location for posting on rjl's webpage:
+        # jsMathScript = "http://www.amath.washington.edu/~rjl/jsMath/easy/load.js"
+    
+        ofile.write("    \n")
+        ofile.write(" \n"  % jsMathScript)
+
+    
+        ofile.write("""
+            
+            $\phantom{******** If you see this on the webpage then the 
+                               browser could not locate *********}$

+            $\phantom{******** the jsMath file load.js *********}$

+            \n""")
+        
+        # define any latex macros that you want to use in jsMath: 
+        
+        ofile.write("""
+          
+          $\\newcommand{\\vector}[1]{\\left[\\begin{array}{c} #1 \\end{array}\\right]}$ 
+          $\\newenvironment{matrix}{\\left[\\begin{array}{cccccccccc}} {\\end{array}\\right]}$ 
+          $\\newcommand{\\A}{{\\cal A}}$
+          $\\newcommand{\\W}{{\\cal W}}$
+          \n""")
+        #
+        # end of jsMath stuff
+    
+
+    # start writing input file to output file...
+    
+    # code is in pre-formatted environment:
+    ofile.write('
 \n')
+    
+    insidehtml = 0;   # set to 1 when we're processing html comments
+    lineno = 0;       # line number counter for error message
+    
+    for line in lines:
+    
+        lineno += 1
+    
+        if string.count(line,"begin_html"):
+            regexp = re.compile(r"\[color:(?P[^\]]*)\]")
+            result = regexp.search(line)
+	    if result:
+	        font_color = result.group('color')
+	    else:
+	        font_color = default_color
+    
+            if insidehtml:
+                print '  Error at line ', lineno, '\n'
+                print '  Unexpected begin_html  when already in html mode\n'
+                print '  Missing end_html? \n'
+                sys.exit(1)
+    
+            # switch out of pre-formatted mode and create table to indent
+            ofile.write('
\n\n')
+    
+            # the next column of the table has the comment itself:
+            ofile.write('
\n')
+    
+            # The first column of the table is spaces for indentation 
+            # to match surrounding source code.
+            # Count how many spaces there are before the begin_html
+            #  or to the first comment character preceeding that string:
+            regexp = re.compile(r"(?P[ ]*)(#|%|begin)")
+            result = regexp.search(line)
+            if result:
+                numindent = len(leadingindent) + len(result.group('spaces'))
+                numindent = numindent
+                ofile.write('
')
+                for i in range(numindent):
+                    ofile.write(' ')
+                ofile.write('
')
+            else:
+                print '  Strange error in clawcode2html - should not be here'
+                print '     at line number ', lineno
+              
+    
+            ofile.write('\n		\n')
+            if ext not in ('.txt', ''):
+                # use colored font for comments except for text files.
+                ofile.write('\n'  % font_color)
+            insidehtml = 1;
+    
+        elif string.count(line,"end_html"):
+            # switch back to pre-formatted environment
+            ofile.write('
\n')
+            ofile.write('
 \n')
+            insidehtml = 0;
+    
+        else:
+            if insidehtml:
+    
+                # replace blank line in html comment by new paragraph 
:
+                blankline = (string.split(line) == [])
+                if not blankline:
+                   firstchar = string.split(line)[0][0]
+                   if ((ext in ['.f','.f95']) & (firstchar not in firstfort)): 
+                       if firstchar not in commentchar[ext]:
+                           print '  Error... in line ', lineno,'\n' \
+                                 '  In html but not in a comment.'\
+                                 '   Forgotten "end_html" ?'
+                           sys.exit(1)
+    
+                # fortran comments may have comment symbol in column 1
+                # strip lines inside an html comment of leading symbol:
+                if ext == '.f':
+                    if line[0] in firstfort:
+                       line = ' ' + line[1:]
+                if ext == '.f95':
+                    if line[0] in firstfort95:
+                       line = ' ' + line[1:]
+    
+                # replace any comment character by ' ' 
+                if commentchar[ext]:
+                    for char in commentchar[ext]:
+                        line = string.replace(line,char,' ')  
+    
+    
+                blankline = (string.split(line) == [])
+                if blankline:
+                   line = ('
\n')
+
+
+                # Allow wiki formatting of links:
+                # -------------------------------
+
+		# Replace [name: placemark] by 
+                # (to jump to a different spot in the same html file)
+                regexp = re.compile(r"\[name:[ ]*(?P[^ ^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    placemark = result.group('placemark')
+                    oldpat = result.group()
+		    newpat = '' % placemark
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+                # Replace links of the form [code: target]
+                # by html links to both target and target.html.
+		# Also allows [code: target#placemark] with links to target 
+		# and target.html#placemark.
+
+                regexp = re.compile(r"\[code:[ ]*(?P[^ ^\]^#]*)([#]?)" + \
+                                    r"(?P[^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    targetname = result.group('target')
+                    placemark = result.group('placemark')
+                    oldpat = result.group()
+		    if placemark:
+                        newpat = '%s' \
+			             % (targetname,targetname) + \
+                                 ' [.html]' \
+			             % (targetname,placemark) 
+		    else:
+                        oldpat = result.group()
+                        newpat = '%s' \
+			             % (targetname,targetname) + \
+                                 ' [.html]' \
+			             % targetname 
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+
+                # replace links of the form [link: target text]
+                # by an html link from text to the target page.
+                regexp = re.compile(r"\[link:[ ]?(?P[^ ^\]]*)" + \
+                                    r"([ ]*)(?P[^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    targetname = result.group('target')
+                    text = result.group('text')
+                    oldpat = result.group()
+                    if text=='': 
+                        text = targetname
+                    newpat = '' + \
+                                text + '  '
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+
+                # replace links of the form [http:etc text]
+                # by an html link from text to the http page.
+                regexp = re.compile(r"\[http:(?P[^ ^\]]*)" + \
+                                    r"([ ]*)(?P[^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    targetname = result.group('target')
+                    text = result.group('text')
+                    oldpat = result.group()
+                    if text=='': 
+                        text = targetname[2:]
+                    newpat = '' + \
+                                text + '  '
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+
+                # replace links of the form [www.etc text]
+                # by an html link from text to the http://www.etc page.
+                regexp = re.compile(r"\[www.(?P[^ ^\]]*)" + \
+                                    r"([ ]*)(?P[^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    targetname = result.group('target')
+                    text = result.group('text')
+                    oldpat = result.group()
+                    if text=='': 
+                        text = 'www.' + targetname
+                    newpat = '' + \
+                                text + '  '
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+
+		# special things for CLAWPACK:
+
+                # replace links of the form [clawcode:clawpack/1d/lib/step1.f]
+                # for example by links relative to clawaddr, 
+		# along with a link to the .html version.
+                regexp = re.compile(r"\[clawcode:[ ]*(?P[^ ^\]^#]*)([#]?)" + \
+                                    r"(?P[^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    targetname = result.group('target').lstrip()
+                    placemark = result.group('placemark')
+                    oldpat = result.group()
+		    if placemark:
+                        newpat = 'claw/%s' \
+			             % (clawaddr,targetname,targetname) + \
+                                 ' [.html]' \
+			             % (clawaddr,targetname,placemark) 
+		    else:
+                        newpat = '%s' \
+			             % (clawaddr,targetname,targetname) + \
+                                 ' [.html]' \
+			             % (clawaddr,targetname) 
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+
+                # replace links of the form [claw:clawpack/1d/lib]
+                # for example by links relative to clawaddr,
+		# with no .html version.
+                regexp = re.compile(r"\[claw:[ ]?(?P[^ ^\]]*)" + \
+                                    r"([ ]*)(?P[^\]]*)\]")
+                result = regexp.search(line)
+                while result:
+                    targetname = result.group('target')
+                    text = result.group('text')
+                    oldpat = result.group()
+                    if text=='': 
+                        text = '$CLAW/' + targetname
+                    newpat = '' + text + '  ' 
+                    line = line.replace(oldpat,newpat)
+                    result = regexp.search(line)
+
+		# place text surrounded by triple braces with 
+		# pre environment with background color:
+		newpat = '
'
+                line = line.replace('{{{',newpat)
+                line = line.replace('}}}','
')
+
+          
+	    else:
+                # not insidehtml - make regular comments default_color.
+                # Determine if this line contains a comment and if so,
+                # what column the comment starts in:
+
+		startcomment = 1000
+	        if (ext == '.f') & (line[0] in firstfort):
+	            startcomment = 0
+	        elif (ext == '.f95') & (line[0] in firstfort95):
+	            startcomment = 0
+		else:
+		    if commentchar[ext]:
+                        for c in commentchar[ext]:
+		            commentcol = string.find(line,c)
+		            if (commentcol>-1)&(commentcol'  % default_color + \
+		           line[startcomment:-1] + '\n'
+
+
+            # output the (possibly modified) line to the output file:
+            ofile.write('%s' % leadingindent+line)
+    
+    # Done with all lines.  Add closing stuff at bottom of html file:
+    ofile.write('
\n')
+    
+    ifile.close()
+    ofile.close()
+