extrai rFup

csv2vtk_particles.py

@@ -13,6 +13,7 @@
 import numpy as np
 import csv, os, shutil
 import configparser
+from zipfile import ZipFile
 try:
     import progressbar
     pbar = True 
@@ -28,13 +29,14 @@
 folder = 'result'
 i = 1
 
+
 while aux:
     try:
         os.mkdir(folder)
         aux = False
     except FileExistsError:
         print('Folder {} exists'.format(folder))
-        opt = input('Overwrite? [y/n]')
+        opt = input('Overwrite? [y/n] ')
         if opt == 'y' or 'opt' == 'Y':
             aux =False 
         else:
@@ -54,6 +56,7 @@
 N = int(config['global']['N'].split()[0])
 nimpre =  int(config['global']['nimpre'].split()[0])
 ntype = int(config['global']['Ntype'].split()[0])
+print_TC = int(config['global']['print_TC'].split()[0])
 quant = []
 rs = [] # raio sólido
 sigma = []
@@ -82,11 +85,6 @@
         rsol[j+k] = rs[i]
     k = sum(quant[0:i+1])
 
-
-# a = input("a")
-# for i in range(len(rsol)):
-#     print("{} {}".format(i,rsol[i]))
-
 # Ler os arquivos e colocá-los em vetores
 
 x = np.zeros(N)
@@ -103,9 +101,12 @@
 
 nID = np.linspace(1,N,N)
 
+zip_positions = ZipFile(via+'/'+folder+'/positions.zip','w')
+zip_velocities = ZipFile(via+'/'+folder+'/velocities.zip','w')
+
 print('Converting...')
 if pbar:
-    bar = progressbar.ProgressBar(max_value=nimpre)
+    bar = progressbar.ProgressBar(max_value=nimpre+1)
 for fnum in range(0,nimpre+1):
     with open('temp/position.csv.'+str(fnum),encoding='utf-8') as file_locus:
         csv_lector = csv.reader(file_locus,delimiter = ',')
@@ -114,8 +115,8 @@
             x[i] = linea[0]
             y[i] = linea[1]
             i = i+1
-    shutil.move(via+'/temp/position.csv.'+str(fnum),via+'/'+folder+'/position.csv.'+str(fnum)) 
-
+    zip_positions.write(via+'/temp/position.csv.'+str(fnum), 'position.csv.'+str(fnum))
+    # shutil.move(via+'/temp/position.csv.'+str(fnum),via+'/'+folder+'/position.csv.'+str(fnum)) 
     with open('temp/velocity.csv.'+str(fnum),encoding='utf-8') as file_velocitas:
         csv_lector = csv.reader(file_velocitas,delimiter = ',')
         i = 0
@@ -124,7 +125,8 @@
             vy[i] = linea[1]
 
             i = i+1
-    shutil.move(via+'/temp/velocity.csv.'+str(fnum),via+'/'+folder+'/velocity.csv.'+str(fnum))
+    zip_velocities.write(via+'/temp/velocity.csv.'+str(fnum),'velocity.csv.'+str(fnum))
+    # shutil.move(via+'/temp/velocity.csv.'+str(fnum),via+'/'+folder+'/velocity.csv.'+str(fnum))
 
     fin = 0
     grupo = 0
@@ -144,8 +146,21 @@
 
     if pbar:
         bar.update(fnum)
+
+
+zip_positions.close()
+zip_velocities.close()
+
 shutil.rmtree('temp')
-
+
+if print_TC == 1:
+    a = os.listdir('temp2')
+    zip_rFup = ZipFile(via+'/'+folder+'/rFuP.zip','w')
+    for f in a:
+        zip_rFup.write(via+'/temp2/'+f,f)
+        # shutil.move(via+'/temp2/'+f,via+'/'+folder + '/' + f)
+    zip_rFup.close()
+    shutil.rmtree('temp2')
 
 with open("settings.txt","a") as settingstxt:
     settingstxt.write("[out_files]\n")
@@ -168,6 +183,7 @@
     with open('.gitignore','a+') as file:
         file.write(folder+'\n')
 
+
     #with open('cell.csv.'+str(fnum),encoding='utf-8') as file_velocitas:
         #csv_lector = csv.reader(file_velocitas,delimiter = ',')
         #i = 0

makefile

@@ -2,10 +2,10 @@
 # Defining variables
 objects = m_config.o linkedlist.o mod1.o saida.o lennard.o data.o mod0.o matprint.o randnormal.o 
 f90comp = mpiifort
-switch = -O3
+switch = -O3 -assume protect_parens,minus0 -prec-div -prec-sqrt 
 # Makefile
 execname: $(objects)
-	$(f90comp) -o lennard.out $(switch) $(objects)
+	$(f90comp) -o lennard $(switch) $(objects)
 randnormal.mod: randnormal.o randnormal.f90
 	$(f90comp) -c $(switch) randnormal.f90
 mod1.mod: mod1.o mod1.f90

part_gen_pequeno.py

@@ -86,6 +86,8 @@
         p1[cont,:] = [i*spac+refe[0],j*spac+refe[1]]
         cont = cont+1   
 
+# np.random.shuffle(p1)        
+
 with open(arquivo1,'w') as file:
     for i in range(N):
         file.write('{},{}\n'.format(p1[i,0],p1[i,1]))

pos_e_vel_inicial_usando_sim_anterior.py

@@ -7,6 +7,7 @@
 from glob import glob
 import os, shutil
 import configparser
+from zipfile import ZipFile
 
 dirname = os.getcwd() #os.path.dirname(os.path.abspath(__file__))
 dirlist = glob(dirname + "/*/")
@@ -16,8 +17,11 @@
 a = int(input("Enter the number of the folder\n"))
 res_dir = dirlist[a]
 
+zip_positions = ZipFile(res_dir+'/positions.zip','r')
+zip_velocities = ZipFile(res_dir+'/velocities.zip','r')
+
 config = configparser.ConfigParser()
-list_files = os.listdir(res_dir)
+len_list_files =  len(zip_positions.namelist()+zip_velocities.namelist())
 
 if os.path.isfile(res_dir + 'settings.txt'):
     config.read(res_dir + 'settings.txt')
@@ -26,7 +30,7 @@
     print('The still not converted to vtk. Probable incomplete simulation.\n'+\
           'settings.ini will be used.\n')
     config.read(dirname + '/settings.ini') 
-    nimpre = len(list_files)/2    
+    nimpre = len(len_list_files)/2    
 
 
 N = int(config['global']['N'].split()[0])
@@ -39,27 +43,42 @@
     quant.append(int(config['par_'+str(i)]['quantidade'].split()[0]))
     x_files.append(config['par_'+str(i)]['x'].split()[0])
     x_files[-1]  = x_files[-1][1:len(x_files[-1])-1] 
-    v_files.append(config['par_'+str(i)]['v_file'].split()[0])
-    v_files[-1]  = v_files[-1][1:len(v_files[-1])-1]
+    try:
+        v_files.append(config['par_'+str(i)]['v_file'].split()[0])
+        v_files[-1]  = v_files[-1][1:len(v_files[-1])-1]
+    except:
+        print("no velocity file used")
+        v_files.append('v_file_'+str(i))
+        pass 
 
 step = input('Extract step no. (max {}) '.format(nimpre-1))
 
 positions = []
-with open(res_dir + 'position.csv.'+step) as file:
+with zip_positions.open('position.csv.'+step) as file:
     for line in file:
         positions.append(line)
 velocities = []
-with open(res_dir + 'velocity.csv.'+step) as file:
+with zip_velocities.open('velocity.csv.'+step) as file:
     for line in file:
         velocities.append(line)
 
+
+# positions = []
+# with open(res_dir + 'position.csv.'+step) as file:
+#     for line in file:
+#         positions.append(line)
+# velocities = []
+# with open(res_dir + 'velocity.csv.'+step) as file:
+#     for line in file:
+#         velocities.append(line)
+
 # verificar se não é desejavel fazer backup de arquivos de posição e velocidade
 a == 'n'
 i = 0
 for f in x_files + v_files:
     if os.path.isfile(f) and a == 'n':
-        a = input('Old positions files exist. Backup? y/n')
-    if a != 'n' or a != 'N':
+        a = input('Old positions files exist. Backup? y/n ')
+    if a != 'n' or a != 'N': 
         try:
             if i == 0:
                 bkp = 'bkp'
@@ -80,14 +99,14 @@
 
 k = 0            
 for i in range(ntype):
-    with open(x_files[i],'w') as file:
+    with open(x_files[i],'wb') as file:
         for j in range(quant[i]):
             file.write(positions[k])
             k += 1
 
 k = 0        
 for i in range(ntype):
-    with open(v_files[i],'w') as file:
+    with open(v_files[i],'wb') as file:
         for j in range(quant[i]):
             file.write(velocities[k])
             k += 1        

saida.f90

@@ -12,9 +12,15 @@ subroutine vec2csv(v,n,d,prop,step,t,nimpre,start)
         character(4) :: extensao = '.csv', passo
         real(dp) :: time
         real(dp), save :: timep, etc, dtimepp
+        character(LEN=*),parameter :: fmt5 = '(f32.16, ", ",f32.16, ", ",f32.16, ", ",f32.16, ", ",f32.16 )'
+        character(LEN=*),parameter :: fmt6 = '(f5.0, ", ",f32.16, ", ",f32.16, ", ",f32.16, ", ",f32.16, ", ",f32.16 )'
 
         write(passo,'(i0)') step
-        open(10,file='temp/'//prop//extensao//'.'//trim(passo),status="replace")
+        if (d <= 3) then
+            open(10,file='temp/'//prop//extensao//'.'//trim(passo),status="replace")
+        else
+            open(10,file='temp2/'//prop//extensao//'.'//trim(passo),status="replace")
+        end if
         if (d == 1) then
             do i = 1,n
                 write(10,*) v(i,1)
@@ -33,9 +39,14 @@ subroutine vec2csv(v,n,d,prop,step,t,nimpre,start)
             end do
         else if (d == 5) then 
             do i = 1,n
-                write(10,*) v(i,1),',',v(i,2),',',v(i,3),',',v(i,4),',',v(i,5)
+                write(10,fmt5) v(i,1),v(i,2),v(i,3),v(i,4),v(i,5)
+            end do          
+        else if (d == 6) then 
+            do i = 1,n
+                write(10,fmt6) v(i,1),v(i,2),v(i,3),v(i,4),v(i,5),v(i,6)
             end do          
         end if
+
         close(10)
 
         if (prop == "position") then 

settings.ini

@@ -1,9 +1,9 @@
 # PARAMETROS GLOBAIS
 [global]
-    nimpre  = 5000 # quntidade de saidas 
-    N = 1089 # número de partículas 
+    nimpre  = 50 # quntidade de saidas 
+    N = 108 #9 # número de partículas 
     Ntype = 1 # número de tipos de partícula
-    t_fim = 50  # tempo de execução 
+    t_fim = 5  # tempo de execução 
     nimpre_init = 0 # começa a simular a partir no tempo referente ao snapshot (nimpre). 
     dt = 0.0001 # passo de tempo
     dimX = 410 # Dimensões da região de cálculo
@@ -20,7 +20,7 @@
     vd = 2 2 # velocidade distribuida com Maxwell Boltzmann
     NMPT = 100 # Número máximo de partículas que poderá mudar de process. Se não souber estimar, usar -1 ou o valor de N.
     GField = 0 0 # Campo de força gravitacional que afeta todas as partículas
-    print_TC = 0 # imprimir dados para calcular coeficiente de transporte
+    print_TC = 1 # imprimir dados para calcular coeficiente de transporte
 # PARTICLE PROPERTIES
 # v é velocidade global, entrar dois número correspondentes ao vetor vx vy que serão aplicadas em todas as partículas
 # se v_file é dada, então ela será usada para dar a velocidade às partículas. Deve ser arquivo .csv. Deixar "%" se não usar. 
@@ -32,7 +32,7 @@
     nome = 'g1'
     sigma = 2 # Lennard Jones
     epsilon = 1 # Lennard Jones
-    quantidade = 1089
+    quantidade = 108 #9
     x_lockdelay = 0 # só vai poder mudar de posição a partir de t = x_lockdelay
     rs = 0 # raio sólido. Posição de partículas na superfície de um sólido de raio rs
     fric_term = 0 # fricção artifical				

teste.f90

@@ -1,11 +1,23 @@
 program teste
-    use mod1
+    ! use mod1
 
-    call system('mkdir temp')
-    open(10,file='temp/test.txt',status="replace")
-    write(10,*) 'lalalala'
-    print*,'a'
+    ! call system('mkdir temp')
+    ! open(10,file='temp/test.txt',status="replace")
+    ! write(10,*) 'lalalala'
+    ! print*,'a'
 
+    implicit none
+    real :: a,b,c,d
+    character(LEN=*), parameter :: fmt = '(f16.0, ", ",f32.16, ", ",f32.16, ", ",f32.16, ", ",f32.16 )'
+    character(170) :: out
+
+    a = 12.0
+    b = 1.2
+    c = sqrt(2.0)
+    d = -sqrt(3.0)
+    write(out,fmt) a,b,c,d,d
+    out = trim(out)
+    write(*,*) out