LCPQ/Crystal-MET
3
0
Fork 0
mirror of https://github.com/NehZio/Crystal-MEC synced 2024-09-27 12:01:01 +02:00
Code Issues Releases Wiki Activity

added progress bar

Browse Source
This commit is contained in:
Léo Gaspard 2019-04-27 16:50:13 +02:00
parent 32dc7234d3
commit 71fddec7cb
1 changed files with 87 additions and 30 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

117
generer.py
View File

@ -3,6 +3,7 @@ import numpy as np
import os import os
import operator import operator
import sys import sys
import datetime
###### CONSTANTS ####### ###### CONSTANTS #######
dr = 0.001 dr = 0.001
@ -35,6 +36,7 @@ opti = 0
trsl = 'x' trsl = 'x'
notIn = 'x' notIn = 'x'
evj = 0 evj = 0
norep = 0
chO = -2.00 chO = -2.00
chIr = 4.00 chIr = 4.00
@ -44,6 +46,37 @@ dIrO = 2.50
dSrO = 3.10 dSrO = 3.10
dBaO = 3.10 dBaO = 3.10
####################### #######################
def printProgressBar (start, now, iteration, total, prefix = '', suffix = '', decimals = 1, length = 100, fill = '\u2588'):
"""
Call in a loop to create terminal progress bar
@params:
iteration - Required : current iteration (Int)
total - Required : total iterations (Int)
prefix - Optional : prefix string (Str)
suffix - Optional : suffix string (Str)
decimals - Optional : positive number of decimals in percent complete (Int)
length - Optional : character length of bar (Int)
fill - Optional : bar fill character (Str)
"""
percent = ("{0:." + str(decimals) + "f}").format(100 * (iteration / float(total)))
filledLength = int(length * iteration // total)
bar = fill * filledLength + '-' * (length - filledLength)
hours = now.hour-start.hour
if now.minute-start.minute < 0:
minuts = 60 + now.minute-start.minute
else:
minuts = now.minute-start.minute
if now.second-start.second < 0:
second = 60 + now.second-start.second
else:
second = now.second-start.second
print('\r%s |%s| %s%% %s Elapsed time : %2i h %2i m %2i s' % (prefix, bar, percent, suffix,hours,minuts,second), end = '\r')
# Print New Line on Complete
if iteration == total:
print()
def read_input(inputFile): def read_input(inputFile):
global cif_file global cif_file
global rBath global rBath
@ -71,6 +104,7 @@ def read_input(inputFile):
global opti global opti
global trsl global trsl
global notIn global notIn
global norep
f = open(inputFile,'r') f = open(inputFile,'r')
line = 'x' line = 'x'
@ -163,6 +197,8 @@ def read_input(inputFile):
seefrag = 1 seefrag = 1
elif line[0] == 'EVJEN': elif line[0] == 'EVJEN':
evj = 1 evj = 1
elif line[0] == 'NOREP':
norep = 1
def parse(fileName): def parse(fileName):
f = open(fileName,'r') f = open(fileName,'r')
@ -224,7 +260,10 @@ def rotation(coord, rMat): #Apply a rotation to coordinates
def cut_bath(rBath, coords): #Select which atoms are in the bath with distance constraint (sphere) def cut_bath(rBath, coords): #Select which atoms are in the bath with distance constraint (sphere)
bath = [] bath = []
start = datetime.datetime.now()
for i in range(len(coords)): for i in range(len(coords)):
now = datetime.datetime.now()
printProgressBar(start,now,i+1,len(coords),prefix='Cutting the bath',length=50)
if distance([0,0,0],[coords[i][0],coords[i][1],coords[i][2]]) <= rBath: if distance([0,0,0],[coords[i][0],coords[i][1],coords[i][2]]) <= rBath:
bath.append([coords[i][0], coords[i][1], coords[i][2], coords[i][3], 'C']) bath.append([coords[i][0], coords[i][1], coords[i][2], coords[i][3], 'C'])
@ -233,8 +272,10 @@ def cut_bath(rBath, coords): #Select which atoms are in the bath with distance c
def set_pp(rPP,coords, notIn): #Select which atoms are in the first shell of pseudopotential def set_pp(rPP,coords, notIn): #Select which atoms are in the first shell of pseudopotential
pp = [] pp = []
start = datetime.datetime.now()
for i in range(len(coords)): for i in range(len(coords)):
now = datetime.datetime.now()
printProgressBar(start,now,i+1,len(coords),prefix='Finding the first shell',length=50)
for j in range(len(coords)): for j in range(len(coords)):
if coords[i][4] == 'O': if coords[i][4] == 'O':
if coords[j][4] == 'C' and coords[j][3] not in notIn: if coords[j][4] == 'C' and coords[j][3] not in notIn:
@ -248,13 +289,16 @@ def set_pp(rPP,coords, notIn): #Select which atoms are in the first shell of pse
def find_frag(pattern, n, coords): #We mark the atoms in the bath corresponding to def find_frag(pattern, n, coords): #We mark the atoms in the bath corresponding to
#the fragment according to user input #the fragment according to user input
inFrag = [] inFrag = []
start = datetime.datetime.now()
for k in range(n): for k in range(n):
closest = [100,100,100] closest = [100,100,100]
now = datetime.datetime.now()
printProgressBar(start,now,k+1,n,prefix='Finding the fragment',length=50)
for j in coords: for j in coords:
if j[3] == pattern[1]: if j[3] == pattern[1]:
if distance(j,[0,0,0]) < distance([0,0,0],closest) and [j[0],j[1],j[2],distance(j,j), coords.index(j)] not in inFrag: if distance(j,[0,0,0]) < distance([0,0,0],closest) and [j[0],j[1],j[2],distance(j,j), coords.index(j)] not in inFrag:
closest = [j[0],j[1],j[2],distance(j,j), coords.index(j)] closest = [j[0],j[1],j[2],distance(j,j), coords.index(j)]
for i in range(1,len(pattern)/2): for i in range(1,len(pattern)//2):
inPattern = [closest] inPattern = [closest]
for j in range(int(pattern[2*i])): for j in range(int(pattern[2*i])):
inPattern.append([100,100,100,distance([100,100,100],closest)]) inPattern.append([100,100,100,distance([100,100,100],closest)])
@ -273,6 +317,8 @@ def find_frag(pattern, n, coords):
def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the coordinates def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the coordinates
newCoord = [] newCoord = []
total = len(coord)
start = datetime.datetime.now()
while coord != []: while coord != []:
toDel = [] toDel = []
@ -304,18 +350,17 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
newCoord[-1].append(charges[index]) newCoord[-1].append(charges[index])
toDel.append(index) toDel.append(index)
elif da < distance(t,d) and distance(t,d) < DA: elif da < distance(t,d) and distance(t,d) < DA:
print "Error : This atom should not be there",distance(t,d),t,d,a,charges[index] print("Error : This atom should not be there",distance(t,d),t,d,a,charges[index])
print "Are you sure about the xOz symmetry operation ?" print("Are you sure about the xOz symmetry operation ?")
break break
if 'yOz' in operations: if 'yOz' in operations:
if distance(t,b) <= da: if distance(t,b) <= da:
newCoord.append(b) newCoord.append(b)
newCoord[-1].append(name+'b') newCoord[-1].append(name+'b')
newCoord[-1].append(charges[index]) newCoord[-1].append(charges[index])
toDel.append(index)
elif da < distance(t,b) and distance(t,b) < DA: elif da < distance(t,b) and distance(t,b) < DA:
print "Error : This atom should not be there",distance(t,b),t,b,a,charges[index] print("Error : This atom should not be there",distance(t,d),t,d,a,charges[index])
print "Are you sure about the yOz symmetry operation ?" print("Are you sure about the xOz symmetry operation ?")
break break
if 'C2z' in operations: if 'C2z' in operations:
if distance(t,c) <= da: if distance(t,c) <= da:
@ -324,8 +369,8 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
newCoord[-1].append(charges[index]) newCoord[-1].append(charges[index])
toDel.append(index) toDel.append(index)
elif da < distance(t,c) and distance(t,c) < DA: elif da < distance(t,c) and distance(t,c) < DA:
print "Error : This atom should not be there",distance(t,c),t,c,a,charges[index] print("Error : This atom should not be there",distance(t,d),t,d,a,charges[index])
print "Are you sure about the C2z axis ?" print("Are you sure about the xOz symmetry operation ?")
break break
if 'xOy' in operations: if 'xOy' in operations:
if distance(t,e) <= da: if distance(t,e) <= da:
@ -334,8 +379,8 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
newCoord[-1].append(charges[index]) newCoord[-1].append(charges[index])
toDel.append(index) toDel.append(index)
elif da < distance(t,e) and distance(t,e) < DA: elif da < distance(t,e) and distance(t,e) < DA:
print "Error : This atom should not be there",distance(t,e),t,e,a,charges[index] print("Error : This atom should not be there",distance(t,d),t,d,a,charges[index])
print "Are you sure about the xOy operation ?" print("Are you sure about the xOz symmetry operation ?")
break break
if 'C2y' in operations: if 'C2y' in operations:
if distance(t,f) <= da: if distance(t,f) <= da:
@ -344,8 +389,8 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
newCoord[-1].append(charges[index]) newCoord[-1].append(charges[index])
toDel.append(index) toDel.append(index)
elif da < distance(t,f) and distance(t,f) < DA: elif da < distance(t,f) and distance(t,f) < DA:
print "Error : This atom should not be there",distance(t,f),t,f,a,charges[index] print("Error : This atom should not be there",distance(t,d),t,d,a,charges[index])
print "Are you sure about the C2y axis ?" print("Are you sure about the xOz symmetry operation ?")
break break
if 'C2x' in operations: if 'C2x' in operations:
if distance(t,g) <= da: if distance(t,g) <= da:
@ -354,8 +399,8 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
newCoord[-1].append(charges[index]) newCoord[-1].append(charges[index])
toDel.append(index) toDel.append(index)
elif da < distance(t,g) and distance(t,g) < DA: elif da < distance(t,g) and distance(t,g) < DA:
print "Error : This atom should not be there",distance(t,g),t,g,a,charges[index] print("Error : This atom should not be there",distance(t,d),t,d,a,charges[index])
print "Are you sure about the C2x axis ?" print("Are you sure about the xOz symmetry operation ?")
break break
if 'i' in operations: if 'i' in operations:
if distance(t,h) <= da: if distance(t,h) <= da:
@ -364,8 +409,8 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
newCoord[-1].append(charges[index]) newCoord[-1].append(charges[index])
toDel.append(index) toDel.append(index)
elif da < distance(t,h) and distance(t,h) < DA: elif da < distance(t,h) and distance(t,h) < DA:
print "Error : This atom should not be there",distance(t,h),t,h,a,charges[index] print("Error : This atom should not be there",distance(t,d),t,d,a,charges[index])
print "Are you sure about the i operation ?" print("Are you sure about the xOz symmetry operation ?")
break break
@ -373,6 +418,8 @@ def symmetry(coord,atoms,charges, operations): #Find symmetry elements in the co
del coord[toDel[m]-m] del coord[toDel[m]-m]
del atoms[toDel[m]-m] del atoms[toDel[m]-m]
del charges[toDel[m]-m] del charges[toDel[m]-m]
now = datetime.datetime.now()
printProgressBar(start,now,total-len(coord),total,prefix='Treating Symmetry',length=50,decimals=3)
return newCoord return newCoord
@ -394,8 +441,8 @@ def write_input(fragCoord,ppCoord,bathCoord,fileName, sym):
g.write('CHARGES\n') g.write('CHARGES\n')
g.write('LABEL X Y Z CHARGE\n') g.write('LABEL X Y Z CHARGE\n')
for i in range(len(bathCoord)): for i in range(len(bathCoord)):
# if bathCoord[i][3][-1] == 'a': if bathCoord[i][3][-1] == 'a':
g.write('%8s % 7.3f % 7.3f % 7.3f % 8.5f\n'%(bathCoord[i][3]+str(i+1),bathCoord[i][0],bathCoord[i][1],bathCoord[i][2],bathCoord[i][4])) g.write('%8s % 7.3f % 7.3f % 7.3f % 8.5f\n'%(bathCoord[i][3].replace('a','')+str(i+1),bathCoord[i][0],bathCoord[i][1],bathCoord[i][2],bathCoord[i][4]))
if sym == 'x': if sym == 'x':
g.write('FRAGMENT\n') g.write('FRAGMENT\n')
g.write('LABEL X Y Z CHARGE\n') g.write('LABEL X Y Z CHARGE\n')
@ -473,9 +520,12 @@ def optimization(coords):
return coords return coords
def count_neighbours(coords): def count_neighbours(coords):
start = datetime.datetime.now()
for i in coords: for i in coords:
neighbour = 0 neighbour = 0
for j in coords: for j in coords:
now = datetime.datetime.now()
printProgressBar(start,now,coords.index(j)+coords.index(i),2*len(coords),prefix='Counting neighbours',length=50)
if distance(i,j) < atoms[atoms.index(i[3])+3] and i[3] != j[3]: if distance(i,j) < atoms[atoms.index(i[3])+3] and i[3] != j[3]:
neighbour += 1 neighbour += 1
if neighbour == atoms[atoms.index(i[3])+2]: if neighbour == atoms[atoms.index(i[3])+2]:
@ -620,11 +670,15 @@ def main():
if sym != 'x': if sym != 'x':
rep = 0 if norep == 0:
for i in range(len(coords)-1): rep = 0
for j in range(i+1,len(coords)): start = datetime.datetime.now()
rep += (coords[i][5]*coords[j][5])/distance(coords[i],coords[j]) for i in range(len(coords)-1):
print("Nuclear repulsion before symmetry : %f"%rep) for j in range(i+1,len(coords)):
now = datetime.datetime.now()
printProgressBar(start,now,i*len(coords)+j,len(coords)**2,prefix='Calculating nuclear repulsion',length=50)
rep += (coords[i][5]*coords[j][5])/distance(coords[i],coords[j])
print("Nuclear repulsion before symmetry : %f"%rep)
frag = symmetry([[i[0],i[1],i[2]] for i in frag],[i[3] for i in frag], [i[5] for i in frag], sym) frag = symmetry([[i[0],i[1],i[2]] for i in frag],[i[3] for i in frag], [i[5] for i in frag], sym)
pp = symmetry([[i[0],i[1],i[2]] for i in pp],[i[3] for i in pp], [i[5] for i in pp], sym) pp = symmetry([[i[0],i[1],i[2]] for i in pp],[i[3] for i in pp], [i[5] for i in pp], sym)
@ -633,12 +687,15 @@ def main():
coords = frag+pp+bath coords = frag+pp+bath
rep = 0 if norep == 0:
for i in range(len(coords)-1): start = datetime.datetime.now()
for j in range(i+1,len(coords)): rep = 0
rep += (coords[i][4]*coords[j][4])/distance(coords[i],coords[j]) for i in range(len(coords)-1):
for j in range(i+1,len(coords)):
print("Nuclear repulsion after symmetry : %f"%rep) now = datetime.datetime.now()
printProgressBar(start,now,i*len(coords)+j,len(coords)**2,prefix='Calculating nuclear repulsion',length=50)
rep += (coords[i][4]*coords[j][4])/distance(coords[i],coords[j])
print("Nuclear repulsion after symmetry : %f"%rep)
else: else:
frag = [[i[0],i[1],i[2],i[3],i[5]] for i in frag] frag = [[i[0],i[1],i[2],i[3],i[5]] for i in frag]
pp = [[i[0],i[1],i[2],i[3],i[5]] for i in pp] pp = [[i[0],i[1],i[2],i[3],i[5]] for i in pp]