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Add possibility to make an initial translation, can be useful to reach precise geometry

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Léo Gaspard 2019-04-05 17:55:18 +02:00
parent b3344adfdf
commit 65904c8769
1 changed files with 16 additions and 8 deletions
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22
generer.py
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@ -5,9 +5,9 @@ import operator
###### CONSTANTS #######
a = 5.48463
b = 5.48463
c = 25.7977
a = 4.030
b = 4.030
c = 13.333
alpha = 90
beta = 90
@ -21,6 +21,7 @@ DA = 1.5
chO = -2.00
chIr = 4.00
chSr = 2.00
chBa = 2.00
dIrO = 2.50
dSrO = 3.10
#######################
@ -283,7 +284,7 @@ def write_input(fragCoord,ppCoord,bathCoord,fileName, sym):
g.write('%4s % 5.3f % 5.3f % 5.3f angstrom\n' %(ppCoord[i][3].replace('a','')+str(i+1),ppCoord[i][0],ppCoord[i][1],ppCoord[i][2]))
g.write("\n\n")
for i in range(len(bathCoord)):
if bathCoord[i][3][-1] == 'a':
# if bathCoord[i][3][-1] == 'a':
g.write('% 5.3f % 5.3f % 5.3f % 5.3f 0. 0. 0. \n'%(bathCoord[i][0],bathCoord[i][1],bathCoord[i][2],bathCoord[i][4]))
if sym == 'n':
for i in range(len(fragCoord)):
@ -330,6 +331,13 @@ def main():
labels = [i[3] for i in coords]
if raw_input("Do you want to make an initial translation ? (y/n) ") == "y":
trsl = raw_input("Enter the coordinates of the translation ").split()
trsl[0] = float(trsl[0])
trsl[1] = float(trsl[1])
trsl[2] = float(trsl[2])
translation(trsl,coords)
center = raw_input("Specify the center of the fragment (if between atoms, specify them all) ").split() #Searching for the center according to user
centers = [] #input, and translating the coordinates
for i in range(len(center)):
@ -343,7 +351,6 @@ def main():
if i[3] in center:
if distance(i,[0,0,0]) <= centers[-1][3]:
centers[-1] = [i[0],i[1],i[2],distance(i,[0,0,0])]
newOgn = np.mean(np.array(centers),axis=0)
newOgn = [newOgn[0], newOgn[1], newOgn[2]]
@ -416,7 +423,7 @@ def main():
g.write('%s % 6.2f % 6.2f % 6.2f \n'%(j[3],j[0],j[1],j[2]))
g.close()
os.system('avogadro tmp.xyz')
#os.system('rm tmp.xyz')
os.system('rm tmp.xyz')
while sym != 'y' and sym != 'n':
sym = raw_input("Do you want to treat the symmetry ? (y/n) ")
@ -431,7 +438,8 @@ def main():
frag = symmetry([[i[0],i[1],i[2]] for i in frag],[i[3] for i in frag], [i[5] for i in frag], operation)
pp = symmetry([[i[0],i[1],i[2]] for i in pp],[i[3] for i in pp], [i[5] for i in pp], operation)
bath = symmetry([[i[0],i[1],i[2]] for i in bath],[i[3] for i in bath], [i[5] for i in bath], operation)
#bath = symmetry([[i[0],i[1],i[2]] for i in bath],[i[3] for i in bath], [i[5] for i in bath], operation)
bath = [[i[0],i[1],i[2],i[3],i[5]] for i in bath]
coords = frag+pp+bath