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CopyCluster.py
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CopyCluster.py
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# -*- coding: utf-8 -*-
"""
@author: Ani Chattaraj
"""
import numpy as np
import matplotlib.pyplot as plt
from numpy import mean, pi, array
import re
font = {'family' : 'Arial',
'size' : 16}
plt.rc('font', **font)
def calc_RadGy(posList):
# posList = N,3 array for N sites
com = np.mean(posList, axis=0) # center of mass
Rg2 = np.mean(np.sum((posList - com)**2, axis=1))
return com, np.sqrt(Rg2)
def readFile(file):
with open(file,'r') as tf:
lines = tf.readlines()
return lines
def getBlock(lines, str1='', str2='', skipName=True):
# skipName => whether to return heading
i1, i2 = 0, 0
for i, line in enumerate(lines):
if re.search(str1, line):
i1 = i
if re.search(str2, line):
i2 = i
if str2 == '':
i2 = len(lines)
if skipName:
return lines[i1+1:i2]
else:
return lines[i1:i2]
def processCoorBlock(cBlock):
tmp_frame = array([line.strip().split() for line in cBlock[1:-1]])
atomId = tmp_frame[:,0].astype(np.int32)
atomTyp = tmp_frame[:,2].astype(np.int32)
charge = tmp_frame[:,3].astype(np.float32)
mId = tmp_frame[:,1].astype(np.int32)
pos = tmp_frame[:,[4,5,6]].astype(np.float32)
return atomId, mId, atomTyp, charge, pos, max(atomId), max(mId)
def processBondBlock(bBlock):
tmp_frame = array([line.strip().split() for line in bBlock[1:-1]])
bId = tmp_frame[:,0].astype(np.int32)
bTyp = tmp_frame[:,1].astype(np.int32)
bPair = tmp_frame[:,[-2,-1]].astype(np.int32)
return bId, bTyp, bPair, max(bId)
def processAngleBlock(aBlock):
tmp_frame = array([line.strip().split() for line in aBlock[1:]])
aId = tmp_frame[:,0].astype(np.int32)
aTyp = tmp_frame[:,1].astype(np.int32)
angle = tmp_frame[:,[2,3,4]].astype(np.int32)
return aId, aTyp, angle, max(aId)
def copyCoorBlock(cBlock, dist=300):
# dist: distance between two clusters along z direction
atomId, mId, atomTyp, charge, pos, aCount, mCount = processCoorBlock(cBlock)
# first copy
aId1 = atomId[:, np.newaxis] # row to column vector
mId1 = mId[:, np.newaxis]
charge1 = charge[:, np.newaxis]
aTyp1 = atomTyp[:, np.newaxis]
cluster1 = np.concatenate((aId1,mId1,aTyp1,charge1,pos), axis=1)
# second copy
aId2 = (atomId + aCount)[:, np.newaxis] # row to column vector
mId2 = (mId + mCount)[:, np.newaxis]
charge2 = charge[:, np.newaxis]
aTyp2 = atomTyp[:, np.newaxis]
pos2 = np.copy(pos)
c1, Rg1 = calc_RadGy(pos)
dist = 3*Rg1
pos2[:,2] = pos[:,2] + dist
c2, Rg2 = calc_RadGy(pos2)
print(f'Radius of Gyration of the Cluster : {Rg1:.2f} A')
cluster2 = np.concatenate((aId2,mId2,aTyp2,charge2,pos2), axis=1)
return np.concatenate((cluster1, cluster2), axis=0), (c1,c2), Rg1
def copyBondBlock(bBlock, cBlock):
atomId, mId, atomTyp, charge, pos, aCount, mCount = processCoorBlock(cBlock)
bId, bTyp, bp, bCount = processBondBlock(bBlock)
# first copy
bId1 = bId[:, np.newaxis] # row to column vector
bTyp1 = bTyp[:, np.newaxis]
cluster1 = np.concatenate((bId1, bTyp1, bp), axis=1)
# second copy
bId2 = (bId + bCount)[:, np.newaxis]
bTyp2 = bTyp[:, np.newaxis]
bp2 = bp + aCount
cluster2 = np.concatenate((bId2, bTyp2, bp2), axis=1)
return np.concatenate((cluster1, cluster2), axis=0)
def copyAngleBlock(aBlock, cBlock):
atomId, mId, atomTyp, charge, pos, atomCount, mCount = processCoorBlock(cBlock)
aId, aTyp, angle, aCount = processAngleBlock(aBlock)
# first copy
aId1 = aId[:, np.newaxis] # row to column vector
aTyp1 = aTyp[:, np.newaxis]
cluster1 = np.concatenate((aId1, aTyp1, angle), axis=1)
# second copy
aId2 = (aId + aCount)[:, np.newaxis]
aTyp2 = aTyp[:, np.newaxis]
angle2 = angle + atomCount
cluster2 = np.concatenate((aId2, aTyp2, angle2), axis=1)
return np.concatenate((cluster1, cluster2), axis=0)
def writeLines(fileStream, Lines, arr=True):
if arr:
for line in Lines:
fileStream.writelines([f'{l} ' for l in line])
fileStream.write('\n')
else:
fileStream.writelines([f'{line} ' for line in Lines])
fileStream.write('\n')
def writeFile(fName, mB, cB, bB, aB, centers, Rg):
# fileName, mass, coordinates, bond, angle (block),
# centers of two clusters, RadGy of the clusters
atomCount, _ = cB.shape
bondCount, _ = bB.shape
angleCount, _ = aB.shape
atomTypes = len(set(cB[:,2]))
bTypes = len(set(bB[:,1]))
aTypes = len(set(aB[:,1]))
c1, c2 = centers
x1, y1, z1 = c1
x2, y2, z2 = c2
bound = Rg + 200
x_low = int(x1 - bound)
x_hi = int(x1 + bound)
y_low = int(y1 - bound)
y_hi = int(y1 + bound)
z_min, z_max = min(z1, z2), max(z1,z2)
z_low = int(z_min - Rg - 100)
z_hi = int(z_max + Rg + 100)
CV_max = (z_hi - z_low) - 2*Rg
#print('ColVar_max along Z: ', round(CV_max))
with open(fName, 'w') as of:
of.write('LAMMPS Description \n\n')
of.write(f'{atomCount} atoms\n')
of.write(f'{bondCount} bonds\n')
of.write(f'{angleCount} angles\n\n')
of.write(f'{atomTypes} atom types\n')
of.write(f'{bTypes} bond types\n')
of.write('10 extra bond per atom\n')
of.write(f'{aTypes} angle types\n\n')
of.write(f'{x_low} {x_hi} xlo xhi\n')
of.write(f'{y_low} {y_hi} ylo yhi\n')
of.write(f'{z_low} {z_hi} zlo zhi\n\n')
writeLines(of, mB, arr=False)
of.write('Atoms\n\n')
#writeLines(of, cB[:])
# converting atomID, Type and molID into intergers
cList = [[int(e[0]), int(e[1]), int(e[2]), e[3],e[4],e[5],e[6]] for e in cB]
writeLines(of, cList)
of.write('\nBonds\n\n')
writeLines(of, bB[:])
of.write('\nAngles\n\n')
writeLines(of, aB[:])
print('Copied the cluster and wrote the data in ', fName)