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Updated and added utility scripts

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This commit is contained in:
Oliver Henrich
2022-04-28 19:00:40 +01:00
parent e8606a51da
commit c5fc65433a
2 changed files with 190 additions and 28 deletions
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57
examples/PACKAGES/cgdna/util/lmp2vis.py
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@ -37,9 +37,9 @@ import sys, math, subprocess
# converts quaternion DOF into local body reference frame
def q_to_exyz(q1,q2,q3,q4):
q=[q1, q2, q3, q4]
ex= [0, 0, 0]
ey = [0, 0,0]
q = [q1, q2, q3, q4]
ex = [0, 0, 0]
ey = [0, 0, 0]
ez = [0, 0, 0]
ex[0]=q[0]*q[0]+q[1]*q[1]-q[2]*q[2]-q[3]*q[3]
@ -57,22 +57,22 @@ def q_to_exyz(q1,q2,q3,q4):
return ex,ey,ez
# processes line by line of LAMMPS trajectory
def transform(line):
def transform(line, colind):
list1 = line.split()
ident, mol, typ = int(list1[0]), int(list1[1]), int(list1[2])
ident, mol, typ = int(list1[colind[0]]), int(list1[colind[1]]), int(list1[colind[2]])
typb = typ + 10 # defines new backbone types, here offset is 10 from atom (base) type
x, y, z = float(list1[3]), float(list1[4]), float(list1[5])
vx, vy, vz = float(list1[9]), float(list1[10]), float(list1[11])
x, y, z = float(list1[colind[3]]), float(list1[colind[4]]), float(list1[colind[5]])
vx, vy, vz = float(list1[colind[6]]), float(list1[colind[7]]), float(list1[colind[8]])
c_quat1, c_quat2, c_quat3, c_quat4 = \
float(list1[12]), float(list1[13]), float(list1[14]), float(list1[15])
float(list1[colind[9]]), float(list1[colind[10]]), float(list1[colind[11]]), float(list1[colind[12]])
ex, ey, ez = q_to_exyz(c_quat1, c_quat2, c_quat3, c_quat4)
# position of sugar-phosphate backbone interaction site in oxDNA2
x1, y1, z1 = x -0.34*ex[0]+0.3408*ey[0],y -0.34*ex[1]+0.3408*ey[1], z-0.34*ex[2]+0.3408*ey[2]
# position of base interaction site in oxDNA2
# position of base interaction site in oxDNA/oxDNA2
x2, y2, z2 = x +0.4*ex[0], y + 0.4*ex[1], z+0.4*ex[2]
# compose basic output data: id, molecule id, type, position, velocity quaternion
@ -96,7 +96,7 @@ def transform(line):
line1 += '\n'
line2 += '\n'
line= line1 + line2
line = line1 + line2
return line
### main part ###
@ -132,24 +132,25 @@ except:
r=open(infilename,'r')
w=open(outfilename,'w+')
line=r.readline() # read first line in file
pass1 = 0
while line != '':
for line in r:
sys.stdout.write('# Processed %3d %%\r' % (100*n/nlines))
# find number of atoms in timestep and double
if line.find('NUMBER OF ATOMS') != -1:
# find number of atoms in timestep
if line.find('ITEM: NUMBER OF ATOMS') != -1:
w.write(line)
N=int(r.readline())
# write to output file and read next line
w.write('%d'%int(2*N)+'\n')
line=r.readline()
n+=2
# find beginning of atom data section
if line.find('ITEM: ATOMS') != -1:
# first pass: extract column number of ID, molecule ID, type, postion, velocity, quaternion
if n==0:
# first pass: extract column number of ID, molecule ID, type, postion, velocity, quaternion in header line
if pass1 == 0:
linestring=line.split()
idindex = linestring.index('id')
molindex = linestring.index('mol')
@ -177,24 +178,24 @@ while line != '':
header += ' shape[0] shape[1] shape[2]'
header += '\n'
### begin processing atom data
i=0
# store column number in data line, -2 offset form header line
colind = [idindex-2,molindex-2,typeindex-2,xindex-2,yindex-2,zindex-2,\
vxindex-2,vyindex-2,vzindex-2,qwindex-2,qxindex-2,qyindex-2,qzindex-2]
pass1 = 1
# begin processing atom data in timestep
w.write(header)
# tranform each atom and write to output file
while i<N:
for i in range(N):
line=r.readline()
w.write(transform(line))
i +=1
n +=1
else:
line=r.readline() # read next line
### end processing atom data
w.write(transform(line,colind))
n+=1
# end processing atom data
# duplicate all lines that are not in atom data section
# duplicate all lines that are not in any other section
else:
w.write(line)
line=r.readline()
n+=1
print('# Done ')

161
examples/PACKAGES/cgdna/util/nbps.py Executable file
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@ -0,0 +1,161 @@
#!/usr/bin/env python
"""
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/ Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Oliver Henrich (University of Strathclyde, Glasgow)
------------------------------------------------------------------------- */
Program:
Usage:
$$ python
Requirements:
The LAMMPS trajectory input file needs to contain the following data columns:
id mol type x y z c_quat[1] c_quat[2] c_quat[3] c_quat[4]
"""
import sys, math, subprocess
# converts quaternion DOF into local body reference frame
def q_to_exyz(q1,q2,q3,q4):
q = [q1, q2, q3, q4]
ex = [0, 0, 0]
ey = [0, 0, 0]
ez = [0, 0, 0]
ex[0]=q[0]*q[0]+q[1]*q[1]-q[2]*q[2]-q[3]*q[3]
ex[1]=2*(q[1]*q[2]+q[0]*q[3])
ex[2]=2*(q[1]*q[3]-q[0]*q[2])
ey[0]=2*(q[1]*q[2]-q[0]*q[3])
ey[1]=q[0]*q[0]-q[1]*q[1]+q[2]*q[2]-q[3]*q[3]
ey[2]=2*(q[2]*q[3]+q[0]*q[1])
ez[0]=2*(q[1]*q[3]+q[0]*q[2])
ez[1]=2*(q[2]*q[3]-q[0]*q[1])
ez[2]=q[0]*q[0]-q[1]*q[1]-q[2]*q[2]+q[3]*q[3]
return ex,ey,ez
# processes line by line of LAMMPS trajectory
def transform(line, colind):
list1 = line.split()
ident, mol, typ = int(list1[colind[0]]), int(list1[colind[1]]), int(list1[colind[2]])
x, y, z = float(list1[colind[3]]), float(list1[colind[4]]), float(list1[colind[5]])
c_quat1, c_quat2, c_quat3, c_quat4 = \
float(list1[colind[6]]), float(list1[colind[7]]), float(list1[colind[8]]), float(list1[colind[9]])
ex, ey, ez = q_to_exyz(c_quat1, c_quat2, c_quat3, c_quat4)
# position of base interaction site in oxDNA/oxDNA2
x2, y2, z2 = x +0.4*ex[0], y + 0.4*ex[1], z+0.4*ex[2]
# compose basic output data: id, molecule id, type, position
line2 = [ident, mol, typ, x2, y2, z2]
return line2
### main part ###
# digest command line input
if len(sys.argv)<3:
print("Syntax: $$ python nbps.py input_filename output_filename")
sys.exit(1)
if len(sys.argv)==3:
infilename = sys.argv[1]
outfilename = sys.argv[2]
print('# Calculating number of base paris from LAMMPS trajectory output')
# count lines to process for progress report
n = 0
try:
result = subprocess.run(['wc', '-l', '%s'%infilename], stdout=subprocess.PIPE)
reslist=str(result).split()
nlines=float(reslist[5])
except:
nlines = 100
r=open(infilename,'r')
w=open(outfilename,'w+')
pass1 = 0
for line in r:
sys.stdout.write('# Processed %3d %%\r' % (100*n/nlines))
# find timestep number
if line.find('ITEM: TIMESTEP') != -1:
t=int(r.readline())
n+=1
# find number of atoms in timestep
if line.find('ITEM: NUMBER OF ATOMS') != -1:
N=int(r.readline())
n+=1
# find beginning of atom data section
if line.find('ITEM: ATOMS') != -1:
# first pass: extract column number of ID, molecule ID, type, postion, velocity, quaternion in header line
if pass1 == 0:
linestring=line.split()
idindex = linestring.index('id')
molindex = linestring.index('mol')
typeindex = linestring.index('type')
xindex = linestring.index('x')
yindex = linestring.index('y')
zindex = linestring.index('z')
qwindex = linestring.index('c_quat[1]')
qxindex = linestring.index('c_quat[2]')
qyindex = linestring.index('c_quat[3]')
qzindex = linestring.index('c_quat[4]')
# store column number in data line, -2 offset form header line
colind = [idindex-2,molindex-2,typeindex-2,xindex-2,yindex-2,zindex-2,\
qwindex-2,qxindex-2,qyindex-2,qzindex-2]
pass1 = 1
# begin processing atom data
atom = []
for i in range(N):
line=r.readline()
atom.append(transform(line,colind))
n +=1
rc2 = 0.2
nbp = 0
for i in range(N):
for j in range(i+1,N):
if (atom[i][2]+atom[j][2])%4 and atom[i][1]!=atom[j][1]:
r2 = (atom[i][3]-atom[j][3])*(atom[i][3]-atom[j][3]) +\
(atom[i][4]-atom[j][4])*(atom[i][4]-atom[j][4]) +\
(atom[i][5]-atom[j][5])*(atom[i][5]-atom[j][5])
if r2<rc2:
nbp += 1
w.write('%d %d\n' % (t,nbp))
# end processing atom data
n+=1
print('# Done ')
r.close()
w.close()