forked from lijiext/lammps
307 lines
8.6 KiB
Python
307 lines
8.6 KiB
Python
#! /usr/freeware/bin/python
|
|
|
|
#
|
|
# This is dump2trj, a program written by Keir E. Novik to convert
|
|
# Lammps position dump files to Amber trajectory files.
|
|
#
|
|
# Copyright 2000, 2001 Keir E. Novik; all rights reserved.
|
|
#
|
|
# Modified by Vikas Varshney, U Akron, 5 July 2005, as described in README
|
|
#
|
|
|
|
#============================================================
|
|
|
|
def Convert_files():
|
|
'Handle the whole conversion process'
|
|
|
|
print
|
|
print 'Welcome to dump2trj, a program to convert Lammps position dump files to\nAmber trajectory format!'
|
|
print
|
|
|
|
Basename_list = Find_dump_files()
|
|
|
|
for Basename in Basename_list:
|
|
t = Trajectory()
|
|
if t.Read_dump(Basename):
|
|
t.Write_trj(Basename)
|
|
del t
|
|
print
|
|
|
|
#============================================================
|
|
|
|
def Find_dump_files():
|
|
'Look for sets of Lammps position dump files to process'
|
|
|
|
'''If passed something on the command line, treat it as a list of
|
|
files to process. Otherwise, look for *.dump in the current
|
|
directory.
|
|
'''
|
|
|
|
import os, sys
|
|
|
|
Basename_list = []
|
|
|
|
# Extract basenames from command line
|
|
for Name in sys.argv[1:]:
|
|
if Name[-5:] == '.dump':
|
|
Basename_list.append(Name[:-5])
|
|
else:
|
|
Basename_list.append(Name)
|
|
|
|
if Basename_list == []:
|
|
print 'Looking for Lammps dump files...',
|
|
Dir_list = os.listdir('.')
|
|
for Filename in Dir_list:
|
|
if Filename[-5:] == '.dump':
|
|
Basename_list.append(Filename[:-5])
|
|
Basename_list.sort()
|
|
if Basename_list != []:
|
|
print 'found',
|
|
for i in range(len(Basename_list)-1):
|
|
print Basename_list[i] + ',',
|
|
print Basename_list[-1] + '\n'
|
|
|
|
if Basename_list == []:
|
|
print 'none.\n'
|
|
|
|
return Basename_list
|
|
|
|
#============================================================
|
|
|
|
class Snapshot:
|
|
def __init__(self, The_trajectory):
|
|
'Initialize the Snapshot class'
|
|
|
|
self.timestep = The_trajectory.timestep
|
|
self.atoms = The_trajectory.atoms
|
|
self.xlo = The_trajectory.xlo
|
|
self.xhi = The_trajectory.xhi
|
|
self.ylo = The_trajectory.ylo
|
|
self.yhi = The_trajectory.yhi
|
|
self.zlo = The_trajectory.zlo
|
|
self.zhi = The_trajectory.zhi
|
|
|
|
#--------------------------------------------------------
|
|
|
|
def Read_dump(self, Lines):
|
|
'Read a snapshot (timestep) from a Lammps position dump file'
|
|
|
|
'''Trajectory.Read_dump() will pass us only the lines we need.
|
|
'''
|
|
|
|
self.Atom_list = Lines
|
|
|
|
#--------------------------------------------------------
|
|
|
|
def Write_trj(self, F):
|
|
'Write a snapshot (timestep) to an Amber trajectory file'
|
|
|
|
'''The Atom_list must be sorted, as it may not be in order
|
|
(for example, in a parallel Lammps simulation).
|
|
'''
|
|
|
|
import string
|
|
|
|
xBOX = (self.xhi - self.xlo)
|
|
yBOX = (self.yhi - self.ylo)
|
|
zBOX = (self.zhi - self.zlo)
|
|
|
|
Min = min(self.xlo, self.ylo, self.zlo)
|
|
Max = max(self.xhi, self.yhi, self.zhi, xBOX, yBOX, zBOX)
|
|
if Min <= -1000 or Max >= 10000:
|
|
print '(error: coordinates too large!)'
|
|
return
|
|
|
|
Print_list = []
|
|
|
|
for Line in NumericalSort(self.Atom_list):
|
|
Item_list = string.split(Line)
|
|
x = xBOX * (Float(Item_list[2])+Float(Item_list[5])) # Modified main box x-coordinate to actual x-coordinate
|
|
y = yBOX * (Float(Item_list[3])+Float(Item_list[6])) # Modified main box y-coordinate to actual y-coordinate
|
|
z = zBOX * (Float(Item_list[4])+Float(Item_list[7])) # Modified main box z-coordinate to actual z-coordinate
|
|
Print_list.append('%(x)8.3f' % vars())
|
|
Print_list.append('%(y)8.3f' % vars())
|
|
Print_list.append('%(z)8.3f' % vars())
|
|
|
|
if len(Print_list) > 9:
|
|
Line = ''
|
|
for j in range(10):
|
|
Line = Line + Print_list[j]
|
|
Line = Line + '\n'
|
|
Print_list = Print_list[10:]
|
|
|
|
try:
|
|
F.write(Line)
|
|
except IOError, Detail:
|
|
print '(error:', Detail[1] + '!)'
|
|
F.close()
|
|
return
|
|
|
|
if len(Print_list) > 0:
|
|
Line = ''
|
|
for j in range(len(Print_list)):
|
|
Line = Line + Print_list[j]
|
|
Line = Line + '\n'
|
|
|
|
try:
|
|
F.write(Line)
|
|
except IOError, Detail:
|
|
print '(error:', Detail[1] + '!)'
|
|
F.close()
|
|
return
|
|
|
|
Line = '%(xBOX)8.3f%(yBOX)8.3f%(zBOX)8.3f\n' % vars()
|
|
try:
|
|
F.write(Line)
|
|
except IOError, Detail:
|
|
print '(error:', Detail[1] + '!)'
|
|
F.close()
|
|
return
|
|
|
|
#============================================================
|
|
|
|
class Trajectory:
|
|
|
|
def Read_dump(self, Basename):
|
|
'Read a Lammps position dump file'
|
|
|
|
import string, sys
|
|
|
|
Filename = Basename + '.dump'
|
|
|
|
print 'Reading', Filename + '...',
|
|
sys.stdout.flush()
|
|
|
|
try:
|
|
F = open(Filename)
|
|
except IOError, Detail:
|
|
print '(error:', Detail[1] + '!)'
|
|
return 0
|
|
|
|
try:
|
|
Lines = F.readlines()
|
|
except IOError, Detail:
|
|
print '(error:', Detail[1] + '!)'
|
|
F.close()
|
|
return 0
|
|
|
|
F.close()
|
|
|
|
i = 0
|
|
self.Snapshot_list = []
|
|
|
|
# Parse the dump
|
|
while i < len(Lines):
|
|
|
|
if string.find(Lines[i], 'ITEM: TIMESTEP') != -1:
|
|
# Read the timestep
|
|
self.timestep = int(Lines[i+1])
|
|
i = i + 2
|
|
|
|
elif string.find(Lines[i], 'ITEM: NUMBER OF ATOMS') != -1:
|
|
# Read the number of atoms
|
|
self.atoms = int(Lines[i+1])
|
|
i = i + 2
|
|
|
|
elif string.find(Lines[i], 'ITEM: BOX BOUNDS') != -1:
|
|
# Read the periodic box boundaries
|
|
Item_list = string.split(Lines[i+1])
|
|
self.xlo = Float(Item_list[0])
|
|
self.xhi = Float(Item_list[1])
|
|
Item_list = string.split(Lines[i+2])
|
|
self.ylo = Float(Item_list[0])
|
|
self.yhi = Float(Item_list[1])
|
|
Item_list = string.split(Lines[i+3])
|
|
self.zlo = Float(Item_list[0])
|
|
self.zhi = Float(Item_list[1])
|
|
i = i + 4
|
|
|
|
elif string.find(Lines[i], 'ITEM: ATOMS') != -1:
|
|
# Read atom positions
|
|
self.Snapshot_list.append(Snapshot(self))
|
|
Start = i + 1
|
|
End = Start + self.atoms
|
|
self.Snapshot_list[-1].Read_dump(Lines[Start:End])
|
|
i = i + self.atoms + 1
|
|
|
|
else:
|
|
print '(error: unknown line in file!)'
|
|
return
|
|
|
|
print 'done.'
|
|
return 1
|
|
|
|
#--------------------------------------------------------
|
|
|
|
def Write_trj(self, Basename):
|
|
'Write an Amber trajectory file'
|
|
|
|
import os, sys
|
|
|
|
Filename = Basename + '.mdcrd'
|
|
|
|
Dir_list = os.listdir('.')
|
|
i = 1
|
|
while Filename in Dir_list:
|
|
Filename = Basename + `i` + '.mdcrd'
|
|
i = i + 1
|
|
del i
|
|
|
|
print 'Writing', Filename + '...',
|
|
sys.stdout.flush()
|
|
|
|
try:
|
|
F = open(Filename, 'w')
|
|
except IOError, Detail:
|
|
print '(error:', Detail[1] + '!)'
|
|
return
|
|
|
|
try:
|
|
F.write(Basename + '\n')
|
|
except IOError, Detail:
|
|
print '(error:', Detail[1] + '!)'
|
|
F.close()
|
|
return
|
|
|
|
for S in self.Snapshot_list:
|
|
S.Write_trj(F)
|
|
|
|
F.close()
|
|
print 'done.'
|
|
|
|
#============================================================
|
|
|
|
def Float(s):
|
|
'Return the string s as a float, if possible'
|
|
|
|
try:
|
|
x = float(s)
|
|
except ValueError:
|
|
if s[-1] == ',':
|
|
s = s[:-1]
|
|
x = float(s)
|
|
|
|
return x
|
|
|
|
#============================================================
|
|
|
|
def NumericalSort(String_list):
|
|
'Sort a list of strings by the integer value of the first element'
|
|
|
|
import string
|
|
|
|
Working_list = []
|
|
for s in String_list:
|
|
Working_list.append((int(string.split(s)[0]), s))
|
|
|
|
Working_list.sort()
|
|
|
|
Return_list = []
|
|
for Tuple in Working_list:
|
|
Return_list.append(Tuple[1])
|
|
return Return_list
|
|
|
|
#============================================================
|
|
|
|
Convert_files()
|