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lammps/tools/amber2lmp/dump2trj.py
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dump2trj.py
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#! /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):
'Initialise 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()
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