#!/usr/bin/env python
#* **************************************************************************
#*
#* CDTK, Chemical Dynamics Toolkit
#* A modular system for chemical dynamics applications and more
#*
#* Copyright (C) 2011, 2012, 2013, 2014, 2015, 2016
#* Oriol Vendrell, DESY, <oriol.vendrell@desy.de>
#*
#* Copyright (C) 2017, 2018, 2019
#* Ralph Welsch, DESY, <ralph.welsch@desy.de>
#*
#* Copyright (C) 2020, 2021, 2022, 2023
#* Ludger Inhester, DESY, ludger.inhester@cfel.de
#*
#* This file is part of CDTK.
#*
#* CDTK is free software: you can redistribute it and/or modify
#* it under the terms of the GNU General Public License as published by
#* the Free Software Foundation, either version 3 of the License, or
#* (at your option) any later version.
#*
#* This program is distributed in the hope that it will be useful,
#* but WITHOUT ANY WARRANTY; without even the implied warranty of
#* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#* GNU General Public License for more details.
#*
#* You should have received a copy of the GNU General Public License
#* along with this program. If not, see <http://www.gnu.org/licenses/>.
#*
#* **************************************************************************
"""
This module has several functions to transform coordinates and velocities obtained
from Gromacs calculation into suitable input files for CDTK. Use ``gmx2cdtk -h``
to find out how to use this program.
Basic units in GMX, please look at the following web.
https://manual.gromacs.org/documentation/2019/reference-manual/definitions.html#table-basicunits
1 Picoseconds = 41341.374575751 Atomic Unit Of Time
1 nm = 18.8973 Bohr
1 nm/ps = 18.8973/41341.374575751 Bohr/A.u = 0.00045710381413114194
1 nm/ps = 4.571038E-04 Bohr/A.u
"""
# TODO: Implement molecular dictionary as a data class (python 3.7+) or similar (python 2.7)
import subprocess
from optparse import OptionParser
import numpy as np
import CDTK.Tools.Conversion as cv
import CDTK.Tools.Utils as uti
import os
[docs]
def get_arg():
parser = OptionParser()
parser = OptionParser(usage="usage: %prog [options]")
parser.add_option(
"-t",
"--output_traj_file",
dest="trajFile",
type="str",
default="traj.xyz",
help="output trajectory file (data from R.log)",
)
parser.add_option(
"-g",
"--output_geom_file",
dest="geomFile",
type="str",
default="geom.xyz",
help="output geometry file (data from atompos)",
)
opts, args = parser.parse_args()
return opts
[docs]
def start():
opts = get_arg()
if os.path.exists('atomlist'):
atomlist = uti.readColumnFile('atomlist')
else:
raise ValueError('atom list (./atomlist) not found')
# - Atomic positions atompos
if os.path.exists('atompos'):
xcart = np.array( uti.readColumnFile('atompos'),float )
geom = np.array([xcart.reshape(-1,3)])
uti.traj2xyz(atomlist, geom, opts.geomFile, comment='data from atompos')
# - Trajectory data R.log
if os.path.exists('R.log'):
t = uti.getTrajectoryTimeSteps('R.log')
geom = uti.atomicCoordinatesFromRlog('R.log')
uti.traj2xyz(atomlist, geom, opts.trajFile, comment='data from CDTK trajectory R.log', timesteps=t)
else:
print(f"R.log not found: skipping output of {opts.trajFile}")
if __name__ == "__main__":
start()