def lammps_to_gromacs(name, gropath='', grosuff='', lmppath='', lmpbin='lmp_openmpi',
energy=True, clean=True):
"""Test lammps to gromacs conversion
"""
lmp_in = os.path.join('Inputs/Lammps/', name, 'data.lmp')
if not os.path.isfile(lmp_in):
raise Exception("File not found: {0}!".format(lmp_in))
top_out = os.path.join('Outputs/LammpsToGromacs/', name, 'topol.top')
gro_out = os.path.join('Outputs/LammpsToGromacs/', name, 'conf.gro')
# calc input energies
if energy:
e_in = lammps_energies(name, 'in', lmppath, lmpbin)
# where the magic happens
Driver.initSystem(name)
Driver.load(lmp_in)
Driver.write(top_out, gro_out)
# calc output energies
if energy:
e_out = gromacs_energies(name, top_out, gro_out, 'LtoG', gropath, grosuff)
# delete gromacs backup files
if clean:
import glob
filelist = glob.glob("Inputs/Gromacs/{name}/#*#".format(name=name))
filelist += glob.glob("Outputs/GromacsToGromacs/{name}/#*#".format(name=name))
for f in filelist:
os.remove(f)
if energy:
return combine_energy_results(e_in, e_out)
def gromacs_to_gromacs(name="system2_GMX", top=None, gro=None, gropath="", grosuff="", energy=True, clean=True):
"""Test gromacs to gromacs conversion
"""
if top == None:
top = os.path.join(name, "topol.top")
if gro == None:
gro = os.path.join(name, "conf.gro")
gro_in = os.path.join("Inputs/Gromacs/", gro)
if not os.path.isfile(gro_in):
raise Exception("File not found: {0}!".format(gro_in))
top_in = os.path.join("Inputs/Gromacs/", top)
if not os.path.isfile(top_in):
raise Exception("File not found: {0}!".format(top_in))
top_out = os.path.join("Outputs/GromacsToGromacs/", name, "topol.top")
gro_out = os.path.join("Outputs/GromacsToGromacs/", name, "conf.gro")
# calc input energies
if energy:
e_in = gromacs_energies(name, top_in, gro_in, "in", gropath, grosuff)
# where the magic happens
Driver.initSystem(name)
Driver.load(top_in, gro_in)
Driver.write(top_out, gro_out)
# calc output energies
if energy:
e_out = gromacs_energies(name, top_out, gro_out, "GtoG", gropath, grosuff)
# delete gromacs backup files
if clean:
import glob
filelist = glob.glob("Inputs/Gromacs/{name}/#*#".format(name=name))
filelist += glob.glob("Outputs/GromacsToGromacs/{name}/#*#".format(name=name))
for f in filelist:
os.remove(f)
if energy:
return combine_energy_results(e_in, e_out)
