def calc_new(self, coords, dirname):
try:
from forcebalance.gmxio import GMX
except ImportError:
raise ImportError(
"ForceBalance is needed to compute energies and gradients using Gromacs."
)
if not os.path.exists(dirname): os.makedirs(dirname)
try:
Gro = Molecule("conf.gro")
Gro.xyzs[0] = coords.reshape(-1, 3) * bohr2ang
cwd = os.getcwd()
shutil.copy2("topol.top", dirname)
shutil.copy2("shot.mdp", dirname)
os.chdir(dirname)
Gro.write("coords.gro")
G = GMX(coords="coords.gro",
gmx_top="topol.top",
gmx_mdp="shot.mdp")
EF = G.energy_force()
Energy = EF[0, 0] / eqcgmx
Gradient = EF[0, 1:] / fqcgmx
os.chdir(cwd)
except (OSError, IOError, RuntimeError, subprocess.CalledProcessError):
raise GromacsEngineError
return {'energy': Energy, 'gradient': Gradient}
def calc_new(self, coords, dirname):
if not os.path.exists(dirname): os.makedirs(dirname)
Gro = Molecule("conf.gro")
Gro.xyzs[0] = coords.reshape(-1, 3) * 0.529
cwd = os.getcwd()
shutil.copy2("topol.top", dirname)
shutil.copy2("shot.mdp", dirname)
os.chdir(dirname)
Gro.write("coords.gro")
G = GMX(coords="coords.gro", gmx_top="topol.top", gmx_mdp="shot.mdp")
EF = G.energy_force()
Energy = EF[0, 0] / eqcgmx
Gradient = EF[0, 1:] / fqcgmx
os.chdir(cwd)
return Energy, Gradient
def calc_new(self, coords, dirname):
try:
from forcebalance.gmxio import GMX
except ImportError:
raise ImportError("ForceBalance is needed to compute energies and gradients using Gromacs.")
if not os.path.exists(dirname): os.makedirs(dirname)
try:
Gro = Molecule("conf.gro")
Gro.xyzs[0] = coords.reshape(-1,3) * bohr2ang
cwd = os.getcwd()
shutil.copy2("topol.top", dirname)
shutil.copy2("shot.mdp", dirname)
os.chdir(dirname)
Gro.write("coords.gro")
G = GMX(coords="coords.gro", gmx_top="topol.top", gmx_mdp="shot.mdp")
EF = G.energy_force()
Energy = EF[0, 0] / eqcgmx
Gradient = EF[0, 1:] / fqcgmx
os.chdir(cwd)
except (OSError, IOError, RuntimeError, subprocess.CalledProcessError):
raise GromacsEngineError
return {'energy':Energy, 'gradient':Gradient}