def step(sys, debug):
config.set_tempdir(sys)
if debug:
os.environ["DMS_DEBUG"] = "TRUE"
s = system.System(sys, "a")
integrator = s.integrator()
integrator.step()
def step(sys,debug) :
config.set_tempdir(sys)
if debug:
os.environ["DMS_DEBUG"] = "TRUE"
s=system.System(sys, "a")
integrator = s.integrator()
integrator.step()
def run(sys, debug) :
config.set_tempdir(sys)
if debug:
os.environ["PROTO_DEBUG"] = "TRUE"
s=system.System(sys, "a")
integrator = s.integrator()
integrator.run()
def sol(sys, debug) :
config.set_tempdir(sys)
if debug:
os.environ["PROTO_DEBUG"] = "TRUE"
s=system.System(sys, "a")
s.begin_timestep()
s.solvate()
s.end_timestep()
def atomistic_step(sys, debug):
config.set_tempdir(sys)
if debug:
os.environ["DMS_DEBUG"] = "TRUE"
s = system.System(sys, "a")
integrator = s.integrator()
s.begin_timestep()
integrator.atomistic_step()
s.end_timestep()
def sol(sys, debug):
config.set_tempdir(sys)
if debug:
os.environ["DMS_DEBUG"] = "TRUE"
s = system.System(sys, "a")
s.begin_timestep()
s.solvate()
s.end_timestep()
print(sys)
def atomistic_step(sys,debug) :
config.set_tempdir(sys)
if debug:
os.environ["DMS_DEBUG"] = "TRUE"
s=system.System(sys, "a")
integrator = s.integrator()
s.begin_timestep()
integrator.atomistic_step()
s.end_timestep()
def cg_step(sys,debug) :
config.set_tempdir(sys)
if debug:
os.environ["DMS_DEBUG"] = "TRUE"
s=system.System(sys, "a")
s._load_ts(s.current_timestep)
integrator = s.integrator()
s.begin_timestep()
integrator.cg_step()
s.end_timestep()
def cg_step(sys, debug):
config.set_tempdir(sys)
if debug:
os.environ["DMS_DEBUG"] = "TRUE"
s = system.System(sys, "a")
s._load_ts(s.current_timestep)
integrator = s.integrator()
s.begin_timestep()
integrator.cg_step()
s.end_timestep()
def md(sys,sol,debug) :
config.set_tempdir(sys)
if debug:
os.environ["PROTO_DEBUG"] = "TRUE"
s=system.System(sys, "a")
s.begin_timestep()
if sol:
sol = s.solvate()
s.md(**sol)
else:
s.md()
s.end_timestep()
def md(sys,sol,debug) :
config.set_tempdir(sys)
if debug:
os.environ["DMS_DEBUG"] = "TRUE"
s=system.System(sys, "a")
s.begin_timestep()
if sol:
sol = s.solvate()
print("sol: {}".format(sol))
s.md(**sol)
else:
s.md()
s.end_timestep()
def md(sys, sol, debug):
config.set_tempdir(sys)
if debug:
os.environ["DMS_DEBUG"] = "TRUE"
s = system.System(sys, "a")
s.begin_timestep()
if sol:
sol = s.solvate()
print("sol: {}".format(sol))
s.md(**sol)
else:
s.md()
s.end_timestep()
def eq(sys, debug):
config.set_tempdir(sys)
if debug:
os.environ["DMS_DEBUG"] = "TRUE"
s = system.System(sys, "a")
s.begin_timestep()
if sol:
sol = s.solvate()
print("sol: {}".format(sol))
eq = s.equilibriate(**sol)
print("eq: {}".format(eq))
else:
s.equilibriate()
s.end_timestep()
def eq(sys,debug) :
config.set_tempdir(sys)
if debug:
os.environ["DMS_DEBUG"] = "TRUE"
s=system.System(sys, "a")
s.begin_timestep()
if sol:
sol = s.solvate()
print("sol: {}".format(sol))
eq = s.equilibriate(**sol)
print("eq: {}".format(eq))
else:
s.equilibriate()
s.end_timestep()
def mneq(sys,sol,debug) :
config.set_tempdir(sys)
if debug:
os.environ["PROTO_DEBUG"] = "TRUE"
s=system.System(sys, "a")
s.begin_timestep()
if sol:
sol = s.solvate()
mn = s.minimize(**sol)
eq = s.equilibriate(**mn)
else:
s.minimize()
s.equilibriate()
s.end_timestep()
def mneqmd(sys,sol,debug) :
config.set_tempdir(sys)
if debug:
os.environ["DMS_DEBUG"] = "TRUE"
s=system.System(sys, "a")
s.begin_timestep()
if sol:
sol = s.solvate()
print("sol: {}".format(sol))
mn = s.minimize(**sol)
print("mn: {}".format(mn))
eq = s.equilibriate(**mn)
print("eq: {}".format(eq))
s.md(**eq)
else:
s.minimize()
s.equilibriate()
s.md()
s.en
s.end_timestep()
def mneqmd(sys, sol, debug):
config.set_tempdir(sys)
if debug:
os.environ["DMS_DEBUG"] = "TRUE"
s = system.System(sys, "a")
s.begin_timestep()
if sol:
sol = s.solvate()
print("sol: {}".format(sol))
mn = s.minimize(**sol)
print("mn: {}".format(mn))
eq = s.equilibriate(**mn)
print("eq: {}".format(eq))
s.md(**eq)
else:
s.minimize()
s.equilibriate()
s.md()
s.en
s.end_timestep()