def optimize(self, shot=0, method="newton", crit=1e-4):
""" Optimize the geometry and align the optimized geometry to the starting geometry. """
if os.path.exists("%s.xyz_2" % self.name):
os.unlink("%s.xyz_2" % self.name)
self.mol[shot].write("%s.xyz" % self.name, ftype="tinker")
if method == "newton":
if self.rigid:
optprog = "optrigid"
else:
optprog = "optimize"
elif method == "bfgs":
if self.rigid:
optprog = "minrigid"
else:
optprog = "minimize"
o = self.calltinker("%s %s.xyz %f" % (optprog, self.name, crit))
# Silently align the optimized geometry.
M12 = Molecule("%s.xyz" % self.name, ftype="tinker") + Molecule("%s.xyz_2" % self.name, ftype="tinker")
if not self.pbc:
M12.align(center=False)
M12[1].write("%s.xyz_2" % self.name, ftype="tinker")
rmsd = M12.ref_rmsd(0)[1]
cnvgd = 0
mode = 0
for line in o:
s = line.split()
if len(s) == 0:
continue
if "Optimally Conditioned Variable Metric Optimization" in line:
mode = 1
if "Limited Memory BFGS Quasi-Newton Optimization" in line:
mode = 1
if mode == 1 and isint(s[0]):
mode = 2
if mode == 2:
if isint(s[0]):
E = float(s[1])
else:
mode = 0
if "Normal Termination" in line:
cnvgd = 1
if not cnvgd:
for line in o:
logger.info(str(line) + "\n")
logger.info("The minimization did not converge in the geometry optimization - printout is above.\n")
return E, rmsd
def Energy_RMSD(systems):
tinkerhome = os.environ["TINKERPATH"]
f1 = open("runAna.sh", "w")
f2 = open("runMin.sh", "w")
i = 0
for sys_ in systems:
opts = systems[sys_]
optimize = (opts['optimize'] if 'optimize' in opts else False)
if not optimize:
if (i+1)%24 == 0:
cmd = "rm -f %s.out\n%s/analyze %s.xyz -k %s.key E > %s.out \n"%(sys_, os.environ["TINKERPATH"], sys_, sys_, sys_)
i += 1
else:
cmd = "rm -f %s.out\n%s/analyze %s.xyz -k %s.key E > %s.out & \n"%(sys_, os.environ["TINKERPATH"], sys_, sys_, sys_)
i += 1
f1.write(cmd)
else:
if (i+1)%24 == 0:
cmd = "rm -f %s.xyz_2 %s.out \n%s/optimize %s.xyz -k %s.key 0.0001 > %s.out \n"%(sys_, sys_, os.environ["TINKERPATH"], sys_, sys_, sys_)
i += 1
else:
cmd = "rm -f %s.xyz_2 %s.out \n%s/optimize %s.xyz -k %s.key 0.0001 > %s.out & \n"%(sys_, sys_, os.environ["TINKERPATH"], sys_, sys_, sys_)
i += 1
f2.write(cmd)
f1.write("wait\n")
f2.write("wait\n")
f1.close()
f2.close()
os.system("sh runAna.sh")
os.system("sh runMin.sh")
for sys_ in systems:
while not os.path.isfile(os.path.join(os.getcwd(), sys_ + ".out")):
time.sleep(1.0)
Es = {}
RMSDs = {}
for sys_ in systems:
energ = 0.0
rmsd = 0.0
for line in open("%s.out"%sys_).readlines():
if "Total Potential Energy" in line:
energ = float(line.split()[-2].replace('D','e'))
Es[sys_] = energ
RMSDs[sys_] = 0.0
if "Final Function Value :" in line:
energ = float(line.split()[-1].replace('D','e'))
Es[sys_] = energ
M1 = Molecule("%s.xyz" % sys_, ftype="tinker")
M2 = Molecule("%s.xyz_2" % sys_, ftype="tinker")
M1 += M2
RMSDs[sys_] = M1.ref_rmsd(0)[1]
return Es,RMSDs
def optimize(self, shot=0, method="newton", crit=1e-4):
""" Optimize the geometry and align the optimized geometry to the starting geometry. """
logger.error(
'Geometry optimizations are not yet implemented in AMBER interface'
)
raise NotImplementedError
# Code from tinkerio.py
if os.path.exists('%s.xyz_2' % self.name):
os.unlink('%s.xyz_2' % self.name)
self.mol[shot].write('%s.xyz' % self.name, ftype="tinker")
if method == "newton":
if self.rigid: optprog = "optrigid"
else: optprog = "optimize"
elif method == "bfgs":
if self.rigid: optprog = "minrigid"
else: optprog = "minimize"
o = self.calltinker("%s %s.xyz %f" % (optprog, self.name, crit))
# Silently align the optimized geometry.
M12 = Molecule("%s.xyz" % self.name, ftype="tinker") + Molecule(
"%s.xyz_2" % self.name, ftype="tinker")
if not self.pbc:
M12.align(center=False)
M12[1].write("%s.xyz_2" % self.name, ftype="tinker")
rmsd = M12.ref_rmsd(0)[1]
cnvgd = 0
mode = 0
for line in o:
s = line.split()
if len(s) == 0: continue
if "Optimally Conditioned Variable Metric Optimization" in line:
mode = 1
if "Limited Memory BFGS Quasi-Newton Optimization" in line:
mode = 1
if mode == 1 and isint(s[0]): mode = 2
if mode == 2:
if isint(s[0]): E = float(s[1])
else: mode = 0
if "Normal Termination" in line:
cnvgd = 1
if not cnvgd:
for line in o:
logger.info(str(line) + '\n')
logger.info(
"The minimization did not converge in the geometry optimization - printout is above.\n"
)
return E, rmsd
