def main():
const = ConstantsClass()
const.k_B = 1.38065e-26
#const.Temp = 298
#const.Temp = 303.15
const.Temp = 300.0
const.N_A = 6.002214e23
const.betainv = const.Temp * const.k_B * const.N_A # 1/beta (kJ / mol)
const.beta = 1.0/const.betainv
const.jobfilepath = "./jobfiles_all/"
const.MarkovNetworkQ = True
const.TSFEmax = 1.0e30
const.EQFEmax = 1.0e30
const.stateQN = 400
#const.Pmax = 1.0e30
const.Pmax = 36.0
#const.samePrange = 2.0
#const.EQFEmax_Prange = 20.0
const.samePrange = 0.0
const.EQFEmax_Prange = 1.0e30
#const.k_min = 1.0e-12 # cut off in order of second
#const.k_min = 1.0e-16 # cut off in order of hour
const.k_min = 1.0e-20
#const.stateNmin = 1.0e-20 #
#const.deltak_th = 1.0e-16
const.deltak_th = 0.0
#const.stateNmin = 1.0e-10
const.stateNmin = 0.0
const.is_bilayer = True
const.diffusionQ = False
const.oneoutsideEQ = True
const.asymmetricQ = True
const.rm_disconnections = False
const.sameEQthreshold = [0.2 for _ in range(4)] + [2.0]
#const.sameEQthreshold = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 2.0]
const.maxtime = 47.0
const.calc_mpiQ = True
const.cythonQ = True
const = mkconst.main(const)
from mpi4py import MPI
const.comm = MPI.COMM_WORLD
const.rank = const.comm.Get_rank()
const.size = const.comm.Get_size()
const.root = 0
const.k_RCMC = 1.0
#const.ksim_Z = 30
const.t_delta = 1.0 / const.k_RCMC / 10
#kSimulation_oneZ.main(const)
for const.ksim_Z in range(31):
if const.ksim_Z % const.size != const.rank:
continue
kSimulation_oneZ.main(const)
def main():
const = ConstantsClass()
const.k_B = 1.38065e-26
#const.Temp = 298
#const.Temp = 303.15
const.Temp = 300.0
const.N_A = 6.002214e23
const.betainv = const.Temp * const.k_B * const.N_A # 1/beta (kJ / mol)
const.MarkovNetworkQ = False
const.TSFEmax = 1.0e30
const.EQFEmax = 1.0e30
const.stateQN = 400
#const.Pmax = 1.0e30
const.Pmax = 35.0
#const.samePrange = 2.0
#const.EQFEmax_Prange = 20.0
const.samePrange = 0.0
const.EQFEmax_Prange = 1.0e30
#const.k_min = 1.0e-12 # cut off in order of second
const.k_min = 1.0e-16 # cut off in order of hour
#const.k_min = 1.0e-20
#const.stateNmin = 1.0e-20 #
#const.deltak_th = 1.0e-16
const.deltak_th = 0.0
#const.stateNmin = 1.0e-10
const.stateNmin = 0.0
const.is_bilayer = False
const.diffusionQ = False
const.oneoutsideEQ = True
const.asymmetricQ = True
const.rm_disconnections = False
const.sameEQthreshold = [0.2 for _ in range(4)] + [2.0]
#const.sameEQthreshold = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 2.0]
const.maxtime = 47.0
const.calc_mpiQ = True
const.cythonQ = True
const = mkconst.main(const)
from mpi4py import MPI
const.comm = MPI.COMM_WORLD
const.rank = const.comm.Get_rank()
const.size = const.comm.Get_size()
const.root = 0
const.jobfilepath = "./"
for i in range(36):
os.chdir("./jobfiles_%s"%i)
RCMC.main(const)
os.chdir("../")
def main():
constC = constClass()
constC.Temp = 300.0 # tempeture (K)
k_B = 1.38065e-26 # Boltzmann constant (kJ / K)
N_A = 6.002214e23 # Avogadro constant (mol^-1)
constC.betainv = constC.Temp * k_B * N_A # 1/beta (kJ / mol)
constC.beta = 1.0 / constC.betainv
constC.initialpointN = 1000
#constC.initialpointN = 0
#constC.calc_cupyQ = True
constC.cythonQ = True
#constC.calc_mpiQ = True
constC.calc_mpiQ = False
constC.use_jacQ = True
constC.sameEQthreshold = [0.2 for _ in range(4)] + [2.0]
constC.IOEsphereA_initial = 0.10
constC.IOEsphereA_dist = 0.02
constC.deltas0 = 0.20
constC.deltas = 0.01
#constC.lADDnQ = True
#constC.IOEl = 10
constC.coeffPickNlist = []
#! SET iteration 400000
#constC.coeffabsmin = 1.0e-3
constC.periodicQ = True
constC.periodicmax = [np.pi for _ in range(4)] + [50.0]
constC.periodicmin = [-np.pi for _ in range(4)] + [-50.0]
constC.wallmax = [1.0e30 for _ in range(4)] + [50.0]
constC.wallmin = [-1.0e30 for _ in range(4)] + [-50.0]
#constC.EQwallmax = [ 1.0e30 for _ in range(4)] + [ 5.0]
#constC.EQwallmin = [-1.0e30 for _ in range(4)] + [-5.0]
#constC.EQwallmax = [ 1.0e30 for _ in range(4)] + [10.0]
#constC.EQwallmin = [-1.0e30 for _ in range(4)] + [ 5.0]
#constC.EQwallmax = [ 1.0e30 for _ in range(4)] + [20.0]
#constC.EQwallmin = [-1.0e30 for _ in range(4)] + [10.0]
#constC.EQwallmax = [ 1.0e30 for _ in range(4)] + [30.0]
#constC.EQwallmin = [-1.0e30 for _ in range(4)] + [20.0]
#constC.EQwallmax = [ 1.0e30 for _ in range(4)] + [40.0]
#constC.EQwallmin = [-1.0e30 for _ in range(4)] + [30.0]
constC.EQwallmax = [1.0e30 for _ in range(4)] + [35.0]
constC.EQwallmin = [-1.0e30 for _ in range(4)] + [-35.0]
constC.abslist = [False for _ in range(4)] + [True]
#constC.x0randomQ = False
#constC.chkBifurcationQ = True
constC.x0randomQ = True
constC.chkBifurcationQ = False
constC.chkinitialTSQ = False
constC.gridQ = True
constC.grid_importQ = True
constC.grid_min = [-np.pi for _ in range(4)] + [-50.0]
constC.grid_max = [np.pi for _ in range(4)] + [50.0]
constC.grid_bin = [100 for _ in range(4)] + [500]
args = sys.argv
currentpoint = sys.argv[2]
#currentpoint = 35
constC.CVfixQ = True
constC.fixlist = [(False, None)] * 4 + [(True, float(currentpoint))]
constC.jobfilepath = "./jobfiles_%s/" % currentpoint
if constC.calc_mpiQ:
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
root = 0
else:
comm = None
rank = 0
root = 0
size = 1
if rank == root:
if not os.path.exists(constC.jobfilepath):
os.mkdir(constC.jobfilepath)
constC = mkconst.main(constC)
if rank == root:
with open("./%s/constants.txt" % constC.jobfilepath, "w") as wf:
wf.write(constC.writestr)
plumedpath = './plumed.dat'
VESclass = SHS4py.VESanalyzer.VESpotential(plumedpath, constC, rank, root,
size, comm)
initialpointlist = []
initialpointTSlist = []
initialpointlist, initialpointTSlist = importinitialpoint(constC)
initialpointlist += importinitialpoint_random(constC)
SHS4py.SHSearch(VESclass.f,
VESclass.grad,
VESclass.hessian,
importinitialpointQ=False,
initialpoints=initialpointlist,
initialTSpoints=initialpointTSlist,
SHSrank=rank,
SHSroot=root,
SHSsize=size,
SHScomm=comm,
const=constC)
def main():
"""
template of the calculation of Metadynamics
"""
constC = constClass()
Temp = 298.0 # tempeture (K) : must same with that of MD simulation
k_B = 1.38065e-26 # Boltzmann constant (kJ / K)
N_A = 6.002214e23 # Avogadro constant (mol^-1)
constC.betainv = Temp * k_B * N_A # 1/beta (kJ / mol)
constC.beta = 1.0 / constC.betainv
constC.threshold = 0.1
constC.sameEQthreshold = 0.05
constC.IOEsphereA_initial = 0.02
constC.IOEsphereA_dist = 0.005
constC.deltas0 = 0.01
constC.deltas = 0.005
constC.initialpointN = 100
constC.periodicQ = False
#If CVs have periodic(like as angles or dihedrals), periodicQ must be True and define periodicmin and periodicmax.
#For example, if you use dihedrals as CVs:
#constC.periodicQ = True
#constC.periodicmin = -np.pi
#constC.periodicmax = np.pi
constC.calc_mpiQ = False # package mpi4py is necessary
constC.calc_cupyQ = False # package cupy is necessary
constC.cythonQ = False # package cython and previous compile are necessary
#If the trajectory is long, I recommend you to use mpi4py & cupy & cython with GPGPU machine.
constC.WellTempairedQ = True
constC.WT_Biasfactor = 6 #BIASFACTOR of the PLUMED setting.
constC.digThreshold = 5
height = 0.5 #HEIGHT of the PLUMED setting.
digTH = -height * constC.digThreshold
constC = mkconst.main(constC)
if constC.calc_mpiQ:
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
root = 0
else:
comm = None
rank = 0
root = 0
size = 1
metaD = SHS4py.metaDanalyzer.Metad_result("./HILLS", constC)
if size != 1:
hillD = len(metaD.hillCs) // (constC.initialpointN // size)
else:
hillD = len(metaD.hillCs) // (constC.initialpointN)
initialpointlist = []
for hillC in metaD.hillCs[::hillD]:
initialpointlist.append(hillC.s)
if size != 1:
initialpointlist = comm.gather(initialpointlist, root=0)
if rank == root:
initialpointlist_gather = []
for initialpointlist_chunk in initialpointlist:
initialpointlist_gather.extend(initialpointlist_chunk)
else:
initialpointlist_gather = None
initialpointlist_gather = comm.bcast(initialpointlist_gather, root=0)
else:
initialpointlist_gather = initialpointlist
SHS4py.SHSearch(metaD.f,
metaD.grad,
metaD.hessian,
importinitialpointQ=False,
initialpoints=initialpointlist_gather,
SHSrank=rank,
SHSroot=root,
SHScomm=comm,
optdigTH=digTH,
const=constC)
def main():
const = ConstantsClass()
const.k_B = 1.38065e-26
#const.Temp = 298
#const.Temp = 303.15
const.Temp = 300.0
const.N_A = 6.002214e23
const.betainv = const.Temp * const.k_B * const.N_A # 1/beta (kJ / mol)
const.MarkovNetworkQ = True
const.TSFEmax = 1.0e30
const.EQFEmax = 1.0e30
const.stateQN = 400
#const.Pmax = 1.0e30
const.Pmax = 36.0
#const.samePrange = 2.0
#const.EQFEmax_Prange = 20.0
const.samePrange = 0.0
const.EQFEmax_Prange = 1.0e30
#const.k_min = 1.0e-12 # cut off in order of second
#const.k_min = 1.0e-16 # cut off in order of hour
const.k_min = 1.0e-20
#const.stateNmin = 1.0e-20 #
#const.deltak_th = 1.0e-16
const.deltak_th = 0.0
#const.stateNmin = 1.0e-10
const.stateNmin = 0.0
const.is_bilayer = True
const.diffusionQ = True
const.oneoutsideEQ = True
const.asymmetricQ = True
const.rm_disconnections = False
const.sameEQthreshold = [0.2 for _ in range(4)] + [2.0]
#const.sameEQthreshold = [0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 2.0]
const.maxtime = 47.0
const.calc_mpiQ = True
const.cythonQ = True
const = mkconst.main(const)
from mpi4py import MPI
const.comm = MPI.COMM_WORLD
const.rank = const.comm.Get_rank()
const.size = const.comm.Get_size()
const.root = 0
const.periodicQ = True
const.periodicmax = np.array([np.pi for _ in range(4)] + [50.0])
const.periodicmin = np.array([-np.pi for _ in range(4)] + [-50.0])
const.useZpozitionQ = True
const.colvarpath = [
#"../VESMW_100ns/run*",
#"../VESMW_200ns/run*",
#"../VESMW_300ns/run*",
#"../VESMW_400ns/run*",
"../VESMW_500ns/run*"
]
#for z in range(36):
#const.zpozition = z
args = sys.argv
const.zpozition = int(sys.argv[1])
const.jobfilepath = "./jobfiles_%s/" % const.zpozition
COV2Diff.main(const)
def main():
"""
"""
constC = constClass()
constC = mkconst.main(constC)
constC.Temp = 300.0 # tempeture (K)
k_B = 1.38065e-26 # Boltzmann constant (kJ / K)
N_A = 6.002214e23 # Avogadro constant (mol^-1)
constC.betainv = constC.Temp * k_B * N_A # 1/beta (kJ / mol)
constC.beta = 1.0 / constC.betainv
comm = None
rank = 0
root = 0
size = 1
plumedpath = './plumed.dat'
VESclass = VESanalyzer.VESpotential(plumedpath, constC, rank, root, size,
comm)
felimit = 99999
zlist = range(36)
eqlist_all = []
tslist_all = []
connections_all = {}
exporteqstr = ""
eqpointindex = 0
exporttsstr = ""
tspointindex = 0
for line in open("./diff_inner.csv"):
angdiff_inner = float(line)
break
for line in open("./diff_outer.csv"):
angdiff_outer = float(line)
break
for z in zlist:
eqlist, tslist, connections, fricdic = importpoints(z)
#eqpoint_femin = eqlist[0]
G = nx.Graph()
#print(len(set([x[0] for x in connections])))
for name1, name2 in connections:
if "EQ" in name1:
eqname = name1
tsname = name2
else:
eqname = name2
tsname = name1
eqpoint = [point for point in eqlist if point.name == eqname]
if len(eqpoint) == 0:
print("ERROR; there is not %s in eqlist.csv" % eqname)
exit()
eqpoint = eqpoint[0]
#if felimit < eqpoint.fe - eqpoint_femin.fe:
#continue
G.add_edge(name1, name2)
G.add_edge(name2, name1)
for eqpoint in eqlist:
if not eqpoint.name in G.nodes():
continue
eqpoint_femin = eqpoint
break
#eqlist_connected = []
#for eqpoint in eqlist:
#if not eqpoint.name in G.nodes():
#continue
#if nx.has_path(G, eqpoint_femin.name, eqpoint.name):
#eqlist_connected.append(eqpoint)
#eqlist = eqlist_connected
tslist_connected = []
for tspoint in tslist:
if not tspoint.name in G.nodes():
continue
if nx.has_path(G, eqpoint_femin.name, tspoint.name):
tslist_connected.append(tspoint)
tslist = tslist_connected
#exit()
for eqpoint in eqlist:
eqpointindex += 1
eqpoint.networkname = "EQ%05d" % eqpointindex
exporteqstr += eqpoint.networkname
for x in eqpoint.point:
exporteqstr += ", %s" % x
exporteqstr += ", %s" % eqpoint.z
exporteqstr += ", %s\n" % eqpoint.fe
for tspoint in tslist:
eqpoints = [x for x in G.neighbors(tspoint.name)]
if len(eqpoints) == 1:
continue
if len(eqpoints) != 2:
print("ERROR; eqpoints = %s" % eqpoints)
exit()
eqpoint1 = [
point for point in eqlist if point.name == eqpoints[0]
][0]
eqpoint2 = [
point for point in eqlist if point.name == eqpoints[1]
][0]
deltafe = tspoint.fe - eqpoint1.fe
#print(tspoint)
#print(fricdic.keys())
k = fricdic[(eqpoint1.name, tspoint.name)] * np.exp(
-constC.beta * deltafe)
#eqedge = (eqpoint1.name, eqpoint2.name)
eqedge = (eqpoint1.networkname, eqpoint2.networkname)
if eqedge in connections_all.keys():
connections_all[eqedge] += k
else:
connections_all[eqedge] = k
deltafe = tspoint.fe - eqpoint2.fe
k = fricdic[(eqpoint2.name, tspoint.name)] * np.exp(
-constC.beta * deltafe)
eqedge = (eqpoint2.networkname, eqpoint1.networkname)
if eqedge in connections_all.keys():
connections_all[eqedge] += k
else:
connections_all[eqedge] = k
tspointindex += 1
tspoint.networkname = "TS%05d" % tspointindex
exporttsstr += tspoint.networkname
for x in tspoint.point:
exporttsstr += ", %s" % x
exporttsstr += ", %s" % tspoint.z
exporttsstr += ", %s\n" % tspoint.fe
zfric = float(open("./jobfiles_%s/fric_z.csv" % z).readline())
z_before = z - 1.0
if z < 25.0:
angfric = angdiff_inner
else:
angfric = angdiff_outer
if z_before < 25.0:
angfric_before = angdiff_inner
else:
angfric_before = angdiff_outer
#if 0 <= z_before < 35:
if z != 0:
connections_all = calcMarcofFric(eqlist, z, zfric, eqlist_before,
zfric_before, angfric,
angfric_before, connections_all,
constC, VESclass)
eqlist_before = eqlist
tslist_before = tslist
connections_before = connections
zfric_before = zfric
print("z = %s" % z)
print("connections_all//Len = %s" % len(connections_all.keys()))
if not os.path.exists("./jobfiles_all"):
os.mkdir("./jobfiles_all")
with open("./jobfiles_all/eqlist.csv", "w") as wf:
wf.write(exporteqstr)
with open("./jobfiles_all/tslist.csv", "w") as wf:
wf.write(exporttsstr)
Kmatstr = ""
for edge in connections_all.keys():
Kmatstr += "%s, %s, %s\n" % (edge[0], edge[1], connections_all[edge])
with open("./jobfiles_all/Kmatrix.csv", "w") as wf:
wf.write(Kmatstr)
def main():
constC = constClass()
#constC.initialpointN = 100
constC.initialpointN = 0
#constC.calc_cupyQ = True
constC.cythonQ = True
constC.calc_mpiQ = True
constC.use_jacQ = True
constC. IOEsphereA_initial = 0.02
constC.IOEsphereA_dist = 0.01
constC.deltas0 = 0.10
constC.deltas = 0.05
constC.lADDnQ = True
constC.IOEl = 8
constC.coeffPickNlist = [300000]
#constC.coeffabsmin = 1.0e-2
constC.periodicQ = True
constC.periodicmax = [ np.pi for _ in range(20)]
constC.periodicmin = [-np.pi for _ in range(20)]
constC.x0randomQ = True
#constC.x0randomQ = False
if constC.calc_mpiQ:
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
root = 0
else:
comm = None
rank = 0
root = 0
size = 1
if rank == root:
if not os.path.exists("./jobfiles_meta"):
os.mkdir("./jobfiles_meta")
constC = mkconst.main(constC)
if rank == root:
with open("./jobfiles_meta/constants.txt", "w") as wf:
wf.write(constC.writestr)
plumedpath = './plumedVES.dat'
VESclass = SHS4py.VESanalyzer.VESpotential(plumedpath, constC, rank, root, size, comm)
initialpointlist = []
# for line in open('./COLVAR'):
# if '#' in line:
# continue
# x = line.replace('\n','').split(' ')
# #print(x)
# initialpointlist.append(np.array(x[2:], dtype = float))
# initialpointlist = random.sample(initialpointlist, k = constC.initialpointN)
#print(initialpointlist)
#for line in open("../VES2D_200ns/jobfiles_meta/eqlist.csv"):
#for line in open("./jobfiles_meta.back1/eqlist.csv"):
#if "#" in line:
#continue
#line = line.split(",")
#initialpointlist.append(np.array(line[1:-1], dtype = float))
#print(initialpointlist[0])
SHS4py.SHSearch(VESclass.f, VESclass.grad, VESclass.hessian,
importinitialpointQ = False, initialpoints = initialpointlist,
SHSrank = rank, SHSroot = root, SHSsize = size, SHScomm = comm,
const = constC)
def main():
constC = constClass()
constC.Temp = 300.0 # tempeture (K)
k_B = 1.38065e-26 # Boltzmann constant (kJ / K)
N_A = 6.002214e23 # Avogadro constant (mol^-1)
constC.betainv = constC.Temp * k_B * N_A # 1/beta (kJ / mol)
constC.beta = 1.0 / constC.betainv
#constC.initialpointN = 100
constC.initialpointN = 0
#constC.calc_cupyQ = True
constC.cythonQ = True
constC.use_jacQ = True
constC.threshold = 1.0
constC.sameEQthreshold = [0.2 for _ in range(4)] + [2.0]
constC.IOEsphereA_initial = 0.05
constC.IOEsphereA_dist = 0.01
constC.deltas0 = 0.05
constC.deltas = 0.01
constC.coeffPickNlist = []
#! SET iteration 400000
#constC.coeffabsmin = 1.0e-3
constC.periodicQ = True
constC.periodicmax = [np.pi for _ in range(4)] + [40.0]
constC.periodicmin = [-np.pi for _ in range(4)] + [-40.0]
constC.wallmax = [1.0e30 for _ in range(4)] + [40.0]
constC.wallmin = [-1.0e30 for _ in range(4)] + [-40.0]
constC.EQwallmax = [1.0e30 for _ in range(4)] + [35.0]
constC.EQwallmin = [-1.0e30 for _ in range(4)] + [-35.0]
constC.abslist = False
constC.x0randomQ = False
constC.chkBifurcationQ = False
constC.chkinitialTSQ = True
constC.gridQ = False
constC.grid_importQ = False
constC.CVfixQ = False
constC.calc_mpiQ = False
if constC.calc_mpiQ:
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
root = 0
else:
comm = None
rank = 0
root = 0
size = 1
#if rank == root:
#if not os.path.exists(constC.jobfilepath):
#os.mkdir(constC.jobfilepath)
constC = mkconst.main(constC)
plumedpath = './plumed.dat'
VESclass = SHS4py.VESanalyzer.VESpotential(plumedpath, constC, rank, root,
size, comm)
eqlist_all = []
for line in open("./jobfiles_all/eqlist.csv"):
if "#" in line:
continue
eqpoint = EQclass(line)
eqlist_all.append(eqpoint)
for z in range(36):
eqlist_z = [eqpoint for eqpoint in eqlist_all if eqpoint.z == z]
femin = 1.0e30
for eqpoint in eqlist_z:
if eqpoint.fe < femin:
femin = eqpoint.fe
targetpoint = eqpoint.cv
writeline = ""
for z_pmf in range(36):
p = np.array(list(targetpoint) + [z_pmf])
print("p = %s" % p)
fe = VESclass.f(p)
writeline += "%s, %s\n" % (z_pmf, fe)
#print(writeline)
#exit()
csvpath = "./jobfiles_all/PMF_%s.csv" % z
with open(csvpath, "w") as wf:
wf.write(writeline)
print("%s is writen" % csvpath)