for di, id in enumerate(idir):
files = os.listdir(id[1])
random.shuffle(files)
dnfo = str(di) + ' of ' + str(
len(idir)) + ') dir: ' + str(id) + ' Selecting: ' + str(
id[0] * len(files))
print(dnfo)
difo.write(dnfo + '\n')
for i in range(id[0]):
for n, m in enumerate(files):
data = hdn.read_rcdb_coordsandnm(id[1] + m)
mols.append(data)
dgen = pmf.dimergenerator(cnstfilecv, saefilecv, nnfprefix, 5, mols)
difo.write('Beginning dimer generation...\n')
Nt = 0
Nd = 0
for i in range(Nr):
dgen.init_dynamics(Nm, V, L, dt, T)
dgen.run_dynamics(Ni, xyzfile, trajfile)
dgen.__fragmentbox__(molfile + str(i).zfill(4) + '_')
Nt += dgen.Nt
Nd += dgen.Nd
print('Step (', i, ') [', str(dgen.Nd), '/', str(dgen.Nt), '] generated ',
def dimer_sampling(self, tid, Nr, dparam, gpuid):
mds_select = dparam['mdselect']
#N = dparam['N']
T = dparam['T']
L = dparam['L']
V = dparam['V']
maxNa = dparam['maxNa']
dt = dparam['dt']
sig = dparam['sig']
Nm = dparam['Nm']
Ni = dparam['Ni']
Ns = dparam['Ns']
mols = []
difo = open(
self.ldtdir + self.datdir + '/info_data_mddimer-' + str(tid) +
'.nfo', 'w')
for di, id in enumerate(dparam['mdselect']):
files = os.listdir(self.idir[id[1]])
random.shuffle(files)
dnfo = str(di) + ' of ' + str(len(
dparam['mdselect'])) + ') dir: ' + str(
self.idir[id[1]]) + ' Selecting: ' + str(
id[0] * len(files))
#print(dnfo)
difo.write(dnfo + '\n')
for i in range(id[0]):
for n, m in enumerate(files):
data = hdt.read_rcdb_coordsandnm(self.idir[id[1]] + m)
if len(data['species']) < maxNa:
mols.append(data)
dgen = pmf.dimergenerator(self.netdict['cnstfile'],
self.netdict['saefile'],
self.netdict['nnfprefix'],
self.netdict['num_nets'], mols, gpuid)
difo.write('Beginning dimer generation...\n')
Nt = 0
Nd = 0
for i in range(Nr):
dgen.init_dynamics(Nm, V, L, dt, T)
for j in range(Ns):
if j != 0:
dgen.run_dynamics(Ni)
fname = self.cdir + 'dimer-' + str(tid).zfill(2) + str(
i).zfill(2) + '-' + str(j).zfill(2) + '_'
max_sig = dgen.__fragmentbox__(fname, sig)
print('MaxSig:', max_sig)
#difo.write('Step ('+str(i)+',',+str(j)+') ['+ str(dgen.Nd)+ '/'+ str(dgen.Nt)+']\n')
difo.write('Step (' + str(i) + ',' + str(j) + ') [' +
str(dgen.Nd) + '/' + str(dgen.Nt) +
'] max sigma: ' + "{:.2f}".format(max_sig) +
' generated ' + str(len(dgen.frag_list)) +
' dimers...\n')
Nt += dgen.Nt
Nd += dgen.Nd
#print('Step (',tid,',',i,') [', str(dgen.Nd), '/', str(dgen.Nt),'] generated ',len(dgen.frag_list), 'dimers...')
#difo.write('Step ('+str(i)+') ['+ str(dgen.Nd)+ '/'+ str(dgen.Nt)+'] generated '+str(len(dgen.frag_list))+'dimers...\n')
if max_sig > 3.0 * sig:
difo.write('Terminating dynamics -- max sigma: ' +
"{:.2f}".format(max_sig) + ' Ran for: ' +
"{:.2f}".format(j * Ni * dt) + 'fs\n')
break
difo.write('Generated ' + str(Nd) + ' of ' + str(Nt) +
' tested dimers. Percent: ' +
"{:.2f}".format(100.0 * Nd / float(Nt)))
difo.close()