Merge pull request #142 from sharc-md/sharc3preview

Sharc3preview

bin/QMout_print.py

@@ -298,7 +298,10 @@ def main():
     qminfile = options.i
     initial = options.S - 1
     target = options.t
-    qmoutfile = args[0]
+    if len(args)<1:
+        qmoutfile = 'QM.out'
+    else:
+        qmoutfile = args[0]
 
     QMin = {'states': 1, 'natom': options.n}
     if qminfile != '':

bin/SHARC_ORCA.py

@@ -2179,7 +2179,8 @@ def readQMin(QMinfilename):
              'unrestricted_triplets': False,
              'qmmm': False,
              'cobramm': False,
-             'picture_change': False
+             'picture_change': False,
+             'dotrans': False
              }
     strings = {'basis': '6-31G',
                'auxbasis': '',
@@ -2375,6 +2376,9 @@ def readQMin(QMinfilename):
         if len(QMin['states']) >= 3 and QMin['states'][2] > 0:
             print('Request "SOC" is not compatible with "unrestricted_triplets"!')
             sys.exit(64)
+    if QMin['template']['dotrans'] and 'soc' in QMin:
+        print('dotrans and SOC not compatible (in ORCA 5).')
+        sys.exit(64)
     # if QMin['template']['cosmo'] and 'grad' in QMin: TODO
         # print('COSMO is not compatible with gradient calculations!')
         # sys.exit(65)
@@ -3175,7 +3179,8 @@ def ORCAinput_string(QMin):
         if restr and 'soc' in QMin:
             string += 'dosoc true\n'
             string += 'printlevel 3\n'
-        # string+="dotrans all\n" #TODO
+        if 'dm' in QMin and QMin['template']['dotrans']: 
+            string+="dotrans all\n" #TODO
         if dograd:
             if multigrad:
                 if singgrad:
@@ -4261,7 +4266,7 @@ def runTHEODORE(WORKDIR, THEODIR):
         sys.stdout.flush()
     os.chdir(prevdir)
     if runerror >0 and os.path.isfile(os.path.join(THEODIR,'bin','theodore')): 
-        sys.stdout.write('Error code is not 0 for TheoDORE 3.x. Please make sure to use at least TheoDORE 3.2 with SHARC_ORCA.py. ' 
+        sys.stdout.write('Error code is not 0 for TheoDORE 3.x. Please make sure to use at least TheoDORE 3.2 with SHARC_ORCA.py. ') 
     return runerror
 
 # =============================================================================================== #
@@ -4497,6 +4502,8 @@ def getQMout(QMin):
         for job in joblist:
             logfile = os.path.join(QMin['scratchdir'], 'master_%i/ORCA.log' % (job))
             dipoles = gettdm(logfile, job, QMin)
+            if QMin['template']['dotrans']:
+                tdms = get_e2e_tdm(logfile, job, QMin)
             mults = QMin['multmap'][-job]
             if 3 in mults and QMin['OrcaVersion'] < (4, 1):
                 mults = [3]
@@ -4531,6 +4538,16 @@ def getQMout(QMin):
                     elif s2 == 1:
                         for ixyz in range(3):
                             QMout['dm'][ixyz][i][j] = dipoles[(m1, s1)][ixyz]
+                    elif QMin['template']['dotrans'] and m1 == m2 == 1:
+                        if (i,j) in tdms:
+                            for ixyz in range(3):
+                                QMout['dm'][ixyz][i][j] = tdms[(i, j)][ixyz]
+                                QMout['dm'][ixyz][j][i] = tdms[(i, j)][ixyz]
+                        elif (j,i) in tdms:
+                            for ixyz in range(3):
+                                QMout['dm'][ixyz][i][j] = tdms[(j, i)][ixyz]
+                                QMout['dm'][ixyz][j][i] = tdms[(j, i)][ixyz]
+
 
 
     # Gradients
@@ -4951,6 +4968,75 @@ def gettdm(logfile, ijob, QMin):
     # print dipoles
     return dipoles
 
+# ======================================================================= #
+
+def get_e2e_tdm(logfile, ijob, QMin):
+
+    # open file
+    f = readfile(logfile)
+    if PRINT:
+        print('e2e Dipoles:  ' + shorten_DIR(logfile))
+
+    # figure out the excited state settings
+    mults = QMin['jobs'][ijob]['mults']
+    if not 1 in mults:
+        return {}
+    restr = QMin['jobs'][ijob]['restr']
+    gsmult = mults[0]
+    estates_to_extract = deepcopy(QMin['states'])
+    estates_to_extract[gsmult - 1] -= 1
+    for imult in range(len(estates_to_extract)):
+        if not imult + 1 in mults:
+            estates_to_extract[imult] = 0
+
+
+    dipoles = {}
+    for imult in mults:
+        if not imult == gsmult:
+            continue
+        nstates = estates_to_extract[imult - 1]
+        if nstates == 0:
+            continue
+        iline = 0
+        while True:
+            line = f[iline]
+            if 'TRANSIENT TD-DFT/TDA-EXCITATION SPECTRA' in line:
+                break
+            iline += 1
+
+        for istate in range(1,nstates):
+            while True:
+                iline += 1
+                line = f[iline]
+                if 'Transitions starting from IROOT' in line:
+                    state = int(line.replace(':','').split()[-1])
+                    print(iline,state)
+                    if state == istate:
+                        break 
+            for jstate in range(1+istate,1+nstates):
+                line = f[iline+7-istate+jstate]
+                #print(line)
+                dm = [ float(i) for i in line.split()[5:8] ]
+                dipoles[ (istate,jstate) ] = dm
+
+    #print(dipoles)
+#            for iline, line in enumerate(f):
+#                if '  ABSORPTION SPECTRUM VIA TRANSITION ELECTRIC DIPOLE MOMENTS' in line:
+#                    # print line
+#                    for istate in range(nstates):
+#                        shift = 5 + istate
+#                        s = f[iline + shift].split()
+#                        dm = [float(i) for i in s[5:8]]
+#                        dipoles[(imult, istate + 1 + (gsmult == imult))] = dm
+    # print dipoles
+    return dipoles
+
+
+
+
+
+
+
 # ======================================================================= #
 
 

bin/setup_traj.py

@@ -2634,7 +2634,7 @@ def check_MOLCAS_qmmm(filename):
     data = f.readlines()
     f.close()
     for line in data:
-        if 'qmmm' in line.lower():
+        if 'qmmm' in re.sub('#.*$', '', line).strip().lower():
             return True
     return False
 

tests/INPUT/scripts_setup_traj/KEYSTROKES.setup_traj

@@ -7,12 +7,15 @@
                                          #Number of trajectories: [1] 
 1234                                     #RNG Seed:  [!] 
 3                                        #Interface number: 
+                                         #Method: [1]
                                          #Simulation time (fs): [1000.0] 
                                          #Simulation timestep (fs): [0.5] 
+                                         #Integrator: [2
                                          #Nsubsteps: [25] 
                                          #Do you want to prematurely terminate trajectories? [False] 
                                          #SHARC dynamics? [True] 
                                          #Coupling number: [3] 
+                                         #GradCorrect: [1]
                                          #EkinCorrect: [2] 
                                          #Reflect frustrated: [1] 
                                          #Decoherence scheme: [2] 

tests/RESULTS/scripts_setup_traj/State_2/TRAJ_00001/input

@@ -8,13 +8,15 @@ nstates 2
 actstates 2 
 state 2 diag
 coeff auto
-rngseed 30569
+rngseed 24999
 
 ezero    -329.5062895400
 tmax 1000.000000
 stepsize 0.500000
 nsubsteps 25
+integrator fvv
 
+method tsh
 surf diagonal
 coupling overlap
 nogradcorrect
@@ -25,6 +27,7 @@ decoherence_param 0.1
 hopping_procedure sharc
 grad_select
 eselect 0.001000
+select_directly
 nospinorbit
 write_overlap
 output_format ascii

tests/RESULTS/scripts_setup_traj/State_2/TRAJ_00001/run.sh

@@ -1,10 +1,10 @@
 #!/bin/bash
 
-#$-N traj_00001
+# $-N traj_00001
 
 
 
-PRIMARY_DIR=/user/mai/Documents/NewSHARC/SHARC_2.1/TESTS/pysharc/RUNNING_TESTS/scripts_setup_traj/State_2/TRAJ_00001/
+PRIMARY_DIR=/global/mai/SHARC_3.0_tests/tests/RUNNING_TESTS/scripts_setup_traj/State_2/TRAJ_00001/
 
 cd $PRIMARY_DIR