adding fssh feature to pysurf

.readthedocs.yaml

@@ -0,0 +1,35 @@
+# Read the Docs configuration file for Sphinx projects
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the OS, Python version and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+    # You can also specify other tool versions:
+    # nodejs: "20"
+    # rust: "1.70"
+    # golang: "1.20"
+
+# Build documentation in the "docs/" directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
+  # builder: "dirhtml"
+  # Fail on all warnings to avoid broken references
+  # fail_on_warning: true
+
+# Optionally build your docs in additional formats such as PDF and ePub
+# formats:
+#   - pdf
+#   - epub
+
+# Optional but recommended, declare the Python requirements required
+# to build your documentation
+# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+# python:
+#   install:
+#     - requirements: docs/requirements.txt

README.rst

@@ -1,19 +1,14 @@
-==============================================================
-PySurf: A Framework for Database Accelerated Quantum Chemistry
-==============================================================
+==============================================================================
+PySurf-FSSH: New Plugin for PySurf to Perform Nonadiabatic Dynamics using FSSH
+==============================================================================
 
-::
-
-     _____          _____                __ 
-    |  __ \        / ____|              / _|
-    | |__) |_   _ | (___   _   _  _ __ | |_ 
-    |  ___/| | | | \___ \ | | | || '__||  _|
-    | |    | |_| | ____) || |_| || |   | |  
-    |_|     \__, ||_____/  \__,_||_|   |_|  
-             __/ |                          
-            |___/                           
+.. image:: docs/logo_pysurf_fssh.jpeg
+   :alt: Schematic description of the code structure
+   :width: 700px
 
+The FSSH Plugin is based on the standard FSSH algorithm proposed by Tully plus a decoherence correction to avoid overcoherence and a velocity adjustment to conserve the total energy. A comprehensive comparison using this plugin between the conventional Tully’s fewest switches surface hopping (FSSH) scheme and the Landau–Zener surface hopping (LZSH) to study photoinduced ring-opening of 1,3-cyclohexadiene to 1,3,5-hexatriene at SF-TDDFT level can be found here_.
 
+.. _here: https://pubs.acs.org/doi/10.1021/acs.jctc.4c00012
 
 Requirements
 ------------
@@ -23,8 +18,6 @@ Requirements
 
 Both can be installed by:
 
-::
-
     pip install pycolt qctools
 
 Additionally:
@@ -45,9 +38,32 @@ ____________
     - Light-weight 
     - Developer/user friendly
 
+Interfaces:
+____________
+
+    - Q-Chem_: TDDFT, SF-TDDFT & EOM-CCSD
+    - OpenMolcas_: SA-CASSCF, XMS-CASPT2 
+    - BAGEL_: XMS-CASPT2
+    - SA-OO-VQE_ (Quantum Algorithm)
+.. _Q-Chem: https://manual.q-chem.com/latest/
+.. _OpenMolcas: https://gitlab.com/Molcas/OpenMolcas
+.. _BAGEL: https://nubakery.org/
+.. _SA-OO-VQE: https://github.com/qc2nl/SAOOVQE
+
+Thermostat:
+____________
+
+     - Nose-Hoover_ 
+.. _Nose-Hoover: https://pubs.aip.org/aip/jcp/article/83/8/4069/219065/The-Nose-Hoover-thermostatThe-Nose-Hoover
+
+Documentation:
+--------------
+
+https://pysurf-fssh.readthedocs.io/
+
 
-Credits
--------
+Credits:
+--------
 
 This work was supported by the Innovational Research Incentives Scheme Vidi 2017 with project number 016.Vidi.189.044, (partly) funded by the Dutch Research Council (NWO).
 

bin/setup_propagation.py

@@ -6,9 +6,11 @@
 from pysurf.setup import SetupBase
 from pysurf.spp import SurfacePointProvider
 from pysurf.dynamics import RunTrajectory
+from pysurf.fssh import State
 from pysurf.utils import exists_and_isfile
 
 
+
 class SetupPropagation(SetupBase):
 
     folder = 'prop'
@@ -19,22 +21,26 @@ class SetupPropagation(SetupBase):
     n_traj = -1 :: int
 
     # Database containing all the initial conditions
-    sampling_db = :: existing_file
+    sampling_db = sampling.db :: existing_file
 
     # Filepath for the inputfile of the Surface Point Provider
     spp = spp.inp :: file
 
     # initial excited state for the trajectory
     initial state =  :: int
 
-    #Filepath for the inputfile of the Propagation
+    # Filepath for the inputfile of the Propagation
     prop = prop.inp :: file
 
     # Decide whether database for the propagation should be copied to the trajectory folder
     copy_db = none :: str
+
+    ## Run LZ or FSSH 
+    #tsh_method =  :: str :: FSSH, LZ
     """
 
     def __init__(self, config):
+        #self.tsh_method = config['tsh_method']
         """ Class to create initial conditions due to user input. Initial conditions are saved 
             in a file for further usage.
         """
@@ -47,16 +53,28 @@ def __init__(self, config):
 
         #Make sure that inputfile for the SPP exists and is complete
 
-        if exists_and_isfile(config['spp']): lconfig = config['spp']
+        if exists_and_isfile(config['spp']):lconfig = config['spp']
         else: lconfig = None
-        SurfacePointProvider.generate_input(config['spp'], config=lconfig)
+        spp_config = SurfacePointProvider.generate_input(config['spp'], config=lconfig)
+        if spp_config['mode'] == 'ab-initio':
+            self.model = None
+            self.basis = spp_config['mode']['software']['basis']        
+        elif spp_config['mode']['model'] == 'LVC':
+            self.model = "LVC"
+            self.basis = None
+        else:
+            self.basis = None
+            self.model = None
 
         #Make sure that inputfile for RunTrajectory exists and is complete
         if exists_and_isfile(config['prop']): lconfig = config['prop']
         else: lconfig = None
-        RunTrajectory.generate_input(config['prop'], config=lconfig)
-
+        #if self.tsh_method == 'FSSH':
+        #    State.from_questions(config = "prop.inp") 
+        #elif self.tsh_method == 'LZ':
+        #    RunTrajectory.generate_input(config['prop'], config=lconfig)
         #
+        State.from_questions(config = "prop.inp") 
         if config['n_traj'] == -1:
             ntraj = len(sampling._db)
         else:
@@ -74,12 +92,21 @@ def from_config(cls, config):
     def setup_folder(self, number, foldername, config, sampling):
         copy(config['prop'], foldername)
         copy(config['spp'], foldername)
+        if self.model == 'LVC':
+            copy('pyrmod6.inp', foldername)
+
+        if self.basis == 'gen':
+            copy('basis_gen.ini', foldername)
 
         if config['copy_db'] != 'none':
             copy(config['copy_db'], foldername)
 
-        initname = os.path.join(foldername, 'init.db')
+        #if self.tsh_method == 'FSSH':
+        #    initname = os.path.join(foldername, 'sampling.db')
+        #elif self.tsh_method == 'LZ':
+        #    initname = os.path.join(foldername, 'init.db')
         #setup new database 
+        initname = os.path.join(foldername, 'sampling.db')
         new_sampling = Sampling.create_db(initname, sampling.info['variables'], sampling.info['dimensions'], sampling.system, sampling.modes, model=sampling.model, sp=True)
         #copy condition to new db
         condition = sampling.get_condition(number)
@@ -88,4 +115,5 @@ def setup_folder(self, number, foldername, config, sampling):
 
 
 if __name__=="__main__":
-    SetupPropagation.from_commandline()
+    SetupPropagation.from_questions(config = "setup_propagation.inp")
+    #SetupPropagation.from_commandline()

bin/submit_traj.py

@@ -0,0 +1,63 @@
+import os
+from subprocess import run, CalledProcessError
+
+class SubmitTrajectories:
+
+    def read_sampling(self):
+        prop = open("sampling.inp", 'r+')
+        for line in prop:
+            if "model = " in line:
+                model = str(line.split()[2])
+            elif "from = molden" in line:
+                model = "molecule"
+        return model 
+
+    def read_spp(self):
+        prop = open("spp.inp", 'r+')
+        for line in prop:
+            if "use_db =" in line:
+                use_db = str(line.split()[2])
+        return use_db 
+
+    def read_prop(self):
+        prop = open("prop.inp", 'r+')
+        for line in prop:
+            if "method =" in line:
+                method = str(line.split()[2])
+        return method 
+
+    def trajectories(self):
+        model = self.read_sampling()
+        use_db = self.read_spp()
+        method = self.read_prop()
+        for traj in os.listdir("prop"):
+            subfolder = os.path.join("prop",traj)
+            try:
+                if method == "LandauZener":
+                    if use_db == "yes":
+                        run(['sbatch db_lz_run.sh'], cwd=subfolder, check=True, shell=True)
+                    else:
+                        run(['sbatch lz_run_om.sh'], cwd=subfolder, check=True, shell=True)
+                        #run(['sbatch lz_run.sh'], cwd=subfolder, check=True, shell=True)
+                elif method == "Surface_Hopping":
+                    if model == "Tully_1":
+                        run(['sbatch model_fssh_run.sh'], cwd=subfolder, check=True, shell=True)
+                    elif model == "LVC":
+                        run(['sbatch lvc_fssh_run.sh'], cwd=subfolder, check=True, shell=True)
+                    else:
+                        #run(['sbatch lz_nacs.sh'], cwd=subfolder, check=True, shell=True)
+                        #run(['sbatch saoovqe.sh'], cwd=subfolder, check=True, shell=True)
+                        run(['sbatch in_saoovqe.sh'], cwd=subfolder, check=True, shell=True)
+                        #run(['sbatch test_open_molcas.sh'], cwd=subfolder, check=True, shell=True)
+                        #run(['sbatch open_molcas.sh'], cwd=subfolder, check=True, shell=True)
+                        #run(['sbatch bagel.sh'], cwd=subfolder, check=True, shell=True)
+                        #run(['sbatch lvc_fssh_run.sh'], cwd=subfolder, check=True, shell=True)
+                        #run(['sbatch fssh_run.sh'], cwd=subfolder, check=True, shell=True)
+            except KeyboardInterrupt or CalledProcessError:
+                break
+            print("Submitting", subfolder)            
+
+
+if __name__=='__main__':
+    all_traj = SubmitTrajectories()
+    all_traj.trajectories()