Fix errors in interface_builder execution and portability

.gitignore

@@ -0,0 +1,12 @@
+__pycache__/
+*.pyc
+*.egg-info/
+log.lammps
+log_*.lammps
+*.data
+*.dump
+amorphous_*/
+quartz*/
+heatofimmersion*/
+Q4*/
+seed.txt

examples/generate_amorphous_system.py

@@ -1,15 +1,19 @@
 from interface_builder import Silica
+import os
 
 # Generate 10 sample of silica surface! 
 for indx in range(2):
     # prepare the surface 
+    output_folder = f'amorphous_{indx}'
+    os.makedirs(output_folder, exist_ok=True)
+
     silica_params = {
         'lx' : 4, 
         'ly' : 4, 
         'lz' : 4, 
         'vacuum' : 30,
         'filename' : 'silica_amorphous.data',
-        'output_folder' : f'amorphous_{indx}',
+        'output_folder' : output_folder,
         'input_folder' : 'test', 
         'sio2_potential' : './data/SiO2.vashishta',
         'sio2_h2o_potential' : "./data/SiOH2O_199_16_adjusted.vashishta",
@@ -19,7 +23,7 @@
     # initilize the silica system 
     silica = Silica(**silica_params)
 
-    silica_file = silica.build_amorphous(16, "lmp", run=True)
+    silica_file = silica.build_amorphous(mpirun_n=16, lmp_exec="lmp", run=True)
 
     # silica_surface = silica.resize_z(silica_file, 90, "silica_surface.data")
     # silica_annealed = silica.anneal(silica_surface, mpirun_n=16, lmp_exec="lmp", run=True)

examples/test_quartz.py

@@ -32,7 +32,7 @@
 passivated_silica = silica_thermalize 
 for _ in range(3):
     passivated_silica = silica.passivate(passivated_silica , T, 'passivated_quartz.data',
-                                    thickness=5, mpirun_n=16, lmp_exec='lmp_usc', run=False)
+                                    water_thickness=5, mpirun_n=16, lmp_exec='lmp_usc', run=False)
 
 silica_passivated_thermalize = silica.thermalize_passivated(passivated_silica, time=50, temp=300, 
                                                             output_filename= "silica_passivated_thermalize.data",

interface_builder/interface_builder.py

@@ -73,7 +73,8 @@ def __init__(
         self.sio2_h2o_potential = sio2_h2o_potential
 
         # create the output directory
-        os.system(f'mkdir {output_folder}')
+        if output_folder:
+            os.makedirs(output_folder, exist_ok=True)
         if lx is None and ly is None and lz is None:
             # copy the input file into the working directory
             shutil.copyfile(
@@ -459,9 +460,6 @@ def set_silanol(
             'potential_filename': self.sio2_h2o_potential,
             'output_folder': self.output_folder
         }
-        lmp_exec = os.path.join(
-            "/home/users/anthonca/silica-water-interface_sandbox/interface_builder/interface_builder/lmp_exec/",
-            "lmp")
         if run:
             script_path = os.path.join(script_dir, 'script', 'in.set_silanol')
             self.execute_lammps(
@@ -542,7 +540,8 @@ def execute_lammps(
             mpirun_n=4,
             lmp_exec='lmp',
             script=None,
-            slurm=False):
+            slurm=False,
+            oversubscribe=True):
         '''Execute a LAMMPS simulation with the given arguments.
         This method executes a LAMMPS simulation using the specified LAMMPS executable and input script, along with additional arguments provided in the lmps_args dictionary.
 
@@ -556,6 +555,8 @@ def execute_lammps(
         :type script: str or None
         :param slurm: (Optional) If True, run the simulation using Slurm on a HPC cluster. Default is False.
         :type slurm: bool
+        :param oversubscribe: (Optional) If True, run mpirun with --oversubscribe. Default is True.
+        :type oversubscribe: bool
 
         :return: None
         '''
@@ -573,8 +574,11 @@ def execute_lammps(
                 **lmps_args)
             sim.run(computer=computer)
         else:
+            mpi_args = f"-n {mpirun_n}"
+            if oversubscribe:
+                mpi_args += " --oversubscribe"
             os.system(
-                f"mpirun -n {mpirun_n} {lmp_exec} -in {script} {lmps_args_list}")
+                f"mpirun {mpi_args} {lmp_exec} -in {script} {lmps_args_list}")
 
     def add_water(
             self,

interface_builder/script/in.passivated_thermalized

@@ -2,10 +2,10 @@ units metal
 boundary p p p
 atom_style atomic
 
-read_data /Users/anthonca/Documents/PhD/silica-water-sim/contact_angle-amorphous/data/new_set/passivation/data/WCA_system_clean/system2_87SiOH_6436.data
+read_data ${input_filename}
 
 pair_style  usc
-pair_coeff  * * ./data/SiOH2O_nm_0_0.vashishta H O Si
+pair_coeff  * * ${potential_filename} H O Si
 pair_modify coord 2 3 2.0 0.3
 pair_modify coord 2 1 1.4 0.3
 mass            1 1.00794
@@ -27,7 +27,7 @@ variable thermalising_time equal  5 # ps
 variable thermalising_steps equal ${thermalising_time}/${dt}
 
 fix 1 all nvt temp 300 300 $(100*dt)
-dump silica all custom 100 ./data/silica-passivated.dump id type x y z
+dump silica all custom 100 ${output_folder}/silica-passivated.dump id type x y z
 
 log log_passivated-thermalized.lammps 
 thermo_style custom step time temp etotal spcpu cpuremain
@@ -36,4 +36,4 @@ thermo 10
 timestep ${dt}
 run ${thermalising_steps}
 
-write_data ./data/passivated-system2_thermalized.data
+write_data ${output_filename}

setup.py

@@ -20,7 +20,9 @@
     packages=find_packages(),
     install_requires=[
         "numpy",
-        "molecular-builder"
+        "molecular-builder",
+        "lammps-logfile",
+        "pandas"
     ],
     classifiers=[
         "Programming Language :: Python :: 3.9",