Merge pull request #237 from jan-janssen/clear_no_close

Extend external LammpsLibrary interface

Author: srmnitc

calphy/alchemy.py

@@ -127,7 +127,7 @@ def run_averaging(self):
 
         # close object and process traj
         lmp = ph.write_data(lmp, "conf.equilibration.data")
-        lmp.close()
+        self.lammps_close(lmp=lmp)
         # Preserve log file
         logfile = os.path.join(self.simfolder, "log.lammps")
         try:
@@ -503,7 +503,7 @@ def run_integration(self, iteration=1):
             for idx in range(len(swap_combos)):
                 lmp.command(f"unfix swap{idx}")
             # lmp.command("unfix swap_print")
-        lmp.close()
+        self.lammps_close(lmp=lmp)
         # Preserve log file
         logfile = os.path.join(self.simfolder, "log.lammps")
         try:

calphy/liquid.py

@@ -131,7 +131,7 @@ def melt_structure(self, lmp):
 
         # if melting cycle is over and still not melted, raise error
         if not melted:
-            lmp.close()
+            self.lammps_close(lmp=lmp)
             # Preserve log file
             logfile = os.path.join(self.simfolder, "log.lammps")
             try:
@@ -215,7 +215,7 @@ def run_averaging(self):
         self.check_if_solidfied(lmp, "traj.equilibration_stage1.dat")
         self.dump_current_snapshot(lmp, "traj.equilibration_stage2.dat")
         lmp = ph.write_data(lmp, "conf.equilibration.data")
-        lmp.close()
+        self.lammps_close(lmp=lmp)
         # Preserve log file
         logfile = os.path.join(self.simfolder, "log.lammps")
         try:
@@ -437,7 +437,7 @@ def run_integration(self, iteration=1):
         lmp.command("uncompute        c2")
 
         # close object
-        lmp.close()
+        self.lammps_close(lmp=lmp)
         # Preserve log file
         logfile = os.path.join(self.simfolder, "log.lammps")
         try:

calphy/phase.py

@@ -279,7 +279,7 @@ def check_if_melted(self, lmp, filename):
         """ """
         solids = ph.find_solid_fraction(os.path.join(self.simfolder, filename))
         if solids / lmp.natoms < self.calc.tolerance.solid_fraction:
-            lmp.close()
+            self.lammps_close(lmp=lmp)
             # Preserve log file on error
             logfile = os.path.join(self.simfolder, "log.lammps")
             try:
@@ -296,7 +296,7 @@ def check_if_solidfied(self, lmp, filename):
         """ """
         solids = ph.find_solid_fraction(os.path.join(self.simfolder, filename))
         if solids / lmp.natoms > self.calc.tolerance.liquid_fraction:
-            lmp.close()
+            self.lammps_close(lmp=lmp)
             # Preserve log file on error
             logfile = os.path.join(self.simfolder, "log.lammps")
             try:
@@ -611,7 +611,7 @@ def run_iterative_pressure_convergence(self, lmp):
             laststd = std
 
         if not converged:
-            lmp.close()
+            self.lammps_close(lmp=lmp)
             # Preserve log file on error
             logfile = os.path.join(self.simfolder, "log.lammps")
             try:
@@ -736,7 +736,7 @@ def run_iterative_constrained_pressure_convergence(self, lmp):
         lmp.command("unfix            2")
 
         if not converged:
-            lmp.close()
+            self.lammps_close(lmp=lmp)
             # Preserve log file on error
             logfile = os.path.join(self.simfolder, "log.lammps")
             try:
@@ -1249,7 +1249,7 @@ def reversible_scaling(self, iteration=1):
             lmp.command("undump           d1")
 
         # close the object
-        lmp.close()
+        self.lammps_close(lmp=lmp)
         # Preserve log file
         logfile = os.path.join(self.simfolder, "log.lammps")
         if os.path.exists(logfile):
@@ -1449,8 +1449,8 @@ def temperature_scaling(self, iteration=1):
         )
         lmp.command("run               %d" % self.calc._n_sweep_steps)
 
-        lmp.close()
-        # Preserve log file
+        self.lammps_close(lmp=lmp)
+    # Preserve log file
         logfile = os.path.join(self.simfolder, "log.lammps")
         if os.path.exists(logfile):
             os.rename(
@@ -1587,7 +1587,7 @@ def pressure_scaling(self, iteration=1):
         )
         lmp.command("run               %d" % self.calc._n_sweep_steps)
 
-        lmp.close()
+        
         # Preserve log file
         logfile = os.path.join(self.simfolder, "log.lammps")
         if os.path.exists(logfile):
@@ -1643,3 +1643,9 @@ def clean_up(self):
 
         with open(os.path.join(self.simfolder, "metadata.yaml"), "w") as fout:
             yaml.safe_dump(metadata, fout)
+
+    def lammps_close(self, lmp):
+        if self._lmp is None:
+            lmp.close()
+        else:
+            lmp.clear()

calphy/solid.py

@@ -293,7 +293,7 @@ def run_interactive_averaging(self):
         self.check_if_melted(lmp, "traj.equilibration_stage2.dat")
         lmp = ph.write_data(lmp, "conf.equilibration.data")
         # close object and process traj
-        lmp.close()
+        self.lammps_close(lmp=lmp)
         # Preserve log file
         logfile = os.path.join(self.simfolder, "log.lammps")
         try:
@@ -593,7 +593,7 @@ def run_integration(self, iteration=1):
 
         # close object
         if not self.calc.script_mode:
-            lmp.close()
+            self.lammps_close(lmp=lmp)
             # Preserve log file
             logfile = os.path.join(self.simfolder, "log.lammps")
             try: