Fixed issues for thermal conductivity and running in parallel.

HISTORY.rst

@@ -1,6 +1,10 @@
 =======
 History
 =======
+2024.3.22 -- Corrected issue with e.g. heat flux calculations
+   * Corrected an issue running LAMMPS via Python, intorduced in the new scheme for
+     executing. It ignored parallelism.
+
 2024.3.21 -- Switched to new installation scheme
    * Fully support ~/SEAMM/lammps.ini
    * Updated to new installer

lammps_step/data/configuration.txt

@@ -21,24 +21,3 @@
 # they can be viewed without the SEAMM Dashboard.
 
 # html = False
-
-#
-# SEAMM picks up the environment variables such as SLURM_NTASKS, strips the
-# prefix from them and replaces any instances in the command line that are
-# enclosed in braces. Hopefully this lets you construct the correct command
-# line.
-#
-# The LAMMPS installer does not handle these variables! They are here
-# just in case!
-
-# lammps-serial = lmp_serial
-# lammps-mpi = lmp_mpi
-# mpiexec = mpiexec
-
-# Optional command-line arguments for LAMMPS. These are usually used with accelerators
-# such as Kokkos or GPU to automatically apply the accelerator. Again there is a normal
-# and GPU version
-
-# cmd-args = -k on -sf kk
-# gpu-cmd-args = -k on g {ngpus} -sf kk -pk kokkos gpu/aware on newton on neigh full neigh/thread on neigh/transpose off comm device
-

lammps_step/data/lammps.ini

@@ -15,6 +15,14 @@
 # code = mpirun -n {NTASKS} -H {NODELIST} -npernode {NTASKS_PER_NODE}
 
 code = mpirun -n {NTASKS} lmp
+python = python
+
+# Optional command-line arguments for LAMMPS. These are usually used with accelerators
+# such as Kokkos or GPU to automatically apply the accelerator. Again there is a normal
+# and GPU version
+
+# cmd-args = -k on -sf kk
+# gpu-cmd-args = -k on g {ngpus} -sf kk -pk kokkos gpu/aware on newton on neigh full neigh/thread on neigh/transpose off comm device
 
 # The name and location of the Docker container to use, optionally with the version
 
@@ -53,7 +61,15 @@ installation = conda
 #
 # code = mpirun -n {NTASKS} -H {NODELIST} -npernode {NTASKS_PER_NODE}
 
-code = mpirun -n {NTASKS} lmp
+code = mpirun -np {NTASKS} lmp
+python = mpirun -np {NTASKS} python
+
+# Optional command-line arguments for LAMMPS. These are usually used with accelerators
+# such as Kokkos or GPU to automatically apply the accelerator. Again there is a normal
+# and GPU version
+
+# cmd-args = -k on -sf kk
+# gpu-cmd-args = -k on g {ngpus} -sf kk -pk kokkos gpu/aware on newton on neigh full neigh/thread on neigh/transpose off comm device
 
 ######################### conda section ############################
 # The full path to the conda executable:

lammps_step/data/seamm-lammps.yml

@@ -5,6 +5,6 @@ dependencies:
   - python
     # Executables, etc.
   - openmpi
-  - lammps
+  - lammps * *mpi_openmpi*
   - openkim-models
   - mpi4py

lammps_step/lammps.py

@@ -663,27 +663,34 @@
 
             if path.exists():
                 full_config.read(ini_dir / "lammps.ini")
+                full_config.set("local", "_origin_", f"{ini_dir / 'lammps.ini'}")
 
             # If the section we need doesn't exists, get the default
             if not path.exists() or executor_type not in full_config:
                 resources = importlib.resources.files("lammps_step") / "data"
                 ini_text = (resources / "lammps.ini").read_text()
                 full_config.read_string(ini_text)
+                full_config.set("local", "_origin_", "lammps default ini file")
 
             # Getting desperate! Look for an executable in the path
             if executor_type not in full_config:
-                path = shutil.which("lammps")
+                path = shutil.which("lmp")
                 if path is None:
                     raise RuntimeError(
                         f"No section for '{executor_type}' in LAMMPS ini file "
                         f"({ini_dir / 'lammps.ini'}), nor in the defaults, nor "
                         "in the path!"
                     )
                 else:
-                    full_config[executor_type] = {
-                        "installation": "local",
-                        "code": str(path),
-                    }
+                    full_config.add_section(executor_type)
+                    full_config.set(executor_type, "installation", "local")
+                    full_config.set(executor_type, "code", str(path))
+
+            # And we may need python!
+            full_config.set("local", "items", f"{full_config.items('local')}")
+            if not full_config.has_option(executor_type, "python"):
+                full_config.set(executor_type, "python", "mpirun -np {NTASKS} python")
+                full_config.set(executor_type, "_python source_", "default value")
 
             # If the ini file does not exist, write it out!
             if not path.exists():
@@ -707,11 +714,19 @@
             # Setup the command lines
             cmd = []
 
-            if "python script" in files:
+            if "run_lammps" in files:
                 cmd = ["{python}", "run_lammps"]
-                if "GPUS" not in ce and config["cmd_args"] != "":
+                if (
+                    "GPUS" not in ce
+                    and "cmd_args" in config
+                    and config["cmd_args"] != ""
+                ):
                     cmd.extend(["--cmd-args", config["cmd_args"]])
-                if "GPUS" in ce and config["gpu_cmd_args"] != "":
+                if (
+                    "GPUS" in ce
+                    and "gpu_cmd_args" in config
+                    and config["gpu_cmd_args"] != ""
+                ):
                     cmd.extend(["--cmd-args", config["gpu_cmd_args"]])
             else:
                 cmd = ["{code}"]
@@ -723,7 +738,7 @@
                     cmd.extend(config["cmd_args"].split())
                 if (
                     "GPUS" in ce
-                    and config["gpu_cmd_args"] != ""
+                    and "gpu_cmd_args" in config
                     and config["gpu_cmd_args"] != ""
                 ):
                     cmd.extend(config["gpu_cmd_args"].split())