Merge pull request #59 from molssi-seamm/dev

Dev
molssi-seamm · Jul 31, 2024 · 6e0ca76 · 6e0ca76
2 parents 3720a68 + ddaae32
commit 6e0ca76
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Showing 4 changed files with 19 additions and 15 deletions.
diff --git a/HISTORY.rst b/HISTORY.rst
@@ -1,6 +1,13 @@
 =======
 History
 =======
+2024.7.31 -- Bugfix and improvements for parallel runs
+   * There was an issue saving the pressure and volume as properties due to a mismatch
+     in the names used. This has been corrected.
+   * Improved how the code determines the number of processors to use for parallel runs,
+     giving salience to the number of atoms in the system, but limiting to the LAMMPS and
+     global limits on numbers of cores as well as the hardware available.
+
 2024.7.25 -- Bugfix and improvements
    * Bugfix: Fixed issue with the initial seamm.ini file, created if it is missing from
      the installation.

diff --git a/lammps_step/data/properties.csv b/lammps_step/data/properties.csv
@@ -15,10 +15,10 @@ Property,Type,Units,Description,URL
 "density, stderr#LAMMPS#{model}",float,g/mL,"The standard error of the density.",https://en.wikipedia.org/wiki/Standard_error
 "density, tau#LAMMPS#{model}",float,fs,"The autocorrelation time of the density.",https://en.wikipedia.org/wiki/Autocorrelation
 "density, inefficiency#LAMMPS#{model}",float,,"The statistical inefficiency of the density sampling.",https://en.wikipedia.org/wiki/Efficiency_(statistics)
-"V#LAMMPS#{model}",float,g/mL,"The volume.",https://en.wikipedia.org/wiki/volume
-"V, stderr#LAMMPS#{model}",float,g/mL,"The standard error of the volume.",https://en.wikipedia.org/wiki/Standard_error
-"V, tau#LAMMPS#{model}",float,fs,"The autocorrelation time of the volume.",https://en.wikipedia.org/wiki/Autocorrelation
-"V, inefficiency#LAMMPS#{model}",float,,"The statistical inefficiency of the volume sampling.",https://en.wikipedia.org/wiki/Efficiency_(statistics)
+"volume#LAMMPS#{model}",float,g/mL,"The volume.",https://en.wikipedia.org/wiki/volume
+"volume, stderr#LAMMPS#{model}",float,g/mL,"The standard error of the volume.",https://en.wikipedia.org/wiki/Standard_error
+"volume, tau#LAMMPS#{model}",float,fs,"The autocorrelation time of the volume.",https://en.wikipedia.org/wiki/Autocorrelation
+"volume, inefficiency#LAMMPS#{model}",float,,"The statistical inefficiency of the volume sampling.",https://en.wikipedia.org/wiki/Efficiency_(statistics)
 "pressure#LAMMPS#{model}",float,atm,"The pressure.",https://en.wikipedia.org/wiki/Pressure
 "pressure, stderr#LAMMPS#{model}",float,atm,"The standard error of the pressure.",https://en.wikipedia.org/wiki/Standard_error
 "pressure, tau#LAMMPS#{model}",float,fs,"The autocorrelation time of the pressure.",https://en.wikipedia.org/wiki/Autocorrelation

diff --git a/lammps_step/lammps.py b/lammps_step/lammps.py
@@ -403,14 +403,11 @@ def run(self):
 
         # Whether to run parallel and if so, how many mpi processes
         if global_options["parallelism"] in ("any", "mpi"):
-            np = o["ncores"]
-            if np == "available":
-                np = global_options["ncores"]
-
-            if np == "available":
-                np = n_atoms // o["atoms_per_core"] + 1
-            else:
-                np = int(np)
+            np = n_atoms // o["atoms_per_core"] + 1
+            if o["ncores"] != "available":
+                np = min(np, o["ncores"])
+            if global_options["ncores"] != "available":
+                np = min(np, global_options["ncores"])
         else:
             np = 1
 

diff --git a/lammps_step/metadata.py b/lammps_step/metadata.py
@@ -162,23 +162,23 @@
         ],
         "description": "V",
         "dimensionality": "scalar",
-        "property": "V#LAMMPS#{model}",
+        "property": "volume#LAMMPS#{model}",
         "type": "float",
         "units": "g/ml",
     },
     "V,stderr": {
         "calculation": ["npt"],
         "description": "stderr of V",
         "dimensionality": "scalar",
-        "property": "V, stderr#LAMMPS#{model}",
+        "property": "volume, stderr#LAMMPS#{model}",
         "type": "float",
         "units": "g/ml",
     },
     "V,tau": {
         "calculation": ["npt"],
         "description": "autocorrelation time of V",
         "dimensionality": "scalar",
-        "property": "V, tau#LAMMPS#{model}",
+        "property": "volume, tau#LAMMPS#{model}",
         "type": "float",
         "units": "fs",
     },