Merge pull request #95 from pyiron/extract_variables

extract_vairable()

Author: jan-janssen

pylammpsmpi/mpi/lmpmpi.py

@@ -77,15 +77,10 @@ def convert_data(val, type, length, width):
         val = job.extract_compute(*filtered_args)
         return convert_data(val=val, type=type, length=length, width=width)
     elif style == 1:  # per atom property
-        val = job.numpy.extract_compute(*filtered_args)
-        val_gather = MPI.COMM_WORLD.gather(val, root=0)
+        val = _gather_data_from_all_processors(
+            data=job.numpy.extract_compute(*filtered_args)
+        )
         if MPI.COMM_WORLD.rank == 0:
-            # val_gather.shape [number of cores, atoms on specific core]
-            # the number of atoms on specific cores can vary
-            val = []
-            for vl in val_gather:
-                for v in vl:
-                    val.append(v)
             length = job.get_natoms()
             return convert_data(val=val, type=type, length=length, width=width)
     else:  # Todo
@@ -165,15 +160,20 @@ def extract_fix(funct_args):
 def extract_variable(funct_args):
     # in the args - if the third one,
     # which is the type is 1 - a lammps array is returned
-    if MPI.COMM_WORLD.rank == 0:
-        # if type is 1 - reformat file
-        try:
-            data = job.extract_variable(*funct_args)
-        except ValueError:
-            return []
-        if funct_args[2] == 1:
-            data = np.array(data)
-        return data
+    if funct_args[2] == 1:
+        data = _gather_data_from_all_processors(
+            data=job.numpy.extract_variable(*funct_args)
+        )
+        if MPI.COMM_WORLD.rank == 0:
+            return np.array(data)
+    else:
+        if MPI.COMM_WORLD.rank == 0:
+            # if type is 1 - reformat file
+            try:
+                data = job.extract_variable(*funct_args)
+            except ValueError:
+                return []
+            return data
 
 
 def get_natoms(funct_args):
@@ -472,6 +472,16 @@ def select_cmd(argument):
     return switcher.get(argument)
 
 
+def _gather_data_from_all_processors(data):
+    data_gather = MPI.COMM_WORLD.gather(data, root=0)
+    if MPI.COMM_WORLD.rank == 0:
+        data = []
+        for vl in data_gather:
+            for v in vl:
+                data.append(v)
+        return data
+
+
 if __name__ == "__main__":
     while True:
         if MPI.COMM_WORLD.rank == 0:

tests/test_pylammpsmpi_cluster.py

@@ -59,7 +59,7 @@ def test_extract_variable(self):
         self.assertEqual(np.round(x, 2), 1.13)
 
         x = self.lmp.extract_variable("fx", "all", 1)
-        self.assertEqual(len(x), 128)
+        self.assertEqual(len(x), 256)
         self.assertEqual(np.round(x[0], 2), -0.26)
 
     def test_scatter_atoms(self):

tests/test_pylammpsmpi_local.py

@@ -55,7 +55,7 @@ def test_extract_variable(self):
         x = self.lmp.extract_variable("tt", "all", 0)
         self.assertEqual(np.round(x, 2), 1.13)
         x = self.lmp.extract_variable("fx", "all", 1)
-        self.assertEqual(len(x), 128)
+        self.assertEqual(len(x), 256)
         self.assertEqual(np.round(x[0], 2), -0.26)
 
     def test_scatter_atoms(self):