Merge pull request #668 from ISISNeutronMuon/chi/cp2k-optional-vel-file

Update the CP2K configurator and widget so that the velocity file is optional

MDANSE/Src/MDANSE/Framework/Configurators/OptionalXYZFileConfigurator.py

@@ -0,0 +1,35 @@
+#    This file is part of MDANSE.
+#
+#    MDANSE is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This program is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+#
+from .XYZFileConfigurator import XYZFileConfigurator
+
+
+class OptionalXYZFileConfigurator(XYZFileConfigurator):
+    def configure(self, filepath: str) -> None:
+        """Configure the XYZ file if the filepath is not empty.
+
+        Parameters
+        ----------
+        filepath : str
+            THe filepath of the xyz file.
+        """
+        if not filepath:
+            self._original_input = filepath
+            self["value"] = filepath
+            self["filename"] = filepath
+            self.error_status = "OK"
+            return
+
+        super().configure(filepath)

MDANSE/Src/MDANSE/Framework/Converters/CP2K.py

@@ -122,14 +122,21 @@ class CP2K(Converter):
         },
     )
     settings["vel_file"] = (
-        "XYZFileConfigurator",
+        "OptionalXYZFileConfigurator",
         {
             "wildcard": "XYZ files (*.xyz);;All files (*)",
-            "default": "INPUT_FILENAME.xyz",
-            "optional": True,
+            "default": "",
             "label": "Velocity file (XYZ, optional)",
         },
     )
+    settings["force_file"] = (
+        "OptionalXYZFileConfigurator",
+        {
+            "wildcard": "XYZ files (*.xyz);;All files (*)",
+            "default": "",
+            "label": "Force file (XYZ, optional)",
+        },
+    )
     settings["cell_file"] = (
         "InputFileConfigurator",
         {
@@ -169,7 +176,7 @@ def initialize(self):
         self._atomicAliases = self.configuration["atom_aliases"]["value"]
         self._xyzFile = self.configuration["pos_file"]
 
-        if self.configuration["vel_file"]:
+        if self.configuration["vel_file"]["value"]:
             self._velFile = self.configuration["vel_file"]
             if abs(self._xyzFile["time_step"] - self._velFile["time_step"]) > 1.0e-09:
                 raise CP2KConverterError(
@@ -181,6 +188,18 @@ def initialize(self):
                     "Inconsistent number of frames between pos and vel files"
                 )
 
+        if self.configuration["force_file"]["value"]:
+            self._forceFile = self.configuration["force_file"]
+            if abs(self._xyzFile["time_step"] - self._forceFile["time_step"]) > 1.0e-09:
+                raise CP2KConverterError(
+                    "Inconsistent time step between pos and force files"
+                )
+
+            if self._xyzFile["n_frames"] != self._forceFile["n_frames"]:
+                raise CP2KConverterError(
+                    "Inconsistent number of frames between pos and force files"
+                )
+
         self._cellFile = CellFile(self.configuration["cell_file"]["filename"])
 
         if abs(self._cellFile["time_step"] - self._xyzFile["time_step"]) > 1.0e-09:
@@ -216,8 +235,10 @@ def initialize(self):
         )
 
         data_to_be_written = ["configuration", "time"]
-        if self.configuration["vel_file"]:
+        if self.configuration["vel_file"]["value"]:
             data_to_be_written.append("velocities")
+        if self.configuration["force_file"]["value"]:
+            data_to_be_written.append("forces")
 
     def run_step(self, index):
         """Runs a single step of the job.
@@ -236,10 +257,14 @@ def run_step(self, index):
         )
 
         variables = {}
-        if self.configuration["vel_file"]:
+        if self.configuration["vel_file"]["value"]:
             variables["velocities"] = self._velFile.read_step(index) * measure(
                 1.0, iunit="ang/fs"
             ).toval("nm/ps")
+        if self.configuration["force_file"]["value"]:
+            variables["forces"] = self._forceFile.read_step(index) * measure(
+                1.0, iunit="uma ang / fs2"
+            ).toval("uma nm / ps2")
 
         real_conf = PeriodicRealConfiguration(
             self._trajectory.chemical_system, coords, unitcell, **variables
@@ -284,9 +309,12 @@ def finalize(self):
 
         self._xyzFile.close()
 
-        if self.configuration["vel_file"]:
+        if self.configuration["vel_file"]["value"]:
             self._velFile.close()
 
+        if self.configuration["force_file"]["value"]:
+            self._forceFile.close()
+
         self._cellFile.close()
 
         # Close the output trajectory.

MDANSE/Src/MDANSE/Mathematics/Arithmetic.py

@@ -98,7 +98,6 @@ def assign_weights(
     dim = key.count("%s")
 
     for k in values.keys() & matches:
-
         if symmetric:
             permutations = set(itertools.permutations(matches[k], r=dim))
             w = sum(weights[p] for p in permutations)

MDANSE/Tests/UnitTests/Data/SrTiO3_MD-cell-1.cell

@@ -0,0 +1,11 @@
+#   Step   Time [fs]       Ax [Angstrom]       Ay [Angstrom]       Az [Angstrom]       Bx [Angstrom]       By [Angstrom]       Bz [Angstrom]       Cx [Angstrom]       Cy [Angstrom]       Cz [Angstrom]      Volume [Angstrom^3]
+2 0.6 11.715 0.0 0.0 0.0 11.715 0.0 0.0 0.0 11.715 1607.780950875
+3 1.2 11.715 0.0 0.0 0.0 11.715 0.0 0.0 0.0 11.715 1607.780950875
+4 1.8 11.715 0.0 0.0 0.0 11.715 0.0 0.0 0.0 11.715 1607.780950875
+5 2.4 11.715 0.0 0.0 0.0 11.715 0.0 0.0 0.0 11.715 1607.780950875
+6 3.0 11.715 0.0 0.0 0.0 11.715 0.0 0.0 0.0 11.715 1607.780950875
+7 3.6 11.715 0.0 0.0 0.0 11.715 0.0 0.0 0.0 11.715 1607.780950875
+8 4.2 11.715 0.0 0.0 0.0 11.715 0.0 0.0 0.0 11.715 1607.780950875
+9 4.8 11.715 0.0 0.0 0.0 11.715 0.0 0.0 0.0 11.715 1607.780950875
+10 5.4 11.715 0.0 0.0 0.0 11.715 0.0 0.0 0.0 11.715 1607.780950875
+11 6.0 11.715 0.0 0.0 0.0 11.715 0.0 0.0 0.0 11.715 1607.780950875