Merge pull request #430 from ISISNeutronMuon/lammps-converter-fix

Lammps converter fix

MDANSE/Src/MDANSE/Framework/Configurators/AseInputFileConfigurator.py

@@ -30,7 +30,7 @@ class AseInputFileConfigurator(InputFileConfigurator):
     _default = ""
     _allowed_formats = ["guess"] + [str(x) for x in all_formats.keys()]
 
-    def __init__(self, name, wildcard="All files|*", **kwargs):
+    def __init__(self, name, wildcard="All files (*)", **kwargs):
         """
         Initializes the configurator object.
 

MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py

@@ -26,6 +26,30 @@ class LAMMPSConfigFileError(Error):
     pass
 
 
+def parse_unit_cell(inputs):
+
+    unit_cell = np.zeros(9)
+
+    xlo, xhi, xy = inputs[0], inputs[1], inputs[2]
+    ylo, yhi, xz = inputs[3], inputs[4], inputs[5]
+    zlo, zhi, yz = inputs[6], inputs[7], inputs[8]
+    # The ax component.
+    unit_cell[0] = xhi - xlo
+
+    # The bx and by components.
+    unit_cell[3] = xy
+    unit_cell[4] = yhi - ylo
+
+    # The cx, cy and cz components.
+    unit_cell[6] = xz
+    unit_cell[7] = yz
+    unit_cell[8] = zhi - zlo
+
+    unit_cell = np.reshape(unit_cell, (3, 3))
+
+    return unit_cell
+
+
 class ConfigFileConfigurator(FileWithAtomDataConfigurator):
 
     def parse(self):
@@ -41,15 +65,39 @@ def parse(self):
 
         self["elements"] = []
 
-        unit = open(self._filename, "r")
-        lines = []
-        for l in unit.readlines():
-            l = l.strip()
-            if l:
-                lines.append(l)
-        unit.close()
+        self["atom_types"] = []
+
+        self["unit_cell"] = np.zeros((3, 3))
+
+        with open(self._filename, "r") as source_file:
+            lines = []
+            for l in source_file.readlines():
+                l = l.strip()
+                if l:
+                    lines.append(l)
 
         for i, line in enumerate(lines):
+            toks = line.split()
+
+            if "xlo" in line and "xhi" in line:
+                try:
+                    x_inputs = [float(x) for x in toks[0:3]]
+                except:
+                    xspan = float(toks[1]) - float(toks[0])
+                    self["unit_cell"][0, 0] = xspan
+            elif "ylo" in line and "yhi" in line:
+                try:
+                    y_inputs = [float(x) for x in toks[0:3]]
+                except:
+                    yspan = float(toks[1]) - float(toks[0])
+                    self["unit_cell"][1, 1] = yspan
+            elif "zlo" in line and "zhi" in line:
+                try:
+                    z_inputs = [float(x) for x in toks[0:3]]
+                except:
+                    zspan = float(toks[1]) - float(toks[0])
+                    self["unit_cell"][2, 2] = zspan
+
             if self["n_atoms"] is None:
                 m = re.match("^\s*(\d+)\s*atoms\s*$", line, re.I)
                 if m:
@@ -74,7 +122,7 @@ def parse(self):
                 for j in range(1, self["n_atom_types"] + 1):
                     data_line = (
                         lines[i + j].strip().split("#")[0]
-                    )  # Remove commentary if any
+                    )  # Remove comments, if present
                     idx, mass = data_line.split()[0:2]
                     idx = int(idx)
                     mass = float(mass)
@@ -89,6 +137,22 @@ def parse(self):
                     self["bonds"].append([at1, at2])
                 self["bonds"] = np.array(self["bonds"], dtype=np.int32)
 
+            if re.match("^\s*Atoms\s*$", line):
+                if self["n_atoms"] is not None:
+                    self["atom_types"] = self["n_atoms"] * [0]
+                    for j in range(self["n_atoms"]):
+                        atoks = lines[i + j + 1].split()
+                        self["atom_types"][j] = int(atoks[2])
+
+        if np.trace(np.abs(self["unit_cell"])) < 1e-8:
+            # print(f"Concatenated: {np.concatenate([x_inputs, y_inputs, z_inputs])}")
+            try:
+                self["unit_cell"] = parse_unit_cell(
+                    np.concatenate([x_inputs, y_inputs, z_inputs])
+                )
+            except:
+                print(f"LAMMPS ConfigFileConfigurator failed to find a unit cell")
+
     def get_atom_labels(self) -> list[AtomLabel]:
         """
         Returns

MDANSE/Src/MDANSE/Framework/Configurators/FileWithAtomDataConfigurator.py

@@ -34,7 +34,7 @@ def configure(self, filepath: str) -> None:
             return
         try:
             self.parse()
-        except Exception:
+        except Exception as e:
             self.error_status = "File parsing error"
 
     @abstractmethod

MDANSE/Src/MDANSE/Framework/Configurators/HDFInputFileConfigurator.py

@@ -33,7 +33,7 @@ def __init__(
         self,
         name,
         variables=None,
-        wildcard="MDA analysis results (*.mda)|*.mda|HDF5 files (*.h5)|*.h5|All files|*",
+        wildcard="MDA analysis results (*.mda);;HDF5 files (*.h5);;All files (*)",
         **kwargs,
     ):
         """

MDANSE/Src/MDANSE/Framework/Configurators/InputFileConfigurator.py

@@ -30,7 +30,7 @@ class InputFileConfigurator(IConfigurator):
 
     _default = ""
 
-    def __init__(self, name, wildcard="All files|*", **kwargs):
+    def __init__(self, name, wildcard="All files (*)", **kwargs):
         """
         Initializes the configurator object.
 

MDANSE/Src/MDANSE/Framework/Configurators/MDMCTrajectoryConfigurator.py

@@ -28,7 +28,7 @@ class MDMCTrajectoryConfigurator(IConfigurator):
 
     _default = None
 
-    def __init__(self, name, wildcard="All files|*", **kwargs):
+    def __init__(self, name, wildcard="All files (*)", **kwargs):
         """
         Initializes the configurator object.
 

MDANSE/Src/MDANSE/Framework/Converters/CASTEP.py

@@ -44,7 +44,7 @@ class CASTEP(Converter):
     settings["castep_file"] = (
         "MDFileConfigurator",
         {
-            "wildcard": "MD files (*.md)|*.md|All files|*",
+            "wildcard": "MD files (*.md);;All files (*)",
             "default": "INPUT_FILENAME.md",
             "label": "Input MD file",
         },

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

@@ -111,15 +111,15 @@ class CP2K(Converter):
     settings["pos_file"] = (
         "XYZFileConfigurator",
         {
-            "wildcard": "XYZ files (*.xyz)|*.xyz|All files|*",
+            "wildcard": "XYZ files (*.xyz);;All files (*)",
             "default": "INPUT_FILENAME.xyz",
             "label": "Positions file (XYZ)",
         },
     )
     settings["vel_file"] = (
         "XYZFileConfigurator",
         {
-            "wildcard": "XYZ files (*.xyz)|*.xyz|All files|*",
+            "wildcard": "XYZ files (*.xyz);;All files (*)",
             "default": "INPUT_FILENAME.xyz",
             "optional": True,
             "label": "Velocity file (XYZ, optional)",
@@ -128,7 +128,7 @@ class CP2K(Converter):
     settings["cell_file"] = (
         "InputFileConfigurator",
         {
-            "wildcard": "Cell files (*.cell)|*.cell|All files|*",
+            "wildcard": "Cell files (*.cell);;All files (*)",
             "default": "INPUT_FILENAME.cell",
             "label": "CP2K unit cell file (.cell)",
         },

MDANSE/Src/MDANSE/Framework/Converters/DCD.py

@@ -281,15 +281,15 @@ class DCD(Converter):
     settings["pdb_file"] = (
         "InputFileConfigurator",
         {
-            "wildcard": "PDB files (*.pdb)|*.pdb|All files|*",
+            "wildcard": "PDB files (*.pdb);;All files (*)",
             "default": "INPUT_FILENAME.pdb",
             "label": "Input PDB file",
         },
     )
     settings["dcd_file"] = (
         "InputFileConfigurator",
         {
-            "wildcard": "DCD files (*.dcd)|*.dcd|All files|*",
+            "wildcard": "DCD files (*.dcd);;All files (*)",
             "default": "INPUT_FILENAME.dcd",
             "label": "Input DCD file",
         },

MDANSE/Src/MDANSE/Framework/Converters/DFTB.py

@@ -32,15 +32,15 @@ class DFTB(Forcite):
     settings["xtd_file"] = (
         "XTDFileConfigurator",
         {
-            "wildcard": "XTD files (*.xtd)|*.xtd|All files|*",
+            "wildcard": "XTD files (*.xtd);;All files (*)",
             "default": "INPUT_FILENAME.xtd",
             "label": "The XTD file",
         },
     )
     settings["trj_file"] = (
         "InputFileConfigurator",
         {
-            "wildcard": "TRJ files (*.trj)|*.trj|All files|*",
+            "wildcard": "TRJ files (*.trj);;All files (*)",
             "default": "INPUT_FILENAME.trj",
             "label": "The TRJ file",
         },

MDANSE/Src/MDANSE/Framework/Converters/DL_POLY.py

@@ -239,15 +239,15 @@ class DL_POLY(Converter):
     settings["field_file"] = (
         "FieldFileConfigurator",
         {
-            "wildcard": "FIELD files (FIELD*)|FIELD*|All files|*",
+            "wildcard": "FIELD files (FIELD*);;All files (*)",
             "default": "INPUT_FILENAME",
             "label": "Input FIELD file",
         },
     )
     settings["history_file"] = (
         "InputFileConfigurator",
         {
-            "wildcard": "HISTORY files (HISTORY*)|HISTORY*|All files|*",
+            "wildcard": "HISTORY files (HISTORY*);;All files (*)",
             "default": "INPUT_FILENAME",
             "label": "Input HISTORY file",
         },

MDANSE/Src/MDANSE/Framework/Converters/Discover.py

@@ -253,15 +253,15 @@ class Discover(Converter):
     settings["xtd_file"] = (
         "XTDFileConfigurator",
         {
-            "wildcard": "XTD files (*.xtd)|*.xtd|All files|*",
+            "wildcard": "XTD files (*.xtd);;All files (*)",
             "default": "INPUT_FILENAME.xtd",
             "label": "Input XTD file",
         },
     )
     settings["his_file"] = (
         "InputFileConfigurator",
         {
-            "wildcard": "HIS files (*.his)|*.his|All files|*",
+            "wildcard": "HIS files (*.his);;All files (*)",
             "default": "INPUT_FILENAME.his",
             "label": "Input HIS file",
         },

MDANSE/Src/MDANSE/Framework/Converters/Forcite.py

@@ -279,15 +279,15 @@ class Forcite(Converter):
     settings["xtd_file"] = (
         "XTDFileConfigurator",
         {
-            "wildcard": "XTD files (*.xtd)|*.xtd|All files|*",
+            "wildcard": "XTD files (*.xtd);;All files (*)",
             "default": "INPUT_FILENAME.xtd",
             "label": "Input XTD file",
         },
     )
     settings["trj_file"] = (
         "InputFileConfigurator",
         {
-            "wildcard": "TRJ files (*.trj)|*.trj|All files|*",
+            "wildcard": "TRJ files (*.trj);;All files (*)",
             "default": "INPUT_FILENAME.trj",
             "label": "Input TRJ file",
         },

MDANSE/Src/MDANSE/Framework/Converters/Gromacs.py

@@ -43,15 +43,15 @@ class Gromacs(Converter):
     settings["pdb_file"] = (
         "InputFileConfigurator",
         {
-            "wildcard": "PDB files (*.pdb)|*.pdb|All files|*",
+            "wildcard": "PDB files (*.pdb);;All files (*)",
             "default": "INPUT_FILENAME.pdb",
             "label": "Input PDB file",
         },
     )
     settings["xtc_file"] = (
         "InputFileConfigurator",
         {
-            "wildcard": "XTC files (*.xtc)|*.xtc|TRR files (*.trr)|*.trr|All files|*",
+            "wildcard": "XTC files (*.xtc);;TRR files (*.trr);;All files (*)",
             "default": "INPUT_FILENAME.xtc",
             "label": "xtc or trr file",
         },