RBVI · alphataubio · May 4, 2025 · May 4, 2025 · May 4, 2025 · May 4, 2025
diff --git a/src/bundles/map_data/bundle_info.xml b/src/bundles/map_data/bundle_info.xml
@@ -48,6 +48,7 @@
 		suffixes=".hed,.img" />
     <Provider name="Imaris map" nicknames="ims" category="Volume data" suffixes=".ims" />
     <Provider name="IMOD map" nicknames="imodmap" category="Volume data" suffixes=".rec" />
+    <Provider name="LAMMPS grid3d" nicknames="grid3d" category="Volume data" suffixes=".grid3d" />
     <Provider name="MacMolPlt grid" nicknames="macmolplt" category="Volume data" suffixes=".mmp" />
     <Provider name="MRC density map" nicknames="mrc" category="Volume data" suffixes=".mrc" />
     <Provider name="NetCDF map" nicknames="netcdfmap" category="Volume data"

diff --git a/src/bundles/map_data/src/Makefile b/src/bundles/map_data/src/Makefile
@@ -13,7 +13,7 @@ TOP = ../../../..
 include $(TOP)/mk/config.make
 
 SUBDIRS	= amira apbs brix ccp4 cmap delphi deltavision dock dsn6 emanhdf gaussian \
-	  gopenmol hdf imagestack imagic imod ims macmolplt mrc priism profec \
+	  gopenmol hdf imagestack imagic imod ims lammps macmolplt mrc priism profec \
 	  pif situs spider tom_em uhbd xplor
 
 PKG_DIR = $(PYSITEDIR)/chimerax/map_data

diff --git a/src/bundles/map_data/src/fileformats.py b/src/bundles/map_data/src/fileformats.py
@@ -39,9 +39,12 @@ def __init__(self, description, name, prefixes, suffixes, *,
     self.allow_directory = allow_directory
     self.check_path = check_path
 
+    print(f"*** name {name} suffixes {suffixes}")
+
   @property
   def open_func(self):
     module_name = self.name
+    print(f"*** module_name {module_name}")
     module = __import__(module_name, globals(), level = 1)
     return module.open
 
@@ -90,7 +93,8 @@ def save_func(self):
   MapFileFormat('SPIDER volume data', 'spider', ['spider'], ['spi','vol']),
   MapFileFormat('TOM toolbox EM density map', 'tom_em', ['tom_em'], ['em']),
   MapFileFormat('UHBD grid, binary', 'uhbd', ['uhbd'], ['grd']),
-  ]
+  MapFileFormat('LAMMPS grid3d', 'lammps', ['lammps'], ['grid3d']),
+]
 
 # -----------------------------------------------------------------------------
 # The electrostatics file types are opened using a surface colormapping tool
@@ -146,6 +150,8 @@ def suffix_warning(paths):
 #
 def open_file(path, file_type = None, **kw):
 
+  print("*** open_file()")
+
   if file_type is None:
     p = path if isinstance(path, str) else path[0]
     file_type = file_type_from_suffix(p)
@@ -181,7 +187,9 @@ def open_file(path, file_type = None, **kw):
 # -----------------------------------------------------------------------------
 #
 def file_type_from_suffix(path):
-
+
+  print("*** file_type_from_suffix()")
+
   for ff in file_formats:
     for suffix in ff.suffixes:
       if has_suffix(path, suffix):
@@ -192,6 +200,8 @@ def file_type_from_suffix(path):
 #
 def file_type_from_colon_specifier(path):
 
+  print("*** file_type_from_colon_specifier()")
+
   try:
     colon_position = path.rindex(':')
   except ValueError:
@@ -209,6 +219,9 @@ def file_type_from_colon_specifier(path):
 # -----------------------------------------------------------------------------
 #
 def file_format_by_name(name):
+
+  print("*** file_format_by_name()")
+
   for ff in file_formats:
     if ff.name == name or name in ff.suffixes or name in ff.prefixes:
       return ff

diff --git a/src/bundles/map_data/src/lammps/Makefile b/src/bundles/map_data/src/lammps/Makefile
@@ -0,0 +1,26 @@
+# === UCSF ChimeraX Copyright ===
+# Copyright 2016 Regents of the University of California.
+# All rights reserved.  This software provided pursuant to a
+# license agreement containing restrictions on its disclosure,
+# duplication and use.  For details see:
+# https://www.rbvi.ucsf.edu/chimerax/docs/licensing.html
+# This notice must be embedded in or attached to all copies,
+# including partial copies, of the software or any revisions
+# or derivations thereof.
+# === UCSF ChimeraX Copyright ===
+
+TOP = ../../../../..
+include $(TOP)/mk/config.make
+
+PKG_DIR = $(PYSITEDIR)/chimerax/map_data/lammps
+
+PYSRCS = __init__.py lammps_grid.py lammps_format.py
+
+all: $(PYOBJS)
+
+install: all
+	-mkdir -p $(PKG_DIR)
+	$(RSYNC) $(PYSRCS) $(PKG_DIR)
+
+clean:
+	rm -rf __pycache__
diff --git a/src/bundles/map_data/src/lammps/__init__.py b/src/bundles/map_data/src/lammps/__init__.py
@@ -0,0 +1,24 @@
+# === UCSF ChimeraX Copyright ===
+# Copyright 2016 Regents of the University of California.
+# All rights reserved.  This software provided pursuant to a
+# license agreement containing restrictions on its disclosure,
+# duplication and use.  For details see:
+# https://www.rbvi.ucsf.edu/chimerax/docs/licensing.html
+# This notice must be embedded in or attached to all copies,
+# including partial copies, of the software or any revisions
+# or derivations thereof.
+# === UCSF ChimeraX Copyright ===
+
+# -----------------------------------------------------------------------------
+# LAMMPS grid3d dump file reader.
+#
+
+print("*** ok 1a")
+
+def open(path):
+    from .lammps_grid import LammpsGrid
+    print("*** ok 1b")
+    return [LammpsGrid(path)]
+
+
+# open /Users/mitch/Dropbox/github/hmx/spice/nitrite/nitrite.grid3d
diff --git a/src/bundles/map_data/src/lammps/lammps_format.py b/src/bundles/map_data/src/lammps/lammps_format.py
@@ -0,0 +1,207 @@
+# === UCSF ChimeraX Copyright ===
+# Copyright 2016 Regents of the University of California.
+# All rights reserved.  This software provided pursuant to a
+# license agreement containing restrictions on its disclosure,
+# duplication and use.  For details see:
+# https://www.rbvi.ucsf.edu/chimerax/docs/licensing.html
+# This notice must be embedded in or attached to all copies,
+# including partial copies, of the software or any revisions
+# or derivations thereof.
+# === UCSF ChimeraX Copyright ===
+
+# -----------------------------------------------------------------------------
+# Read LAMMPS grid3d format map data.
+#
+import os
+import numpy
+
+class Lammps_Grid_Data:
+    """
+    Parses LAMMPS grid3d format files produced by the 'dump grid' command.
+    """
+    def __init__(self, path):
+        self.path = path
+        self.name = os.path.basename(path)
+
+        # Parse file to get grid metadata
+        if path.endswith('.gz'):
+            import gzip
+            f = gzip.open(path, 'rt')
+        else:
+            f = open(path, 'r')
+
+        try:
+            self.parse_header(f)
+        finally:
+            f.close()
+
+    def parse_header(self, file):
+        """Parse the LAMMPS grid3d file and extract metadata."""
+        # LAMMPS grid data variables
+        self.timesteps = []
+        self.matrix_size = None  # (nx, ny, nz)
+        self.origin = None       # (x0, y0, z0)
+        self.step = None         # (dx, dy, dz)
+        self.columns = None      # List of data column names
+        self.data_sections = []  # List of (timestep, start_pos, num_entries)
+
+        # Read through file to find all sections
+        lines = file.readlines()
+        line_index = 0
+
+        while line_index < len(lines):
+            line = lines[line_index].strip()
+
+            # Parse ITEM: TIMESTEP
+            if line.startswith("ITEM: TIMESTEP"):
+                line_index += 1
+                timestep = int(lines[line_index].strip())
+                self.timesteps.append(timestep)
+
+            # Parse ITEM: GRID SIZE
+            elif line.startswith("ITEM: GRID SIZE"):
+                line_index += 1
+                parts = lines[line_index].strip().split()
+                if len(parts) >= 3:
+                    # LAMMPS grid dimensions are (nx, ny, nz)
+                    self.matrix_size = (int(parts[0]), int(parts[1]), int(parts[2]))
+
+            # Parse ITEM: GRID ORIGIN
+            elif line.startswith("ITEM: GRID ORIGIN"):
+                line_index += 1
+                parts = lines[line_index].strip().split()
+                if len(parts) >= 3:
+                    self.origin = (float(parts[0]), float(parts[1]), float(parts[2]))
+
+            # Parse ITEM: GRID SPACING
+            elif line.startswith("ITEM: GRID SPACING"):
+                line_index += 1
+                parts = lines[line_index].strip().split()
+                if len(parts) >= 3:
+                    self.step = (float(parts[0]), float(parts[1]), float(parts[2]))
+
+            # Parse ITEM: GRID CELLS
+            elif line.startswith("ITEM: GRID CELLS"):
+                header = line.split()
+                # Skip "ITEM: GRID CELLS" and get column names
+                self.columns = header[3:]
+
+                if self.matrix_size is None:
+                    raise ValueError("Grid size not defined before GRID CELLS section")
+
+                # Record the position in the file for later data reading
+                start_pos = line_index + 1
+
+                # Calculate expected number of data entries
+                nx, ny, nz = self.matrix_size
+                num_entries = nx * ny * nz
+
+                # Record data section info
+                current_timestep = self.timesteps[-1] if self.timesteps else 0
+                self.data_sections.append((current_timestep, start_pos, num_entries))
+
+                # Skip the data section - we'll read it on demand
+                line_index += num_entries
+                continue
+
+            line_index += 1
+
+        # Use first column for the initial grid
+        if len(self.columns) > 0:
+            self.current_column = self.columns[0]
+        else:
+            raise ValueError("No grid data columns found")
+
+        # Set element type
+        from numpy import float32
+        self.element_type = float32
+
+        # Validate that we have all required metadata
+        if self.matrix_size is None:
+            raise ValueError("Grid size not found in file")
+        if self.origin is None:
+            raise ValueError("Grid origin not found in file")
+        if self.step is None:
+            raise ValueError("Grid spacing not found in file")
+        if not self.data_sections:
+            raise ValueError("No grid data sections found in file")
+
+    def read_matrix(self, ijk_origin, ijk_size, ijk_step, progress):
+        """
+        Read and return the specified submatrix from the file.
+        For LAMMPS grid3d format, we need to read and parse the entire grid.
+        """
+        # Currently just read the first data section and first column
+        timestep, start_pos, num_entries = self.data_sections[0]
+        column_idx = self.columns.index(self.current_column)
+
+        # Read the whole file again
+        if self.path.endswith('.gz'):
+            import gzip
+            f = gzip.open(self.path, 'rt')
+        else:
+            f = open(self.path, 'r')
+
+        try:
+            lines = f.readlines()
+
+            # Create numpy array for the data
+            nx, ny, nz = self.matrix_size
+            data = numpy.zeros((nz, ny, nx), dtype=self.element_type)
+
+            # Read the data section
+            for i in range(num_entries):
+                if progress and i % 1000 == 0:
+                    progress.percent = 100.0 * i / num_entries
+
+                line_idx = start_pos + i
+                if line_idx >= len(lines):
+                    break
+
+                line = lines[line_idx].strip()
+                parts = line.split()
+
+                # LAMMPS format: ix iy iz value1 value2 ...
+                # We expect at least 3 + len(columns) values
+                if len(parts) < 3 + len(self.columns):
+                    continue
+
+                ix = int(parts[0])
+                iy = int(parts[1])
+                iz = int(parts[2])
+
+                # Get the value for the current column
+                value = float(parts[3 + column_idx])
+
+                # Store in data array (in ZYX index order)
+                if 0 <= ix < nx and 0 <= iy < ny and 0 <= iz < nz:
+                    data[iz, iy, ix] = value
+
+            # Extract the requested submatrix
+            submatrix = self._submatrix(data, ijk_origin, ijk_size, ijk_step)
+            return submatrix
+
+        finally:
+            f.close()
+
+    def _submatrix(self, data, ijk_origin, ijk_size, ijk_step):
+        """Extract a submatrix from the data array."""
+        ox, oy, oz = ijk_origin
+        sx, sy, sz = ijk_size
+        stx, sty, stz = ijk_step
+
+        # Adjust for our ZYX index order
+        i0, i1, i2 = oz, oy, ox
+        s0, s1, s2 = sz, sy, sx
+        st0, st1, st2 = stz, sty, stx
+
+        # Extract the submatrix
+        if st0 == 1 and st1 == 1 and st2 == 1:
+            submatrix = data[i0:i0+s0, i1:i1+s1, i2:i2+s2].copy()
+        else:
+            submatrix = data[
+                i0:i0+s0*st0:st0,
+                i1:i1+s1*st1:st1,
+                i2:i2+s2*st2:st2].copy()
+
+        return submatrix
diff --git a/src/bundles/map_data/src/lammps/lammps_grid.py b/src/bundles/map_data/src/lammps/lammps_grid.py
@@ -0,0 +1,52 @@
+# === UCSF ChimeraX Copyright ===
+# Copyright 2016 Regents of the University of California.
+# All rights reserved.  This software provided pursuant to a
+# license agreement containing restrictions on its disclosure,
+# duplication and use.  For details see:
+# https://www.rbvi.ucsf.edu/chimerax/docs/licensing.html
+# This notice must be embedded in or attached to all copies,
+# including partial copies, of the software or any revisions
+# or derivations thereof.
+# === UCSF ChimeraX Copyright ===
+
+# === UCSF ChimeraX Copyright ===
+# Copyright 2016 Regents of the University of California.
+# All rights reserved.  This software provided pursuant to a
+# license agreement containing restrictions on its disclosure,
+# duplication and use.  For details see:
+# https://www.rbvi.ucsf.edu/chimerax/docs/licensing.html
+# This notice must be embedded in or attached to all copies,
+# including partial copies, of the software or any revisions
+# or derivations thereof.
+# === UCSF ChimeraX Copyright ===
+
+# -----------------------------------------------------------------------------
+# Wrap LAMMPS grid3d data as grid data for displaying as surfaces, meshes, and volumes.
+#
+from .. import GridData
+
+# -----------------------------------------------------------------------------
+#
+class LammpsGrid(GridData):
+    """
+    Reads LAMMPS grid3d format files produced by the 'dump grid' command in LAMMPS.
+    """
+    def __init__(self, path):
+
+        print("*** ok 2")
+
+
+        from . import lammps_format
+        d = lammps_format.Lammps_Grid_Data(path)
+
+        self.lammps_data = d
+
+        GridData.__init__(self, d.matrix_size, d.element_type, 
+                         origin=d.origin, step=d.step,
+                         path=path, file_type='grid3d',
+                         name=d.name)
+
+    # ---------------------------------------------------------------------------
+    #
+    def read_matrix(self, ijk_origin, ijk_size, ijk_step, progress):
+        return self.lammps_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)