Merge devel into master (#389)

Author: amcadmus

README.md

@@ -1,5 +1,5 @@
 **dpdata** is a python package for manipulating data formats of software in computational science, including DeePMD-kit, VASP, LAMMPS, GROMACS, Gaussian.
-dpdata only works with python 3.x.
+dpdata only works with python 3.7 or above.
 
 
 # Installation

docs/index.rst

@@ -10,6 +10,7 @@ Welcome to dpdata's documentation!
    :maxdepth: 2
    :caption: Contents:
 
+   Overview <self>
    cli
    formats
    api/api

dpdata/lammps/dump.py

@@ -31,11 +31,9 @@ def get_atype(lines, type_idx_zero = False) :
     tidx = keys.index('type') - 2
     atype = []
     for ii in blk :
-        atype.append([int(ii.split()[tidx]), int(ii.split()[id_idx])])
-    # sort with type id
+        atype.append([int(ii.split()[id_idx]), int(ii.split()[tidx])])
     atype.sort()
     atype = np.array(atype, dtype = int)    
-    atype = atype[:, ::-1]
     if type_idx_zero :
         return atype[:,1] - 1
     else :
@@ -78,17 +76,15 @@ def safe_get_posi(lines,cell,orig=np.zeros(3), unwrap=False) :
     assert coord_tp_and_sf is not None, 'Dump file does not contain atomic coordinates!'
     coordtype, sf, uw = coord_tp_and_sf
     id_idx = keys.index('id') - 2
-    tidx = keys.index('type') - 2
     xidx = keys.index(coordtype[0])-2
     yidx = keys.index(coordtype[1])-2
     zidx = keys.index(coordtype[2])-2
-    sel = (xidx, yidx, zidx)
     posis = []
     for ii in blk :
         words = ii.split()
-        posis.append([float(words[tidx]), float(words[id_idx]), float(words[xidx]), float(words[yidx]), float(words[zidx])])
+        posis.append([float(words[id_idx]), float(words[xidx]), float(words[yidx]), float(words[zidx])])
     posis.sort()
-    posis = np.array(posis)[:,2:5]
+    posis = np.array(posis)[:,1:4]
     if not sf:
         posis = (posis - orig) @ np.linalg.inv(cell)  # Convert to scaled coordinates for unscaled coordinates
     if uw and unwrap:
@@ -178,14 +174,16 @@ def system_data(lines, type_map = None, type_idx_zero = True, unwrap=False) :
     orig, cell = dumpbox2box(bounds, tilt)
     system['orig'] = np.array(orig) - np.array(orig)
     system['cells'] = [np.array(cell)]
-    natoms = sum(system['atom_numbs'])
     system['atom_types'] = get_atype(lines, type_idx_zero = type_idx_zero)
     system['coords'] = [safe_get_posi(lines, cell, np.array(orig), unwrap)]
     for ii in range(1, len(array_lines)) :
         bounds, tilt = get_dumpbox(array_lines[ii])
         orig, cell = dumpbox2box(bounds, tilt)
         system['cells'].append(cell)
-        system['coords'].append(safe_get_posi(array_lines[ii], cell, np.array(orig), unwrap))
+        atype = get_atype(array_lines[ii], type_idx_zero = type_idx_zero)
+        # map atom type; a[as[a][as[as[b]]]] = b[as[b][as^{-1}[b]]] = b[id]
+        idx = np.argsort(atype)[np.argsort(np.argsort(system['atom_types']))]
+        system['coords'].append(safe_get_posi(array_lines[ii], cell, np.array(orig), unwrap)[idx])
     system['cells'] = np.array(system['cells'])
     system['coords'] = np.array(system['coords'])
     return system

pyproject.toml

@@ -12,7 +12,11 @@ authors = [
 ]
 license = {file = "LICENSE"}
 classifiers = [
-    "Programming Language :: Python :: 3.6",
+    "Programming Language :: Python :: 3.7",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
     "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
 ]
 dependencies = [

tests/poscars/conf2.dump

@@ -0,0 +1,11 @@
+ITEM: TIMESTEP
+0
+ITEM: NUMBER OF ATOMS
+2
+ITEM: BOX BOUNDS xy xz yz pp pp pp
+0.0 5.0739861 1.2621856
+0.0 2.7916155 1.2874292
+0.0 2.2254033 0.7485898
+ITEM: ATOMS id type x y z
+1 2 0.0 0.0 0.0
+2 1 1.2621856 0.7018028 0.5513885

tests/test_lammps_dump_idx.py

@@ -0,0 +1,21 @@
+# The index should map to that in the dump file
+
+import os
+import numpy as np
+import unittest
+from context import dpdata
+
+class TestLmpDumpIdx(unittest.TestCase):
+    def setUp(self):
+        self.system = dpdata.System(os.path.join('poscars', 'conf2.dump'))
+    
+    def test_coords(self): 
+        np.testing.assert_allclose(self.system['coords'], np.array(
+            [[[0., 0., 0.],
+            [1.2621856, 0.7018028, 0.5513885]]]
+        ))
+    
+    def test_type(self):
+        np.testing.assert_allclose(self.system.get_atom_types(), np.array(
+            [1, 0], dtype=int,
+        ))

tests/test_lammps_read_from_trajs.py

@@ -10,6 +10,7 @@ def setUp(self):
             dpdata.System(os.path.join('lammps', 'traj_with_random_type_id.dump'), fmt = 'lammps/dump', type_map = ["Ta","Nb","W","Mo","V","Al"])
 
     def test_nframes (self) :
+        self.system.sort_atom_types()
         atype = self.system['atom_types'].tolist()
         self.assertTrue(atype == [1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5])