Support of all lammps dump coordinate style

dpdata/lammps/dump.py

@@ -51,45 +51,38 @@ def get_natoms_vec(lines) :
     assert (sum(natoms_vec) == get_natoms(lines))
     return natoms_vec
 
-def get_posi(lines) :
+def get_coordtype_and_scalefactor(keys):
+    # 4 types in total,with different scaling factor
+    key_pc=['x','y','z'] # plain cartesian, sf = 1
+    key_uc=['xu','yu','zu'] # unwraped cartesian, sf = 1
+    key_s=['xs','ys','zs'] # scaled by lattice parameter, sf = lattice parameter
+    key_su = ['xsu','ysu','zsu'] #scaled and unfolded,sf = lattice parameter
+    lmp_coor_type = [key_pc,key_uc,key_s,key_su]
+    sf = [0,0,1,1]
+    for k in range(4):
+        if all(i in keys for i in lmp_coor_type[k]):
+            return lmp_coor_type[k],sf[k]
+
+def safe_get_posi(lines,cell,orig=np.zeros(3)) :
     blk, head = _get_block(lines, 'ATOMS')
     keys = head.split()
+    coord_tp_and_sf = get_coordtype_and_scalefactor(keys)
+    assert coord_tp_and_sf is not None, 'Dump file does not contain atomic coordinates!'
+    coordtype, sf = coord_tp_and_sf
     id_idx = keys.index('id') - 2
-    xidx = keys.index('x') - 2
-    yidx = keys.index('y') - 2
-    zidx = keys.index('z') - 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[id_idx]), float(words[xidx]), float(words[yidx]), float(words[zidx])])
     posis.sort()
-    posis = np.array(posis)     
-    return posis[:,1:4]
-
-def get_posi_frac(lines) :
-    blk, head = _get_block(lines, 'ATOMS')
-    keys = head.split()
-    id_idx = keys.index('id') - 2
-    xidx = keys.index('xs') - 2
-    yidx = keys.index('ys') - 2
-    zidx = keys.index('zs') - 2
-    sel = (xidx, yidx, zidx)
-    posis = []
-    for ii in blk :
-        words = ii.split()
-        posis.append([float(words[id_idx]), float(words[xidx]), float(words[yidx]), float(words[zidx])])
-    posis.sort()
-    posis = np.array(posis)     
-    return posis[:,1:4]
-
-def safe_get_posi(lines, cell, orig = np.zeros(3)):
-    try:
-        posis = get_posi(lines) - orig
-    except ValueError:
-        fposis = get_posi_frac(lines)
-        posis = fposis @ cell
-    return posis
+    posis = np.array(posis)[:,1:4]
+    if not sf:
+        posis = (posis-orig)@np.linalg.inv(cell)# Convert to scaled coordinates for unscaled coordinates
+    return (posis%1)@cell # Convert scaled coordinates back to Cartesien coordinates 
 
 def get_dumpbox(lines) :
     blk, h = _get_block(lines, 'BOX BOUNDS')
@@ -211,16 +204,16 @@ def split_traj(dump_lines) :
     # # print(get_natomtypes(lines))
     # # print(get_natoms_vec(lines))
     # posi = get_posi(lines)
-    # dbox, tilt = get_dumpbox(lines)
-    # orig, box = dumpbox2box(dbox, tilt)
     # dbox1, tilt1 = box2dumpbox(orig, box)
     # print(dbox - dbox1)
     # print(tilt - tilt1)
     # print(orig)
     # print(box)
     # np.savetxt('tmp.out', posi - orig, fmt='%.6f')
     # print(system_data(lines))
-
-    lines = load_file('conf.5.dump', begin = 0, step = 2)
-    with open('tmp.out', 'w') as fp:
-        fp.write('\n'.join(lines))
+    lines = load_file('conf_unfold.dump', begin = 0, step = 1)
+    al = split_traj(lines)
+    s = system_data(lines,['O','H'])
+    #l = np.linalg.norm(s['cells'][1],axis=1)
+    #p = s['coords'][0] + l
+    #np.savetxt('p',p,fmt='%1.10f')

tests/poscars/conf_s_su.dump

@@ -0,0 +1,22 @@
+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 xs ys zs
+1 1 0.0 0.0 0.0
+2 2 0.2472745002 0.2527254533 0.2477701458
+ITEM: TIMESTEP
+1
+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 xsu ysu zsu
+1 1 0.0 0.0 0.0
+2 2 1.2472745002 1.2527254533 1.2477701458

tests/poscars/conf_unfold.dump

@@ -0,0 +1,22 @@
+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 xu yu zu
+1 1 5.073986099999999944e+00 2.791615499999999805e+00 2.225403299999999973e+00  
+2 2 6.336171700000000406e+00 3.493418300000000087e+00 2.776791800099999818e+00
+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
+1.0 3.2254033 0.7485898
+ITEM: ATOMS id type xu yu zu
+1 1 5.073986099999999944e+00 2.791615499999999805e+00 3.225403299999999973e+00  
+2 2 6.336171700000000406e+00 3.493418300000000087e+00 3.776791800099999818e+00

tests/poscars/test_lammps_dump_s_su.py

@@ -0,0 +1,26 @@
+import os
+import numpy as np
+import unittest
+from context import dpdata
+from poscars.poscar_ref_oh import TestPOSCARoh        
+
+class TestDump(unittest.TestCase, TestPOSCARoh):
+
+    def setUp(self): 
+        self.system = dpdata.System(os.path.join('poscars', 'conf_s_su.dump'), 
+                                    type_map = ['O', 'H'])
+
+class TestDump2(unittest.TestCase, TestPOSCARoh):
+
+    def setUp(self): 
+        self.tmp_system = dpdata.System(os.path.join('poscars', 'conf_s_su.dump'), 
+                                        type_map = ['O', 'H'])
+        self.system = self.tmp_system.sub_system([1])
+
+    def test_nframes (self) :
+        self.assertEqual(self.tmp_system.get_nframes(), 2)
+
+
+if __name__ == '__main__':
+    unittest.main()
+

tests/test_lammps_dump_unfold.py

@@ -0,0 +1,26 @@
+import os
+import numpy as np
+import unittest
+from context import dpdata
+from poscars.poscar_ref_oh import TestPOSCARoh        
+
+class TestDump(unittest.TestCase, TestPOSCARoh):
+
+    def setUp(self): 
+        self.system = dpdata.System(os.path.join('poscars', 'conf_unfold.dump'), 
+                                    type_map = ['O', 'H'])
+
+class TestDump2(unittest.TestCase, TestPOSCARoh):
+
+    def setUp(self): 
+        self.tmp_system = dpdata.System(os.path.join('poscars', 'conf_unfold.dump'), 
+                                        type_map = ['O', 'H'])
+        self.system = self.tmp_system.sub_system([1])
+
+    def test_nframes (self) :
+        self.assertEqual(self.tmp_system.get_nframes(), 2)
+
+
+if __name__ == '__main__':
+    unittest.main()
+