Merge pull request #358 from shirtsgroup/bugfix_May20

Bugfixes

intermol/gromacs/__init__.py

@@ -29,6 +29,7 @@
     'CMAP': ['dihedral','cmap'],
     'LJ (SR)': ['vdw total', 'vdw (SR)'],
     'LJ-14': ['vdw total','vdw-14'],
+    'LJ recip.': ['vdw total', 'vdw (LR)'],
     'Disper. corr.': ['vdw total', 'vdw (LR)'],
     'Coulomb (SR)': ['coulomb total','coulomb (SR)'],
     'Coulomb-14': ['coulomb total','coulomb-14'],

intermol/lammps/lammps_parser.py

@@ -412,6 +412,8 @@ def read_data(self, data_file):
                         self.parse_box(line.split(), 1)
                     elif ('zlo' in line) and ('zhi' in line):
                         self.parse_box(line.split(), 2)
+                    elif ('xy xz yz' in line):
+                        self.parse_box(line.split(), 'tilt')
                     # Other headers.
                     else:
                         keyword = line.strip()
@@ -608,12 +610,23 @@ def parse_box(self, line, dim):
             line (str): Current line in input file.
             dim (int): Dimension specified in line.
         """
-        fields = [float(field) for field in line[:2]]
-        box_length = fields[1] - fields[0]
-        if box_length > 0:
-            self.system.box_vector[dim, dim] = box_length * self.DIST
+        if dim == 'tilt':
+            fields = [(float(field) * self.DIST) for field in line[:3]]
+            dirs = line[3:]
+            for f,d in zip(fields,dirs):
+                if d == 'xy':
+                    self.system.box_vector[1,0] = f
+                elif d == 'xz':
+                    self.system.box_vector[2,0] = f
+                elif d == 'yz':
+                    self.system.box_vector[2,1] = f
         else:
-            raise LammpsError("Negative box length specified in data file.")
+            fields = [float(field) for field in line[:2]]
+            box_length = fields[1] - fields[0]
+            if box_length > 0:
+                self.system.box_vector[dim, dim] = box_length * self.DIST
+            else:
+                raise LammpsError("Negative box length specified in data file.")
 
     def parse_masses(self, data_lines):
         """Read masses from data file."""
@@ -1154,6 +1167,10 @@ def write(self, unit_set='real',nonbonded_style=None):
             f.write('{0:11.7f} {1:11.7f} zlo zhi\n'.format(
                     z_min, z_min + self.system.box_vector[2][2].value_in_unit(
                             self.DIST)))
+            f.write('{0:11.7f} {1:11.7f} {2:11.7f} xy xz yz\n'.format(
+                    self.system.box_vector[1][0].value_in_unit(self.DIST),
+                    self.system.box_vector[2][0].value_in_unit(self.DIST),
+                    self.system.box_vector[2][1].value_in_unit(self.DIST)))
 
             for mass in mass_list:
                 f.write(mass)

intermol/tests/lammps/unit_tests/box_vectors_vacuum/box_vectors_vacuum.input

@@ -0,0 +1,18 @@
+units real
+atom_style full
+
+dimension 3
+boundary p p p
+
+pair_style lj/cut/coul/cut 30.0 30.0
+pair_modify mix geometric
+
+bond_style hybrid harmonic morse
+angle_style harmonic
+special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.5
+
+read_data box_vectors_vacuum.lmp
+
+thermo_style custom ebond eangle edihed eimp epair evdwl ecoul elong etail pe
+
+run 0

intermol/tests/lammps/unit_tests/box_vectors_vacuum/box_vectors_vacuum.lmp

@@ -0,0 +1,97 @@
+topol
+
+9 atoms
+8 bonds
+13 angles
+0 dihedrals
+0 impropers
+
+4 atom types
+4 bond types
+6 angle types
+
+ 26.160000  46.266100 xlo xhi
+ 28.470000  48.576100 ylo yhi
+ 26.030000  46.136100 zlo zhi
+  0.0  -4.50000 0.0  xy xz yz
+
+Masses
+
+1  12.0110
+2   1.0080
+3  15.9994
+4   1.0080
+
+Pair Coeffs
+
+1   0.0660   3.5000
+2   0.0300   2.5000
+3   0.1700   3.1200
+4   0.0000   0.0000
+
+Bond Coeffs
+
+1   harmonic 340.00000000         1.09000000
+2   harmonic 553.00000000         0.94500000
+3   morse    320.00000000         1.41000000  1.2
+4   morse    268.00000000         1.52900000  1.3
+
+Angle Coeffs
+
+1        50.00000000       109.50000000
+2        37.50000000       110.70000000
+3        37.50000000       110.70000000
+4        33.00000000       107.80000000
+5        35.00000000       109.50000000
+6        55.00000000       108.50000000
+
+Atoms
+
+     1      1      1  2.0   27.110   29.460   28.030
+     2      1      2  -2.0  27.090   28.470   27.570
+     3      1      2  2.0   26.160   29.540   28.550
+     4      1      3  -2.0  28.040   29.570   29.070
+     5      1      4  2.0   28.830   29.460   28.570
+     6      1      1  -2.0  27.320   30.480   26.870
+     7      1      2  2.0   28.330   30.640   26.490
+     8      1      2  -2.0  27.000   31.450   27.230
+     9      1      2  2.0   26.630   30.350   26.030
+
+Velocities
+
+     1   0.0000   0.0000   0.0000
+     2   0.0000   0.0000   0.0000
+     3   0.0000   0.0000   0.0000
+     4   0.0000   0.0000   0.0000
+     5   0.0000   0.0000   0.0000
+     6   0.0000   0.0000   0.0000
+     7   0.0000   0.0000   0.0000
+     8   0.0000   0.0000   0.0000
+     9   0.0000   0.0000   0.0000
+
+Bonds
+
+     1      1      1      2
+     2      1      6      9
+     3      1      1      3
+     4      1      6      7
+     5      1      6      8
+     6      2      4      5
+     7      3      1      4
+     8      4      1      6
+
+Angles
+
+     1      1      4      1      6
+     2      2      3      1      6
+     3      3      1      6      9
+     4      4      8      6      9
+     5      4      7      6      9
+     6      5      2      1      4
+     7      5      3      1      4
+     8      3      1      6      7
+     9      4      7      6      8
+    10      2      2      1      6
+    11      6      1      4      5
+    12      4      2      1      3
+    13      3      1      6      8

intermol/tests/lammps/unit_tests/box_vectors_vacuum/log.lammps

@@ -0,0 +1,62 @@
+LAMMPS (1 Feb 2014)
+units real
+atom_style full
+
+dimension 3
+boundary p p p
+
+pair_style lj/cut/coul/cut 30.0 30.0
+pair_modify mix geometric
+
+bond_style hybrid harmonic morse
+angle_style harmonic
+special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.5
+
+read_data box_vectors.lmp
+  triclinic box = (26.16 28.47 26.03) to (46.2661 48.5761 46.1361) with tilt (0 -4.5 0)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  9 atoms
+  reading velocities ...
+  9 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  reading bonds ...
+  8 bonds
+  reading angles ...
+  13 angles
+  4 = max # of 1-2 neighbors
+  4 = max # of 1-3 neighbors
+  7 = max # of 1-4 neighbors
+  8 = max # of special neighbors
+
+thermo_style custom ebond eangle edihed eimp epair evdwl ecoul elong etail pe
+
+run 0
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:54)
+Memory usage per processor = 4.88161 Mbytes
+E_bond E_angle E_dihed E_impro E_pair E_vdwl E_coul E_long E_tail PotEng 
+   47.912249     4.808182            0            0     354.9457 -0.086795261     355.0325            0            0    407.66613 
+Loop time of 0 on 1 procs for 0 steps with 9 atoms
+
+Pair  time (%) = 0 (0)
+Bond  time (%) = 0 (0)
+Neigh time (%) = 0 (0)
+Comm  time (%) = 0 (0)
+Outpt time (%) = 0 (0)
+Other time (%) = 0 (0)
+
+Nlocal:    9 ave 9 max 9 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    567 ave 567 max 567 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    767 ave 767 max 767 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 767
+Ave neighs/atom = 85.2222
+Ave special neighs/atom = 7.33333
+Neighbor list builds = 0
+Dangerous builds = 0