LAMMPS DATA WRITER

[ksy141]

Hello, I'm trying to write a LAMMPS data file from a coordinate file. Consider a hydrogen gas,

cat > h2.gro << EOF
MDAnalysis BEST!!
 2
    1HYDR   HH1    1   3.000   3.000   3.000
    1HYDR   HH2    2   3.000   3.000   3.500
    6.00000   6.00000   6.00000
EOF

Now let's make a data file with MDAnalysis. In order to make a LAMMPS data file, the atom types should be changed to positive integers.

import MDAnalysis as mda
u = mda.Universe('h2.gro')
u.atoms.types = ['1', '1']
u.atoms.write('h2.data')

However, I received the error from the LAMMPS.py (~line 431).

attrs = [('bond', 'bonds'), ('angle', 'angles'), ('dihedral', 'dihedrals'), ('improper', 'impropers')]
for btype, attr_name in attrs:
    features[btype] = atoms.__getattribute__(attr_name)
    self.f.write('{:>12d}  {}\n'.format(len(features[btype]), attr_name))
    features[btype] = features[btype].atomgroup_intersection(atoms, strict=True)

I think try, except should be added like this?

for btype, attr_name in attrs:
    try:
        features[btype] = atoms.__getattribute__(attr_name)
        self.f.write('{:>12d}  {}\n'.format(len(features[btype]), attr_name))
        features[btype] = features[btype].atomgroup_intersection(atoms, strict=True)
    except:
        pass

After adding try, except the above example should work. Now let's add a bond between the first hydrogen atom (index: 0) and second hydrogen atom (index: 1)!

import MDAnalysis as mda
u = mda.Universe('h2.gro')
u.atoms.types = ['1', '1']
u.add_TopologyAttr('bonds', [[0, 1]])
u.atoms.write('h2.data')

I received the following error:
TypeError: LAMMPS DATAWriter: Trying to write bond, but bond type ('1', '1') is not numerical.

Trying to change the bond type like this is not allowed, with the error message saying AttributeError: can't set attribute

u.bonds[0].type = 1

Thanks! Anyone can help me how to set a bond properly so that MDAnalysis can understand?

MDAnalysis 1.0.1

[ksy141]

How about the following changes in LAMMPS.py (~ line 340)? I confirmed this works for bonds and angles for a simple water system. Commented lines are the lines included in the original code.

def _write_bonds(self, bonds):
    self.f.write('\n')
    self.f.write('{}\n'.format(btype_sections[bonds.btype]))
    self.f.write('\n')

    bt = {}; t=0
    for bond, i in zip(bonds, range(1, len(bonds)+1)):
        if bond.type not in bt.keys():
            t += 1
            bt[bond.type] = t
        self.f.write('{:d} {:d} '.format(i, bt[bond.type])+\
                ' '.join((bond.atoms.indices + 1).astype(str))+'\n')
    
#        try:
#            self.f.write('{:d} {:d} '.format(i, int(bond.type))+\
#                    ' '.join((bond.atoms.indices + 1).astype(str))+'\n')
#        except TypeError:
#            raise_from(TypeError('LAMMPS DATAWriter: Trying to write bond, '
#                            'but bond type {} is not '
#                            'numerical.'.format(bond.type)),
#                        None)

[1ut]

The codes you provided have been ​rewritten in develop branch like this commit. (0d951a2#diff-b36aa1d8c19a92c6f8918f35d8c0ea354fd051e64b40e789452551e7bc0792ba , PR #2759)

Also, I think some issues you provided have been solved in develop branch.

You may try a development version. The method to build it is here. (https://userguide.mdanalysis.org/stable/contributing_code.html#build-mdanalysis-develop)

[ksy141]

Thanks, closing the issue.