From b07de15e5bbac4252d3d44582e5d21915024b560 Mon Sep 17 00:00:00 2001
From: doublylinkedlist <williamyxl@gmail.com>
Date: Sat, 9 Sep 2023 03:22:43 -0500
Subject: [PATCH] Update write_lammps_data.py

---
 .../cif2lammps/write_lammps_data.py           | 74 +++++++++----------
 1 file changed, 37 insertions(+), 37 deletions(-)

diff --git a/mofa/simulation/cif2lammps/write_lammps_data.py b/mofa/simulation/cif2lammps/write_lammps_data.py
index c536537c..592a1511 100644
--- a/mofa/simulation/cif2lammps/write_lammps_data.py
+++ b/mofa/simulation/cif2lammps/write_lammps_data.py
@@ -344,13 +344,13 @@ def lammps_inputs(args):
             total_charge += charge
             pos = [np.round(v, 8) for v in atom_data['cartesian_position']]
 
-            data.write('{:>5} {:<5} {:<5} {:8.5f} {:12.5f} {:12.5f} {:12.5f}   # {:>5}'.format(index, 
-                                                                                               atom_data['mol_flag'], 
-                                                                                               lammps_type, 
-                                                                                               charge, 
-                                                                                               pos[0], 
-                                                                                               pos[1], 
-                                                                                               pos[2], 
+            data.write('{:>5} {:<5} {:<5} {:8.5f} {:12.5f} {:12.5f} {:12.5f}   # {:>5}'.format(index,
+                                                                                               atom_data['mol_flag'],
+                                                                                               lammps_type,
+                                                                                               charge,
+                                                                                               pos[0],
+                                                                                               pos[1],
+                                                                                               pos[2],
                                                                                                cif_label))
             data.write('\n')
 
@@ -366,11 +366,11 @@ def lammps_inputs(args):
         for bond_type in FF.bond_data['all_bonds']:
             for bond in FF.bond_data['all_bonds'][bond_type]:
                 bond_index += 1
-                data.write('{:>5} {:<5} {:<6} {:<6}   # {:>6} {:>6}'.format(bond_index, 
-                                                                            bond_type, 
-                                                                            bond[0], 
-                                                                            bond[1], 
-                                                                            id2label[bond[0]], 
+                data.write('{:>5} {:<5} {:<6} {:<6}   # {:>6} {:>6}'.format(bond_index,
+                                                                            bond_type,
+                                                                            bond[0],
+                                                                            bond[1],
+                                                                            id2label[bond[0]],
                                                                             id2label[bond[1]]))
                 data.write('\n')
 
@@ -382,13 +382,13 @@ def lammps_inputs(args):
         for angle_type in FF.angle_data['all_angles']:
             for angle in FF.angle_data['all_angles'][angle_type]:
                 angle_index += 1
-                data.write('{:>5} {:<5} {:<6} {:<6} {:<6}   # {:>6} {:>6} {:>6}'.format(angle_index, 
-                                                                                        angle_type, 
-                                                                                        angle[0], 
-                                                                                        angle[1], 
-                                                                                        angle[2], 
-                                                                                        id2label[angle[0]], 
-                                                                                        id2label[angle[1]], 
+                data.write('{:>5} {:<5} {:<6} {:<6} {:<6}   # {:>6} {:>6} {:>6}'.format(angle_index,
+                                                                                        angle_type,
+                                                                                        angle[0],
+                                                                                        angle[1],
+                                                                                        angle[2],
+                                                                                        id2label[angle[0]],
+                                                                                        id2label[angle[1]],
                                                                                         id2label[angle[2]]))
                 data.write('\n')
 
@@ -402,15 +402,15 @@ def lammps_inputs(args):
             for dihedral_type in FF.dihedral_data['all_dihedrals']:
                 for dihedral in FF.dihedral_data['all_dihedrals'][dihedral_type]:
                     dihedral_index += 1
-                    data.write('{:>5} {:<5} {:<6} {:<6} {:<6} {:<6}   # {:>6} {:>6} {:>6} {:>6}'.format(dihedral_index, 
-                                                                                                        dihedral_type, 
-                                                                                                        dihedral[0], 
-                                                                                                        dihedral[1], 
-                                                                                                        dihedral[2], 
-                                                                                                        dihedral[3], 
-                                                                                                        id2label[dihedral[0]], 
-                                                                                                        id2label[dihedral[1]], 
-                                                                                                        id2label[dihedral[2]], 
+                    data.write('{:>5} {:<5} {:<6} {:<6} {:<6} {:<6}   # {:>6} {:>6} {:>6} {:>6}'.format(dihedral_index,
+                                                                                                        dihedral_type,
+                                                                                                        dihedral[0],
+                                                                                                        dihedral[1],
+                                                                                                        dihedral[2],
+                                                                                                        dihedral[3],
+                                                                                                        id2label[dihedral[0]],
+                                                                                                        id2label[dihedral[1]],
+                                                                                                        id2label[dihedral[2]],
                                                                                                         id2label[dihedral[3]]))
                     data.write('\n')
 
@@ -424,15 +424,15 @@ def lammps_inputs(args):
             for improper_type in FF.improper_data['all_impropers']:
                 for improper in FF.improper_data['all_impropers'][improper_type]:
                     improper_index += 1
-                    data.write('{:>5} {:<5} {:<6} {:<6} {:<6} {:<6}   # {:>6} {:>6} {:>6} {:>6}'.format(improper_index, 
-                                                                                                        improper_type, 
-                                                                                                        improper[0], 
-                                                                                                        improper[1], 
-                                                                                                        improper[2], 
-                                                                                                        improper[3], 
-                                                                                                        id2label[improper[0]], 
-                                                                                                        id2label[improper[1]], 
-                                                                                                        id2label[improper[2]], 
+                    data.write('{:>5} {:<5} {:<6} {:<6} {:<6} {:<6}   # {:>6} {:>6} {:>6} {:>6}'.format(improper_index,
+                                                                                                        improper_type,
+                                                                                                        improper[0],
+                                                                                                        improper[1],
+                                                                                                        improper[2],
+                                                                                                        improper[3],
+                                                                                                        id2label[improper[0]],
+                                                                                                        id2label[improper[1]],
+                                                                                                        id2label[improper[2]],
                                                                                                         id2label[improper[3]]))
                     data.write('\n')