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amcadmus merged 2 commits into from
Apr 9, 2020
Merged

support gromacs gro file format #92

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9c3857d
support gromacs gro file format
Apr 9, 2020
14456cd
add missing data files
Apr 9, 2020
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59 changes: 30 additions & 29 deletions README.md
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Expand Up @@ -51,6 +51,34 @@ The labels provided in the `OUTCAR`, i.e. energies, forces and virials (if any),

The `System` or `LabeledSystem` can be constructed from the following file formats with the `format key` in the table passed to argument `fmt`:

| Software| format | multi frames | labeled | class | format key |
| ------- | :--- | :---: | :---: | :--- | :--- |
| vasp | poscar | False | False | System | 'vasp/poscar' |
| vasp | outcar | True | True | LabeledSystem | 'vasp/outcar' |
| vasp | xml | True | True | LabeledSystem | 'vasp/xml' |
| lammps | lmp | False | False | System | 'lammps/lmp' |
| lammps | dump | True | False | System | 'lammps/dump' |
| deepmd | raw | True | False | System | 'deepmd/raw' |
| deepmd | npy | True | False | System | 'deepmd/npy' |
| deepmd | raw | True | True | LabeledSystem | 'deepmd/raw' |
| deepmd | npy | True | True | LabeledSystem | 'deepmd/npy' |
| gaussian| log | False | True | LabeledSystem | 'gaussian/log'|
| gaussian| log | True | True | LabeledSystem | 'gaussian/md' |
| siesta | output | False | True | LabeledSystem | 'siesta/output'|
| siesta | aimd_output | True | True | LabeledSystem | 'siesta/aimd_output' |
| cp2k | output | False | True | LabeledSystem | 'cp2k/output' |
| cp2k | aimd_output | True | True | LabeledSystem | 'cp2k/aimd_output' |
| QE | log | False | True | LabeledSystem | 'qe/pw/scf' |
| QE | log | True | False | System | 'qe/cp/traj' |
| QE | log | True | True | LabeledSystem | 'qe/cp/traj' |
|quip/gap|xyz|True|True|MultiSystems|'quip/gap/xyz'|
| PWmat | atom.config | False | False | System | 'pwmat/atom.config' |
| PWmat | movement | True | True | LabeledSystem | 'pwmat/movement' |
| PWmat | OUT.MLMD | True | True | LabeledSystem | 'pwmat/out.mlmd' |
| Amber | multi | True | True | LabeledSystem | 'amber/md' |
| Gromacs | gro | False | False | System | 'gromacs/gro' |


The Class `dpdata.MultiSystems` can read data from a dir which may contains many files of different systems, or from single xyz file which contains different systems.

Use `dpdata.MultiSystems.from_dir` to read from a directory, `dpdata.MultiSystems` will walk in the directory
Expand Down Expand Up @@ -82,35 +110,8 @@ xyz_multi_systems.systems['B1C9'].to_deepmd_raw('./my_work_dir/B1C9_raw')

# dump all systems
xyz_multi_systems.to_deepmd_raw('./my_deepmd_data/')


```

| Software| format | multi frames | labeled | class | format key |
| ------- | :--- | :---: | :---: | :--- | :--- |
| vasp | poscar | False | False | System | 'vasp/poscar' |
| vasp | outcar | True | True | LabeledSystem | 'vasp/outcar' |
| vasp | xml | True | True | LabeledSystem | 'vasp/xml' |
| lammps | lmp | False | False | System | 'lammps/lmp' |
| lammps | dump | True | False | System | 'lammps/dump' |
| deepmd | raw | True | False | System | 'deepmd/raw' |
| deepmd | npy | True | False | System | 'deepmd/npy' |
| deepmd | raw | True | True | LabeledSystem | 'deepmd/raw' |
| deepmd | npy | True | True | LabeledSystem | 'deepmd/npy' |
| gaussian| log | False | True | LabeledSystem | 'gaussian/log'|
| gaussian| log | True | True | LabeledSystem | 'gaussian/md' |
| siesta | output | False | True | LabeledSystem | 'siesta/output'|
| siesta | aimd_output | True | True | LabeledSystem | 'siesta/aimd_output' |
| cp2k | output | False | True | LabeledSystem | 'cp2k/output' |
| cp2k | aimd_output | True | True | LabeledSystem | 'cp2k/aimd_output' |
| QE | log | False | True | LabeledSystem | 'qe/pw/scf' |
| QE | log | True | False | System | 'qe/cp/traj' |
| QE | log | True | True | LabeledSystem | 'qe/cp/traj' |
|quip/gap|xyz|True|True|MultiSystems|'quip/gap/xyz'|
| PWmat | atom.config | False | False | System | 'pwmat/atom.config' |
| PWmat | movement | True | True | LabeledSystem | 'pwmat/movement' |
| PWmat | OUT.MLMD | True | True | LabeledSystem | 'pwmat/out.mlmd' |
| Amber | multi | True | True | LabeledSystem | 'amber/md' |
## Access data
These properties stored in `System` and `LabeledSystem` can be accessed by operator `[]` with the key of the property supplied, for example
```python
Expand All @@ -130,7 +131,6 @@ Available properties are (nframe: number of frames in the system, natoms: total
| 'virials' | np.ndarray | nframes x 3 x 3 | True | The virial tensor of each frame



## Dump data
The data stored in `System` or `LabeledSystem` can be dumped in 'lammps/lmp' or 'vasp/poscar' format, for example:
```python
Expand All @@ -142,7 +142,6 @@ d_outcar.to('vasp/poscar', 'POSCAR', frame_idx=-1)
```
The last frames of `d_outcar` will be dumped to 'POSCAR'.


The data stored in `LabeledSystem` can be dumped to deepmd-kit raw format, for example
```python
d_outcar.to('deepmd/raw', 'dpmd_raw')
Expand All @@ -157,13 +156,15 @@ dpdata.LabeledSystem('OUTCAR').sub_system([0,-1]).to('deepmd/raw', 'dpmd_raw')
```
by which only the first and last frames are dumped to `dpmd_raw`.


## replicate
dpdata will create a super cell of the current atom configuration.
```python
dpdata.System('./POSCAR').replicate((1,2,3,) )
```
tuple(1,2,3) means don't copy atom configuration in x direction, make 2 copys in y direction, make 3 copys in z direction.


## perturb
By the following example, each frame of the original system (`dpdata.System('./POSCAR')`) is perturbed to generate three new frames. For each frame, the cell is perturbed by 5% and the atom positions are perturbed by 0.6 Angstrom. `atom_pert_style` indicates that the perturbation to the atom positions is subject to normal distribution. Other available options to `atom_pert_style` are`uniform` (uniform in a ball), and `const` (uniform on a sphere).
```python
Expand Down
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55 changes: 55 additions & 0 deletions dpdata/gromacs/gro.py
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@@ -0,0 +1,55 @@
#!/usr/bin/env python3

import numpy as np

nm2ang = 10.

def _get_line(line):
atom_name = line[10:15].split()[0]
atom_idx = int(line[15:20].split()[0])
posis = [float(line[ii:ii+8]) for ii in range(20,44,8)]
posis = np.array(posis) * nm2ang
return atom_name, atom_idx, posis

def _get_cell(line):
cell = np.zeros([3,3])
lengths = [float(ii) for ii in line.split()]
if len(lengths) >= 3:
for dd in range(3):
cell[dd][dd] = lengths[dd]
else:
raise RuntimeError('wrong box format: ', line)
if len(lengths) == 9:
cell[0][1] = lengths[3]
cell[0][2] = lengths[4]
cell[1][0] = lengths[5]
cell[1][2] = lengths[6]
cell[2][0] = lengths[7]
cell[2][1] = lengths[8]
cell = cell * nm2ang
return cell

def file_to_system_data(fname):
names = []
idxs = []
posis = []
with open(fname) as fp:
fp.readline()
natoms = int(fp.readline())
for ii in range(natoms):
n, i, p = _get_line(fp.readline())
names.append(n)
idxs.append(i)
posis.append(p)
cell = _get_cell(fp.readline())
posis = np.array(posis)
system = {}
system['orig'] = np.array([0, 0, 0])
system['atom_names'] = list(set(names))
system['atom_names'].sort()
system['atom_numbs'] = [names.count(ii) for ii in system['atom_names']]
system['atom_types'] = [system['atom_names'].index(ii) for ii in names]
system['atom_types'] = np.array(system['atom_types'], dtype = int)
system['coords'] = np.array([posis])
system['cells'] = np.array([cell])
return system
14 changes: 14 additions & 0 deletions dpdata/system.py
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Expand Up @@ -22,6 +22,7 @@
import dpdata.pwmat.movement
import dpdata.pwmat.atomconfig
import dpdata.fhi_aims.output
import dpdata.gromacs.gro
from copy import deepcopy
from monty.json import MSONable
from monty.serialization import loadfn,dumpfn
Expand Down Expand Up @@ -607,6 +608,19 @@ def from_deepmd_raw(self, folder, type_map = None) :
if tmp_data is not None :
self.data = tmp_data

@register_from_funcs.register_funcs("gro")
@register_from_funcs.register_funcs("gromacs/gro")
def from_gromacs_gro(self, file_name) :
"""
Load gromacs .gro file

Parameters
----------
file_name : str
The input file name
"""
self.data = dpdata.gromacs.gro.file_to_system_data(file_name)

@register_to_funcs.register_funcs("deepmd/npy")
def to_deepmd_npy(self, folder, set_size = 5000, prec=np.float32) :
"""
Expand Down
12 changes: 12 additions & 0 deletions tests/gromacs/1h.gro
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9
1SOL O 1 0.135 0.183 0.341
1SOL H 2 0.177 0.149 0.262
1SOL H 3 0.046 0.149 0.339
2SOL O 4 0.520 0.447 0.111
2SOL H 5 0.567 0.481 0.035
2SOL H 6 0.568 0.481 0.186
3SOL O 7 0.651 0.539 0.335
3SOL H 8 0.653 0.634 0.336
3SOL H 9 0.743 0.512 0.336
0.7822838765564372 0.7353572647182051 0.9036518515423753
12 changes: 12 additions & 0 deletions tests/gromacs/1h.tri.gro
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9
1SOL O 1 0.135 0.183 0.341
1SOL H 2 0.177 0.149 0.262
1SOL H 3 0.046 0.149 0.339
2SOL O 4 0.520 0.447 0.111
2SOL H 5 0.567 0.481 0.035
2SOL H 6 0.568 0.481 0.186
3SOL O 7 0.651 0.539 0.335
3SOL H 8 0.653 0.634 0.336
3SOL H 9 0.743 0.512 0.336
0.7822838765564372 0.7353572647182051 0.9036518515423753 0.0 0.1 0.2 0.3 0.4 0.5
46 changes: 46 additions & 0 deletions tests/test_gromacs_gro.py
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import os
import numpy as np
import unittest
from context import dpdata

class TestGromacsGro(unittest.TestCase):
def test_read_file(self):
system = dpdata.System('gromacs/1h.gro')
self.assertEqual(system['atom_names'], ['H', 'O'])
self.assertEqual(system['atom_numbs'], [6, 3])
for cc,ii in enumerate([1, 0, 0, 1, 0, 0, 1, 0, 0]):
self.assertEqual(system['atom_types'][cc], ii)
self.assertEqual(len(system['cells']), 1)
self.assertEqual(len(system['coords']), 1)
for ii in range(3):
for jj in range(3):
if ii != jj:
self.assertAlmostEqual(system['cells'][0][ii][jj], 0)
self.assertAlmostEqual(system['cells'][0][0][0], 7.822838765564372)
self.assertAlmostEqual(system['cells'][0][1][1], 7.353572647182051)
self.assertAlmostEqual(system['cells'][0][2][2], 9.036518515423753)
self.assertAlmostEqual(system['coords'][0][8][0], 7.43)
self.assertAlmostEqual(system['coords'][0][8][1], 5.12)
self.assertAlmostEqual(system['coords'][0][8][2], 3.36)

def test_read_file_tri(self):
system = dpdata.System('gromacs/1h.tri.gro')
self.assertEqual(system['atom_names'], ['H', 'O'])
self.assertEqual(system['atom_numbs'], [6, 3])
for cc,ii in enumerate([1, 0, 0, 1, 0, 0, 1, 0, 0]):
self.assertEqual(system['atom_types'][cc], ii)
self.assertEqual(len(system['cells']), 1)
self.assertEqual(len(system['coords']), 1)
count = 0
for ii in range(3):
for jj in range(3):
if ii != jj:
self.assertAlmostEqual(system['cells'][0][ii][jj], count)
count += 1
self.assertAlmostEqual(system['cells'][0][0][0], 7.822838765564372)
self.assertAlmostEqual(system['cells'][0][1][1], 7.353572647182051)
self.assertAlmostEqual(system['cells'][0][2][2], 9.036518515423753)
self.assertAlmostEqual(system['coords'][0][8][0], 7.43)
self.assertAlmostEqual(system['coords'][0][8][1], 5.12)
self.assertAlmostEqual(system['coords'][0][8][2], 3.36)
system.to('vasp/poscar', 'POSCAR')