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Merge pull request #92 from amcadmus/devel
support gromacs gro file format
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‎README.md

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@@ -51,6 +51,34 @@ The labels provided in the `OUTCAR`, i.e. energies, forces and virials (if any),
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The `System` or `LabeledSystem` can be constructed from the following file formats with the `format key` in the table passed to argument `fmt`:
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| Software| format | multi frames | labeled | class | format key |
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| ------- | :--- | :---: | :---: | :--- | :--- |
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| vasp | poscar | False | False | System | 'vasp/poscar' |
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| vasp | outcar | True | True | LabeledSystem | 'vasp/outcar' |
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| vasp | xml | True | True | LabeledSystem | 'vasp/xml' |
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| lammps | lmp | False | False | System | 'lammps/lmp' |
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| lammps | dump | True | False | System | 'lammps/dump' |
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| deepmd | raw | True | False | System | 'deepmd/raw' |
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| deepmd | npy | True | False | System | 'deepmd/npy' |
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| deepmd | raw | True | True | LabeledSystem | 'deepmd/raw' |
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| deepmd | npy | True | True | LabeledSystem | 'deepmd/npy' |
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| gaussian| log | False | True | LabeledSystem | 'gaussian/log'|
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| gaussian| log | True | True | LabeledSystem | 'gaussian/md' |
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| siesta | output | False | True | LabeledSystem | 'siesta/output'|
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| siesta | aimd_output | True | True | LabeledSystem | 'siesta/aimd_output' |
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| cp2k | output | False | True | LabeledSystem | 'cp2k/output' |
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| cp2k | aimd_output | True | True | LabeledSystem | 'cp2k/aimd_output' |
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| QE | log | False | True | LabeledSystem | 'qe/pw/scf' |
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| QE | log | True | False | System | 'qe/cp/traj' |
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| QE | log | True | True | LabeledSystem | 'qe/cp/traj' |
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|quip/gap|xyz|True|True|MultiSystems|'quip/gap/xyz'|
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| PWmat | atom.config | False | False | System | 'pwmat/atom.config' |
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| PWmat | movement | True | True | LabeledSystem | 'pwmat/movement' |
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| PWmat | OUT.MLMD | True | True | LabeledSystem | 'pwmat/out.mlmd' |
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| Amber | multi | True | True | LabeledSystem | 'amber/md' |
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| Gromacs | gro | False | False | System | 'gromacs/gro' |
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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.
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Use `dpdata.MultiSystems.from_dir` to read from a directory, `dpdata.MultiSystems` will walk in the directory
@@ -82,35 +110,8 @@ xyz_multi_systems.systems['B1C9'].to_deepmd_raw('./my_work_dir/B1C9_raw')
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# dump all systems
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xyz_multi_systems.to_deepmd_raw('./my_deepmd_data/')
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```
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| Software| format | multi frames | labeled | class | format key |
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| ------- | :--- | :---: | :---: | :--- | :--- |
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| vasp | poscar | False | False | System | 'vasp/poscar' |
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| vasp | outcar | True | True | LabeledSystem | 'vasp/outcar' |
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| vasp | xml | True | True | LabeledSystem | 'vasp/xml' |
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| lammps | lmp | False | False | System | 'lammps/lmp' |
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| lammps | dump | True | False | System | 'lammps/dump' |
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| deepmd | raw | True | False | System | 'deepmd/raw' |
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| deepmd | npy | True | False | System | 'deepmd/npy' |
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| deepmd | raw | True | True | LabeledSystem | 'deepmd/raw' |
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| deepmd | npy | True | True | LabeledSystem | 'deepmd/npy' |
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| gaussian| log | False | True | LabeledSystem | 'gaussian/log'|
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| gaussian| log | True | True | LabeledSystem | 'gaussian/md' |
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| siesta | output | False | True | LabeledSystem | 'siesta/output'|
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| siesta | aimd_output | True | True | LabeledSystem | 'siesta/aimd_output' |
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| cp2k | output | False | True | LabeledSystem | 'cp2k/output' |
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| cp2k | aimd_output | True | True | LabeledSystem | 'cp2k/aimd_output' |
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| QE | log | False | True | LabeledSystem | 'qe/pw/scf' |
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| QE | log | True | False | System | 'qe/cp/traj' |
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| QE | log | True | True | LabeledSystem | 'qe/cp/traj' |
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|quip/gap|xyz|True|True|MultiSystems|'quip/gap/xyz'|
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| PWmat | atom.config | False | False | System | 'pwmat/atom.config' |
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| PWmat | movement | True | True | LabeledSystem | 'pwmat/movement' |
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| PWmat | OUT.MLMD | True | True | LabeledSystem | 'pwmat/out.mlmd' |
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| Amber | multi | True | True | LabeledSystem | 'amber/md' |
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## Access data
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These properties stored in `System` and `LabeledSystem` can be accessed by operator `[]` with the key of the property supplied, for example
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```python
@@ -130,7 +131,6 @@ Available properties are (nframe: number of frames in the system, natoms: total
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| 'virials' | np.ndarray | nframes x 3 x 3 | True | The virial tensor of each frame
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## Dump data
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The data stored in `System` or `LabeledSystem` can be dumped in 'lammps/lmp' or 'vasp/poscar' format, for example:
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```python
@@ -142,7 +142,6 @@ d_outcar.to('vasp/poscar', 'POSCAR', frame_idx=-1)
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```
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The last frames of `d_outcar` will be dumped to 'POSCAR'.
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The data stored in `LabeledSystem` can be dumped to deepmd-kit raw format, for example
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```python
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d_outcar.to('deepmd/raw', 'dpmd_raw')
@@ -157,13 +156,15 @@ dpdata.LabeledSystem('OUTCAR').sub_system([0,-1]).to('deepmd/raw', 'dpmd_raw')
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```
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by which only the first and last frames are dumped to `dpmd_raw`.
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## replicate
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dpdata will create a super cell of the current atom configuration.
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```python
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dpdata.System('./POSCAR').replicate((1,2,3,) )
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```
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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.
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## perturb
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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).
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```python

‎dpdata/gromacs/__init__.py

Whitespace-only changes.

‎dpdata/gromacs/gro.py

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#!/usr/bin/env python3
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import numpy as np
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nm2ang = 10.
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def _get_line(line):
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atom_name = line[10:15].split()[0]
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atom_idx = int(line[15:20].split()[0])
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posis = [float(line[ii:ii+8]) for ii in range(20,44,8)]
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posis = np.array(posis) * nm2ang
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return atom_name, atom_idx, posis
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def _get_cell(line):
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cell = np.zeros([3,3])
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lengths = [float(ii) for ii in line.split()]
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if len(lengths) >= 3:
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for dd in range(3):
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cell[dd][dd] = lengths[dd]
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else:
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raise RuntimeError('wrong box format: ', line)
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if len(lengths) == 9:
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cell[0][1] = lengths[3]
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cell[0][2] = lengths[4]
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cell[1][0] = lengths[5]
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cell[1][2] = lengths[6]
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cell[2][0] = lengths[7]
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cell[2][1] = lengths[8]
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cell = cell * nm2ang
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return cell
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def file_to_system_data(fname):
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names = []
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idxs = []
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posis = []
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with open(fname) as fp:
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fp.readline()
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natoms = int(fp.readline())
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for ii in range(natoms):
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n, i, p = _get_line(fp.readline())
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names.append(n)
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idxs.append(i)
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posis.append(p)
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cell = _get_cell(fp.readline())
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posis = np.array(posis)
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system = {}
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system['orig'] = np.array([0, 0, 0])
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system['atom_names'] = list(set(names))
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system['atom_names'].sort()
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system['atom_numbs'] = [names.count(ii) for ii in system['atom_names']]
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system['atom_types'] = [system['atom_names'].index(ii) for ii in names]
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system['atom_types'] = np.array(system['atom_types'], dtype = int)
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system['coords'] = np.array([posis])
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system['cells'] = np.array([cell])
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return system

‎dpdata/system.py

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@@ -22,6 +22,7 @@
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import dpdata.pwmat.movement
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import dpdata.pwmat.atomconfig
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import dpdata.fhi_aims.output
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import dpdata.gromacs.gro
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from copy import deepcopy
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from monty.json import MSONable
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from monty.serialization import loadfn,dumpfn
@@ -607,6 +608,19 @@ def from_deepmd_raw(self, folder, type_map = None) :
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if tmp_data is not None :
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self.data = tmp_data
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@register_from_funcs.register_funcs("gro")
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@register_from_funcs.register_funcs("gromacs/gro")
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def from_gromacs_gro(self, file_name) :
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"""
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Load gromacs .gro file
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Parameters
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----------
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file_name : str
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The input file name
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"""
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self.data = dpdata.gromacs.gro.file_to_system_data(file_name)
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@register_to_funcs.register_funcs("deepmd/npy")
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def to_deepmd_npy(self, folder, set_size = 5000, prec=np.float32) :
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"""

‎tests/gromacs/1h.gro

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1SOL O 1 0.135 0.183 0.341
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1SOL H 2 0.177 0.149 0.262
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1SOL H 3 0.046 0.149 0.339
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2SOL O 4 0.520 0.447 0.111
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2SOL H 5 0.567 0.481 0.035
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2SOL H 6 0.568 0.481 0.186
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3SOL O 7 0.651 0.539 0.335
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3SOL H 8 0.653 0.634 0.336
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3SOL H 9 0.743 0.512 0.336
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0.7822838765564372 0.7353572647182051 0.9036518515423753

‎tests/gromacs/1h.tri.gro

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1SOL O 1 0.135 0.183 0.341
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1SOL H 2 0.177 0.149 0.262
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1SOL H 3 0.046 0.149 0.339
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2SOL O 4 0.520 0.447 0.111
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2SOL H 5 0.567 0.481 0.035
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2SOL H 6 0.568 0.481 0.186
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3SOL O 7 0.651 0.539 0.335
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3SOL H 8 0.653 0.634 0.336
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3SOL H 9 0.743 0.512 0.336
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0.7822838765564372 0.7353572647182051 0.9036518515423753 0.0 0.1 0.2 0.3 0.4 0.5

‎tests/test_gromacs_gro.py

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

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