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Merge pull request #87 from njzjz/amber
support reading Amber MD trajectory
2 parents 42be217 + d963605 commit 1e0908b

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‎README.md

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@@ -110,6 +110,7 @@ xyz_multi_systems.to_deepmd_raw('./my_deepmd_data/')
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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

‎dpdata/amber/md.py

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import re
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from scipy.io import netcdf
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import numpy as np
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kcalmol2eV= 0.04336410390059322
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energy_convert = kcalmol2eV
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force_convert = energy_convert
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def read_amber_traj(parm7_file, nc_file, mdfrc_file, mden_file):
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"""The amber trajectory includes:
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* nc, NetCDF format, stores coordinates
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* mdfrc, NetCDF format, stores forces
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* mden, text format, stores energies
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* parm7, text format, stores types
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"""
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flag=False
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amber_types = []
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with open(parm7_file) as f:
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for line in f:
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if line.startswith("%FLAG"):
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flag = line.startswith("%FLAG AMBER_ATOM_TYPE")
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elif flag:
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if line.startswith("%FORMAT"):
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fmt = re.findall(r'\d+', line)
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fmt0 = int(fmt[0])
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fmt1 = int(fmt[1])
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else:
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for ii in range(fmt0):
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start_index = ii * fmt1
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end_index = (ii + 1) * fmt1
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if end_index >= len(line):
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continue
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amber_types.append(line[start_index:end_index].strip())
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with netcdf.netcdf_file(nc_file, 'r') as f:
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coords = np.array(f.variables["coordinates"][:])
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cell_lengths = np.array(f.variables["cell_lengths"][:])
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cell_angles = np.array(f.variables["cell_angles"][:])
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if np.all(cell_angles > 89.99 ) and np.all(cell_angles < 90.01):
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# only support 90
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# TODO: support other angles
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shape = cell_lengths.shape
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cells = np.zeros((shape[0], 3, 3))
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for ii in range(3):
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cells[:, ii, ii] = cell_lengths[:, ii]
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else:
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raise RuntimeError("Unsupported cells")
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with netcdf.netcdf_file(mdfrc_file, 'r') as f:
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forces = np.array(f.variables["forces"][:])
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# energy
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energies = []
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with open(mden_file) as f:
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for line in f:
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if line.startswith("L6"):
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s = line.split()
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if s[2] != "E_pot":
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energies.append(float(s[2]))
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atom_names, atom_types, atom_numbs = np.unique(amber_types, return_inverse=True, return_counts=True)
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data = {}
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data['atom_names'] = list(atom_names)
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data['atom_numbs'] = list(atom_numbs)
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data['atom_types'] = atom_types
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data['forces'] = forces * force_convert
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data['energies'] = np.array(energies) * energy_convert
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data['coords'] = coords
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data['cells'] = cells
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data['orig'] = np.array([0, 0, 0])
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return data
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‎dpdata/system.py

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import dpdata.siesta.aiMD_output
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import dpdata.md.pbc
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import dpdata.gaussian.log
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import dpdata.amber.md
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import dpdata.cp2k.output
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from dpdata.cp2k.output import Cp2kSystems
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import dpdata.pwmat.movement
@@ -1171,6 +1172,19 @@ def from_gaussian_log(self, file_name, md=False):
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def from_gaussian_md(self, file_name):
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self.from_gaussian_log(file_name, md=True)
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@register_from_funcs.register_funcs('amber/md')
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def from_amber_md(self, file_name=None, parm7_file=None, nc_file=None, mdfrc_file=None, mden_file=None):
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# assume the prefix is the same if the spefic name is not given
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if parm7_file is None:
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parm7_file = file_name + ".parm7"
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if nc_file is None:
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nc_file = file_name + ".nc"
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if mdfrc_file is None:
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mdfrc_file = file_name + ".mdfrc"
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if mden_file is None:
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mden_file = file_name + ".mden"
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self.data = dpdata.amber.md.read_amber_traj(parm7_file, nc_file, mdfrc_file, mden_file)
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@register_from_funcs.register_funcs('cp2k/output')
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def from_cp2k_output(self, file_name) :
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self.data['atom_names'], \

‎setup.py

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readme = f.read()
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# install_requires = ['xml']
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install_requires=['numpy>=1.14.3', 'monty']
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install_requires=['numpy>=1.14.3', 'monty', 'scipy']
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setuptools.setup(
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name="dpdata",
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long_description=readme,
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long_description_content_type="text/markdown",
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url="https://github.com/deepmodeling/dpdata",
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packages=['dpdata', 'dpdata/vasp', 'dpdata/lammps', 'dpdata/md', 'dpdata/deepmd', 'dpdata/qe', 'dpdata/siesta', 'dpdata/gaussian', 'dpdata/cp2k','dpdata/xyz','dpdata/pwmat'],
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packages=['dpdata', 'dpdata/vasp', 'dpdata/lammps', 'dpdata/md', 'dpdata/deepmd', 'dpdata/qe', 'dpdata/siesta', 'dpdata/gaussian', 'dpdata/cp2k','dpdata/xyz','dpdata/pwmat', 'dpdata/amber'],
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package_data={'dpdata':['*.json']},
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classifiers=[
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"Programming Language :: Python :: 3.6",

‎tests/amber/.02_Heat.mden.swp

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‎tests/amber/02_Heat.mden

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L0 Nsteps time(ps) Etot EKinetic
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L1 Temp T_solute T_solv Pres_scal_solu
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L2 Pres_scal_solv BoxX BoxY BoxZ
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L3 volume pres_X pres_Y pres_Z
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L4 Pressure EKCoM_x EKCoM_y EKCoM_z
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L5 EKComTot VIRIAL_x VIRIAL_y VIRIAL_z
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L6 VIRIAL_tot E_pot E_vdw E_el
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L7 E_hbon E_bon E_angle E_dih
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L8 E_14vdw E_14el E_const E_pol
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L9 AV_permMoment AV_indMoment AV_totMoment Density dV/dlambda
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L0 100 0.2000000000E+00 -.6889864713E+04 0.5501673987E+02
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L1 0.1444218747E+02 0.1444218747E+02 -.6944881453E+10 0.1000000000E+01
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L2 0.1000000000E+01 0.3139785600E+02 0.3410004500E+02 0.2927296600E+02
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L3 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
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‎tests/amber/02_Heat.mdfrc

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‎tests/amber/02_Heat.nc

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