Convert from Amber restart to Geometry.dat file for AIMS🔗
scripts.convert_to_geomdat
🔗
Written by Alice Walker and Ruibin Liang
This script converts from Amber restart format to AIMS Geometry.dat files. It assumes your restart file has velocities.
To run, just give it the paths to your prmtop, restart data and desired output data as below.
main('test_data/parm.prmtop','test_data/','test_data/outs/')
Functions🔗
convert_geometries(prmpath: str, rstpath: str, outpath: str)
🔗
This function creates a directory structure and output to convert a set of geometries from Amber prmtop/rst format to FMS90 Geometry.dat format.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
prmpath |
str |
the path to the prmtop file |
required |
rstpath |
str |
the path to the restart file |
required |
outpath |
str |
the path to the output files |
required |
Returns:
| Type | Description |
|---|---|
|
All converted geometries in the path outpath/filename. |
Source code in scripts/convert_to_geomdat.py
def convert_geometries(
prmpath: str,
rstpath: str,
outpath: str,
):
"""This function creates a directory structure and output to convert a set of geometries from Amber prmtop/rst format to FMS90 Geometry.dat format.
Params:
prmpath: the path to the prmtop file
rstpath: the path to the restart file
outpath: the path to the output files
Returns:
All converted geometries in the path outpath/filename.
"""
findme = "*/*.rst*"
Prmpath = Path(prmpath)
Rstpath = Path(rstpath)
Outpath = Path(outpath)
# Get initial information from parmtop
names, masses = read_prmtop(Prmpath)
# Find all restart files in test data
filenames = list(Rstpath.glob(findme))
# Create new dats
for filename in filenames:
coords, vel, numats = read_rst(filename)
output_geom(names, masses, coords, vel, numats, Outpath, filename)
output_geom(namelist: <built-in function array>, atommass: <built-in function array>, atomcoord: <built-in function array>, atomvel: <built-in function array>, atomnum: int, outpath: str, filename: str)
🔗
This function takes output from read_rst and read_prmtop as input and creates a Geometry.dat file, with appropriate numerical conversions to Bohr coordinates and a.u. time, to be used for AIMS simulations.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
namelist |
<built-in function array> |
the vector of atom names as strings |
required |
atommass |
<built-in function array> |
the vector of atomic masses as floats |
required |
atomcoord |
<built-in function array> |
the 2d N by 3 array of atomic xyz coordinates |
required |
atomvel |
<built-in function array> |
the 2d N by 3 array of atomic velocities |
required |
atomnum |
int |
the total number of atoms in the system |
required |
outpath |
str |
the directory to put all output files/directories |
required |
filename |
str |
the name of the specific restart file to be converted |
required |
Returns:
| Type | Description |
|---|---|
|
A Geometry.dat file in the path outpath/filename-Geometry.dat |
Source code in scripts/convert_to_geomdat.py
def output_geom(
namelist: np.array,
atommass: np.array,
atomcoord: np.array,
atomvel: np.array,
atomnum: int,
outpath: str,
filename: str,
):
"""This function takes output from read_rst and read_prmtop as input and creates a Geometry.dat file, with appropriate numerical conversions to Bohr coordinates and a.u. time, to be used for AIMS simulations.
Params:
namelist: the vector of atom names as strings
atommass: the vector of atomic masses as floats
atomcoord: the 2d N by 3 array of atomic xyz coordinates
atomvel: the 2d N by 3 array of atomic velocities
atomnum: the total number of atoms in the system
outpath: the directory to put all output files/directories
filename: the name of the specific restart file to be converted
Returns:
A Geometry.dat file in the path outpath/filename-Geometry.dat
"""
# Initialize new output directory if it doesn't exist
if not outpath.exists():
Path.mkdir(outpath)
# Create directory structure from original files
newdir = filename.parent
finalpath = outpath.joinpath(newdir.relative_to(newdir.parent))
Path.mkdir(finalpath, parents=True, exist_ok=True)
with open(finalpath.joinpath("Geometry.dat"), "w+") as f:
f.write("UNITS=BOHR\n")
f.write(str(atomnum) + "\n")
for j in range(0, atomnum):
if namelist[j] == "Cl-":
f.write(
"{0:<10s}".format(namelist[j][0:2])
+ "".join(
"{0:>22.16f}".format(x / 0.52917724924) for x in atomcoord[j]
)
+ "\n"
)
else:
f.write(
"{0:<10s}".format(namelist[j][0])
+ "".join(
"{0:>22.16f}".format(x / 0.52917724924) for x in atomcoord[j]
)
+ "\n"
)
f.write("# momenta\n")
for j in range(0, atomnum):
for x in atomvel[j]:
p = x * atommass[j] * 9.3499611711905144e-04 * 1.8228884855409500e03
f.write(
"{0:>22.16f}".format(p)
) # time unit in rst7: 1/20.455 ps length unit in rst7: angstrom mass unit in amber: atomic mass unit
f.write("\n")
read_prmtop(prmpath: str)
🔗
This function parses a prmtop to extract atomic types/names and masses.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
prmpath |
str |
the path to the prmtop file |
required |
Returns:
| Type | Description |
|---|---|
namelist |
the atom names as a vector of strings. atommass: atomic masses as a vector of floats. |
Source code in scripts/convert_to_geomdat.py
def read_prmtop(prmpath: str):
"""This function parses a prmtop to extract atomic types/names and masses.
Params:
prmpath: the path to the prmtop file
Returns:
namelist: the atom names as a vector of strings.
atommass: atomic masses as a vector of floats.
"""
namelist = []
atommass = []
with open(prmpath) as f:
for line in f:
if "ATOM_NAME" in line:
line = next(f)
for line in f:
if "CHARGE" in line:
break
else:
line = line.strip("\n")
for c in range(0, len(line), 4):
namelist = namelist + [line[c : c + 3]]
if "MASS" in line:
line = next(f)
for line in f:
if "ATOM_TYPE_INDEX" in line:
break
else:
a = line.split()
for x in a:
atommass.append(float(x))
return namelist, atommass
read_rst(rstpath: str)
🔗
This function parses a restart file to extract coordinates and velocities.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
rstpath |
str |
the path to the restart file(s) to be processed. Can handle instances in subdirectories. |
required |
Returns:
| Type | Description |
|---|---|
atomcoord |
the xyz coordinates as an N by 3 array. atomvel: the velocities as an N by 3 array. |
Source code in scripts/convert_to_geomdat.py
def read_rst(rstpath: str):
"""This function parses a restart file to extract coordinates and velocities.
Params:
rstpath: the path to the restart file(s) to be processed. Can handle instances in subdirectories.
Returns:
atomcoord: the xyz coordinates as an N by 3 array.
atomvel: the velocities as an N by 3 array.
"""
atomcoord = np.array([])
atomvel = np.array([])
atomnum = 0
with rstpath.open() as f:
f.readline()
line = f.readline()
atomnum = int(line.split()[0])
atomcoord = np.zeros((atomnum, 3))
atomvel = np.zeros((atomnum, 3))
for j in range(0, int((atomnum + 1) / 2)):
line = f.readline()
a = line.split()
atomcoord[j * 2] = np.array([float(a[0]), float(a[1]), float(a[2])])
if len(a) == 6:
atomcoord[j * 2 + 1] = np.array([float(a[3]), float(a[4]), float(a[5])])
for j in range(0, int((atomnum + 1) / 2)):
line = f.readline()
a = line.split()
atomvel[j * 2] = np.array([float(a[0]), float(a[1]), float(a[2])])
if len(a) == 6:
atomvel[j * 2 + 1] = np.array([float(a[3]), float(a[4]), float(a[5])])
return atomcoord, atomvel, atomnum