dynpy_params.py

# This is the standard input file for setting extra paramters needed for initializing and parsing MD trajectories, generating clusters,  

class ParseDynamics:
   # MD_ENGINE = 'QE'
   # traj_dir = './example-data/Iodide/' #Path to directory containing trajectory directories {01..XX} ('./example-data/' for example, or './trajectories/' for default space of your own traj data)
   # start_prod = 30000 #MD step number to start sampling snapshots from. For the default setup and equilibration used in this package, 42000 (~6ps) is recommended
   # end_prod = 30100
   # sample_freq = 10 #number of steps between sampled snapshots. Keep high for testing
   # md_print_freq = 10
   # timestep = 6.0*2.418884254e-5 #timestep of aiMD in picoseconds. May be any expression returning floating point value
   # nat = 192
   # symbols = ['I'] + ['H']*129 + ['O']*64 #Full list of element symbols in the order they appear in 'ATOMIC_SPECIES' block of QE MD input
   # celldm = 24.269 #Simulation cell dimension in bohr. May be any expression returning floating point value
    
    #MD_ENGINE = 'QE'
    #traj_dir = './example-data/QE/water/' #Path to directory containing trajectory directories {01..XX} ('./example-data/' for example, or './trajectories/' for default space of your own traj data)
    #start_prod = 30000 #MD step number to start sampling snapshots from. For the default setup and equilibration used in this package, 42000 (~6ps) is recommended
    #end_prod = 32000
    #sample_freq = 10 #number of steps between sampled snapshots. Keep high for testing
    #md_print_freq = 10
    #timestep = 6.0*2.418884254e-5 #timestep of aiMD in picoseconds. May be any expression returning floating point value
    #nat = 192
    #symbols = ['O','H','H']*64  #Full list of element symbols in the order they appear in 'ATOMIC_SPECIES' block of QE MD input
    #celldm = 23.46 #Simulation cell dimension in bohr. May be any expression returning floating point value

    MD_ENGINE = 'Tinker'
    traj_dir = '../jerschow-trajectories/tinker/300K/'
    trajs = ['01']
    prefix = 'gpl'
    #traj_dir = './example-data/tinker/water/vapor/101kpa/' #Path to directory containing trajectory directories {01..XX} ('./example-data/' for example, or './trajectories/' for default space of your own traj data)
    #traj_dir = './example-data/tinker/water/' #Path to directory containing trajectory directories {01..XX} ('./example-data/' for example, or './trajectories/' for default space of your own traj data)
    ntraj = 1 #number of trajectories to parse
    nat = 896
    #nat = 1408
    start_prod = 1 #MD step number to start sampling snapshots from. For the default setup and equilibration used in this package, 42000 (~6ps) is recommended
    end_prod = 500
    md_print_freq = 5
    sample_freq = 1 #number of steps between sampled snapshots. Keep high for testing
    celldm = 22.32/0.529177 #gpl #Simulation cell dimension in bohr. May be any expression returning floating point value
    #celldm = 25.37/0.529177 #dma
    timestep = 0.001 #timestep of MD in picoseconds. May be any expression returning floating point value
    #parse_vel=True

class SpinRotation:
    mol_type = 'methyl'
    nmol = 64
    C_SR = [0,0,-20.23]
    #C_SR = [-0.37401643,-0.33949459,-0.74248898]
    #identifier = 'C(6)H(7)N(1)' #gpl
    identifier = 'C(9)H(12)O(1)'
    #methyl_indeces = [0,10,11,12,13] #Indeces of atoms that make up the methyl group of interest in the molecule, including the alpha carbon which must start the sequence.
    global_momentum = False
    methyl_indeces = [1,7,13,14,15] #dma-2
    #methyl_indeces = [3,8,16,17,18] #dma-5
    #Indexing is zero-based and is relative to a single molecular unit. All molecules in the system must have atoms ordered the same way!
    #mol_plane_indeces = [0,1,5]
    #mol_type = 'water'
    #C_SR = [33.46,36.9377,35.546]

class Quadrupolar:
    data_set = '/mnt/e/Documents/Akimov-research/ml_efg_AGdensity_ntrain_250.csv'
    analyte = '23Na'
    multiple_trajectories = False
    timestep = 0.01015931
    index_is_frame = True


class Dipolar:
    #identifier = 'C(6)H(7)N(1)' #gpl
    identifier = 'H(2)O(1)'
    #analyte_label = 10
    #analyte_species = '13C'
    pair_type = 'inter'
    rmax = 15

class Snapshots:  #Input parameters file for neighbors.py. Used for parsing qe aiMD, making clusters, and writing inputs for ADF/QE-GIPAW
    write_ADF = True #If True, write input files for ADF EFG calcs
    write_GIPAW = False #If True, write input files for QE-PAW EFG calcs
    analyte_label = 'I' #Element symbol for analyte nucleus. Should be redundant with nuc_symbol and if not provided will be inferred from the latter
    nuc_symbol = '127I' #Analyte symbol prepended with the proper atomic mass number of the isotope
    solute_charge = -1 #Charge of the solute/analyte
    formal_charges = {'H':1,'O':-2}
    write_xyzs = True #If True, write set of xyz files of clusters used for ADF inputs
    nn = 30 #Number of nearest neighbor solvent molecules desired for clusters
    scratch = '/gpfs/scratch' #Scratch space to use for EFG calculations
    skip_compute_neighbors = False #If True, write new ADF inputs from existing xyz data from previous run. Use only if .xyz files exist and you know they are computed correctly



#In most cases, the following templates do not need to be changed
class InputTemplates:  #Templates for ADF inputs
    ADF_in = """ATOMS
{0}
END

RELATIVISTIC Scalar ZORA

BASIS
core None
{3} ZORA/QZ4P/{3}
O ZORA/DZP/O
H ZORA/DZP/H
END

XC
HYBRID PBE0
END

CHARGE {2}

SOLVATION
solv eps=78.54 rad=1.93
END

QTENS

SYMMETRY nosym

NUMERICALQUALITY verygood

COMMENT
{1}
END

SAVE TAPE21 TAPE10"""

#Template for ADF Slurm scripts
    ADF_slm = """#!/usr/bin/env bash
#SBATCH --time=8:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16
#SBATCH --mem=64000
##SBATCH --exclusive
##SBATCH --constraint=IB
#SBATCH --cluster=industry
#SBATCH --partition=scavenger
#SBATCH --qos=scavenger
#SBATCH --job-name=ADF/{0}/{1}
#SBATCH --output={1}.out
#SBATCH --error={1}.err

prefix={1}
scratch={2}/$SLURM_JOB_NAME/
mkdir -p $scratch

source 
export I_MPI_PMI_LIBRARY=/usr/lib64/libpmi.so
export SCM_TMPDIR=$scratch
export SLURMTMPDIR=$scratch

cd $scratch
cp $SLURM_SUBMIT_DIR/$prefix*.inp .
$ADFBIN/adf < $prefix-scf.inp > $prefix-scf.out
cp $prefix*.out $SLURM_SUBMIT_DIR/"""

    #Template for QE-GIPAW scf input
    PAW_scf_in = """&control
!{0}
calculation = 'scf'
prefix = '{1}'
restart_mode = 'from_scratch'
pseudo_dir = ''
outdir = './'
verbosity = 'low'
wf_collect = .true.
/
&system
ibrav = 1
celldm(1) = {2}
nat = {3}
ntyp = {4}
ecutwfc = 100
/
&electrons
electron_maxstep = 200
conv_thr =  1e-7
/
ATOMIC_SPECIES
I  126.90      I.revpbe-dn-kjpaw_psl.1.0.0.UPF
H  2.01355d0   H.revpbe-kjpaw_psl.1.0.0.UPF
O  15.9994     O.revpbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS (angstrom)
{5}
K_POINTS automatic
1 1 1 0 0 0"""

    #Template for QE-GIPAW efg input
    PAW_efg_in = """&inputgipaw
!{0}
job = 'efg'
prefix = '{1}'
tmp_dir = './'
verbosity = high
spline_ps = .true.
Q_efg(1) = {2}
/"""

#Template for QE-GIPAW Slurm scripts
PAW_slm = """#!/bin/bash
#SBATCH --time=60:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=24
#SBATCH --cluster=faculty
#SBATCH --partition=scavenger
#SBATCH --qos=scavenger
##SBATCH --exclusive
#SBATCH --output={0}.out
#SBATCH --error={0}.err
#SBATCH --job-name=GIPAW/{1}/{0}
#SBATCH --mem=187000

# USER VARS
gpfs={2}/$SLURM_JOB_NAME/

#GET INPUT FROM SUBMIT DIR
cd $SLURMTMPDIR
cp $SLURM_SUBMIT_DIR/*.inp $SLURMTMPDIR

# MODULES
module load intel
module load intel-mpi
module load mkl

# ENVIRONMENT VARS
PWSCF=""
GIPAW=""
NPOOL=1                                         # QE specific
export I_MPI_PMI_LIBRARY=/usr/lib64/libpmi.so   # CCR req'd

# SETUP
mkdir -p ${{gpfs}}

# RUN QE
srun $PWSCF/bin/pw.x -npool $NPOOL -input {0}-scf.inp > {0}-scf.out
srun $GIPAW/bin/gipaw.x -npool $NPOOL -input {0}-efg.inp > {0}-efg.out

# SAVE FILES
cp {0}-{{scf,efg}}.out $SLURM_SUBMIT_DIR
cp -r * ${{gpfs}}"""