Cookbook¶

Create an input block with an header¶

These Settings

sett = Settings()
sett.input.ams.SomeInputBlock['_h'] = 'MyHeader'
sett.input.ams.SomeInputBlock.SomeOption = 2

will generate the following text input when used for an AMSJob:

SomeInputBlock MyHeader
    SomeOption 2
End

Create an empty input block¶

These Settings

sett = Settings()
sett.input.ams.SomeInputBlock

will generate the following text input when used for an AMSJob:

SomeInputBlock
End

Create an input block with repeating keys¶

These Settings

sett = Settings()
sett.input.ams.constraints.atom = [1,2,3]

will generate the following text input when used for an AMSJob:

Constraints
    Atom 1
    Atom 2
    Atom 3
End

Repeating input block¶

These Settings

block_1 = Settings()
block_1.SomeOption = 1

block_2 = Settings()
block_2.SomeOption = 7

sett = Settings()
sett.input.ams.SomeInputBlock = [block_1, block_2]

will generate the following text input when used for an AMSJob:

SomeInputBlock
  SomeOption 1
End
SomeInputBlock
  SomeOption 7
End

Convert an AMS text input into an AMS job¶

The from_input() function can be used to convert text input into AMSJob instances.

job = AMSJob.from_input(name='jobname', text_input='''
Task SinglePoint
System
    Atoms
        H 0. 0. 0.
        H 0. 0. 1.
    End
End
Engine Band
    Basis
        Type DZ
        Core None
    End
EndEngine
''')

Convert an AMS text input into settings object¶

The Settings object corresponding to a piece of text input can easily be obtained as the .settings attribute of the AMSJob instance returned by the from_input() method.

settings = AMSJob.from_input("""
Task SinglePoint
Engine Band
    Basis
        Type DZ
        Core None
    End
EndEngine
""").settings

Convert an AMS .run file into an AMS job¶

The from_inputfile() method can be used to convert a .run file generated by the AMS GUI into a PLAMS AMSJob.

job = AMSJob.from_inputfile('/path/to/job.run')

Specify paths to files in the input¶

With PLAMS, you cannot specify relative paths to input files, because every PLAMS job launches in a new directory, which makes the relative paths invalid. To specify an absolute path, use os.path.abspath:

import os

sett = Settings()
sett.input.reaxff.forcefield = os.path.abspath('../my-forcefield.ff')

Restart from a previous job¶

To use restart features in AMS, for example the EngineRestart, or to read the InitialVelocities from the final velocities of a previous molecular dynamics run, you can use a convenient shortcut and simply assign the job to the corresponding settings entry:

sett = Settings()
sett.input.ams.EngineRestart = (previous_ams_job, 'engine') # resolves to the engine.rkf

sett2 = Settings()
sett2.input.ams.MolecularDynamics.InitialVelocities.Type = 'FromFile'
sett2.input.ams.MolecularDynamics.InitialVelocities.File = previous_ams_job # resolves to ams.rkf

Alternatively, call the rkfpath() method on the previous job’s AMSResults:

sett = Settings()
sett.input.ams.EngineRestart = previous_ams_job.results.rkfpath(file='engine')

sett2 = Settings()
sett2.input.ams.MolecularDynamics.InitialVelocities.Type = 'FromFile'
sett2.input.ams.MolecularDynamics.InitialVelocities.File = previous_ams_job.results.rkfpath()

Generate a molecule from a SMILES string¶

See function from_smiles().

# Compute 10 conformers, optimize with UFF and pick the lowest in energy.
ethane = from_smiles('C-C', nconfs=10, forcefield='uff')[0]

Load all files in a folder as molecules¶

See function read_molecules().

molecules = read_molecules('/some_path/folder_containing_structure_files/')

for name, mol in molecules.items():
    print("Name of the file (without extension): ", name)
    print(mol)

Generate a liquid or gas mixture¶

# Generate a 2-to-1 water-acetonitrile mixture with a density of 0.9 g/cm^3 and approximately 200 atoms
water = from_smiles('O')
acetonitrile = from_smiles('CC#N')
mixture = packmol(molecules=[water, acetonitrile],
                  mole_fractions=[0.667, 0.333],
                  n_atoms=200,
                  density=0.9)

See Packmol example for more examples on how to construct liquid or gas mixtures and solid/liquid or solid/gas interfaces.

Write an ams.rkf-like trajectory¶

If you have a list of molecules, it can be convenient to write them to an AMS-like .rkf file so that you can visualize them in the GUI module AMSmovie.

from scm.plams import molecules_to_rkf, from_smiles

molecule_list = [from_smiles('C'), from_smiles('CC')]
molecules_to_rkf(molecule_list, 'output.rkf', overwrite=True)

Convert a trajectory to ams.rkf with bond guessing¶

See Convert to ams.rkf trajectory with bond guessing

Pre-optimize a molecule¶

# pre-optimize with UFF inside AMS
optimized_mol = preoptimize(mol)

See Quick jobs for details and options.

Counting rings¶

Rings inside molecules can be counted in various ways, which are not all giving the same results. With the help of the RDKit library, a vast variety of ring counting approaches is readily available. The general approach to using these functions in a PLAMS scripts is to convert your PLAMS Molecule into an RDKit molecule, see the page on the RDKit interface. This is how one searches for the smallest set of rings in a molecule:

# import RDKit
from rdkit import Chem

# create a PLAMS molecule and convert it to an RDKit Mol
dicyclopentadiene = from_smiles('C1C=CC2C1C3CC2C=C3')
rdmol = to_rdmol(dicyclopentadiene)

# Calculate smalles set of rings
for atoms in Chem.GetSymmSSSR(rdmol):
     print ([atom_id for atom_id in atoms], len(atoms))

For more information see also the RDKit manual.

Directly from Functions¶

Results can be either red from previous calculations (see Accessing Old Jobs) or from an AMSResults instance of a computation just executed within the same workflow. In either case an AMSResults object should be present at runtime:

myAMSJob.run()
myAMSResults = myAMSJob.results if myAMSJob.ok() else None

myAMSEnergy = myAMSResults.get_energy(unit='au')

myAMSStructure = myAMSResults.get_main_molecule()

From the RKF Interface¶

Other properties not listed in the table above should be retrieved using the readrkf() function:

myProperty = myAMSResults.readrkf(section, variable)

It is the responsibility of the user to provide the correct names for section and variable under which the required result is stored in the rkf file.

Finding Section/Variable Pairs¶

Looking up the names of the needed sections and variable within rkf files is typically needed for more intricate properties when writing a new PLAMS workflow. There are two main approaches to search for this information.

myEngineProperty = myAMSResults.readrkf(section, variable, file=<engine>)

From molecular dynamics trajectories¶

kf = KFReader(mdjob.results['ams.rkf'])
hist = KFHistory(kf, "History")
mdhist = KFHistory(kf, "MDHistory")

frame = 0
for E, T, p in zip(hist.iter("Energy"), mdhist.iter("Temperature"), mdhist.iter("Pressure")):
    frame += 1
    print("Frame: {} Energy: {} Temperature: {} Pressure: {}".format(frame, E, T, p))

import numpy as np

# mdjob is a finished AMSJob
coords = mdjob.results.get_history_property('Coords', history_section='History')
coords = np.array(coords).reshape(len(coords), -1, 3) # in bohr
print(coords.shape)

rkf = RKFTrajectoryFile(mdjob.results['ams.rkf'])
mol = rkf.get_plamsmol()

for i in range(rkf.get_length()):
    coords,cell = rkf.read_frame(i,molecule=mol)
    print(coords, cell, mol.get_center_of_mass())

kf = KFReader(mdjob.results['ams.rkf'])
mdhist = KFHistory(kf, "MDHistory")
hist = KFHistory(kf, "History")

# get number of distinct molecule types and all their formulas
number_of_molecules = kf.read('Molecules','Num molecules')
formulas = [ kf.read('Molecules',f'Molecule name {i+1}') for i in range(number_of_molecules) ]

for mols, step in zip( hist.iter("Mols.Type"), mdhist.iter("Step")):
    line = f"{step:8d} "
    for i in sorted(set(mols)): line += f"{formulas[i-1]:s} "
    print(line)

Binding Native PLAMS Jobs¶

From an existing PLAMS working directory with the contents

OLDDIR/
├── OLDJOB1/
|   ├── ams.log
|   ├── ams.rkf
|   ├── OLDJOB1.dill
|   ├── OLDJOB1.err
|   ├── OLDJOB1.in
|   ├── OLDJOB1.out
|   ├── OLDJOB1.run
|   ├── engine.rkf
|   ├── output.xyz
├── input
└── logfile

we can bind an instance of the AMSJob class by making use of the .dill file. The AMSJob object in turn contains a results object, which gives access to the data previously calculated. This can be achieved using the load() function as illustrated in the following snippet:

path       = "OLDDIR/OLDJOB1/OLDJOB1.dill"
single_JOB = load(path)                                       # AMSJob instance
if single_JOB.ok():
   energy     = single_JOB.results.get_energy()               # load the desired properties
   structure  = single_JOB.results.get_main_molecule()
   propertyX  = single_JOB.results.readrkf('AMSResults', 'DipoleMoment', file='engine')

More often than not, the working directory will include multiple individual subdirectories, each containing individual PLAMS job.

OLDDIR/
├── OLDJOB1/
|   ├── ams.log
|   ├── ams.rkf
|   ├── OLDJOB1.dill
|   ├── OLDJOB1.err
|   ├── OLDJOB1.in
|   ├── OLDJOB1.out
|   ├── OLDJOB1.run
|   ├── engine.rkf
|   ├── output.xyz
├── OLDJOB2/
|   ├── ams.log
|   ├── ams.rkf
|   ├── OLDJOB2.dill
|   ├── OLDJOB2.err
|   ├── OLDJOB2.in
|   ├── OLDJOB2.out
|   ├── OLDJOB2.run
|   ├── engine.rkf
|   ├── output.xyz
├── OLDJOB3/
|   ├── ams.log
|   ├── ams.rkf
|   ├── OLDJOB3.dill
|   ├── OLDJOB3.err
|   ├── OLDJOB3.in
|   ├── OLDJOB3.out
|   ├── OLDJOB3.run
|   ├── engine.rkf
|   ├── output.xyz
├── input
└── logfile

These can be loaded using the load_all() function and by providing only the path to the top-level directory:

path       = "OLDDIR"
all_JOBS   = load_all(path)

Note that load_all() wraps the load() function used above and therefore requires existing .dill files in each of the loaded subdirectories. The load_all() function yields a dictionary with the paths of the .dill files as keys and the corresponding job object as values:

print(all_JOBS)

{'/home/user/OLDDIR/OLDJOB1/OLDJOB1.dill': <scm.plams.interfaces.adfsuite.ams.AMSJob object at 0x7f0baad340b8>,
 '/home/user/OLDDIR/OLDJOB2/OLDJOB2.dill': <scm.plams.interfaces.adfsuite.ams.AMSJob object at 0x7f0baacf24a8>,
 '/home/user/OLDDIR/OLDJOB3/OLDJOB3.dill': <scm.plams.interfaces.adfsuite.ams.AMSJob object at 0x7f0baad06cf8>}

We can now access these AMSJob instances:

for this_JOB in all_JOBS.values():
   if this_JOB.ok():
      energy     = this_JOB.results.get_energy()
      structure  = this_JOB.results.get_main_molecule()
      propertyX  = this_JOB.results.readrkf('AMSResults', 'DipoleMoment', file='engine')

Binding old RKF Files¶

In cases where the .dill files are not available any more, it is still possible to load the contents of previously generated .rkf files into a PLAMS workflow:

path       = "OLDDIR/OLDJOB1/"
ext_JOB    = AMSJob.load_external(path)
if ext_JOB.ok():
   energy     = ext_JOB.results.get_energy()
   structure  = ext_JOB.results.get_main_molecule()

If the .rkf file does originate from some other source than any of the direct AMS engines, also an instance of the more generic SingleJob class can be used:

path       = "OLDDIR/OLDJOB1/ams.rkf"
ext_JOB    = SingleJob.load_external(path)

The downside of this latter approach is that the accessibility to the data is very limited and has to be implemented mostly in terms of pattern-matching searches in the output files.

An alternative way is to make use of the KFReader class:

path       = "OLDDIR/OLDJOB1/ams.rkf"
rkf_reader = KFReader(path)
n_steps    = rkf_reader.read("History", "nEntries")
energy     = rkf_reader.read("History", "Energy({})".format(n_steps))
structure  = rkf_reader.read("History", "Coords({})".format(n_steps))

Note that also the KFReader class lacks most of the shortcut functions of a proper AMSResults object so that the access to the data has to be specified manually.

Parallel job execution¶

PLAMS supports running multiple jobs in parallel. Details on the synchronization between parallel job executions can be found here. To make sure your PLAMS script can take maximum advantage of parallel job execution there is a simple rule: Make sure to create and run as many jobs as possible before starting to access any results. (This is because the access to results of a job may block until that job has finished, preventing you to submit more independent jobs in the meantime.)

In the common case where there are no dependencies between jobs, this means that we should set up and run all jobs before starting to access any results. The script below shows how to parallelize the trivially parallel task of just executing the same job on a set of molecules.

mols = read_molecules('my_molecules')
# mols is a dictionary mapping filenames (without
# extension) to plams.Molecule instances, e.g.:
# my_molecules/benzene.xyz would become mols['benzene']

sett = Settings()
# ... all your settings go here ...

config.default_jobrunner = JobRunner(parallel=True, maxjobs=8)
sett.runscript.nproc = 4
# run up to 8 jobs (using 4 cores each) in parallel

jobs    = { n: AMSJob(name=n, settings=sett, molecule=m) for n,m in mols.items() }
results = { n: j.run() for n,j in jobs.items() }
# make and run all jobs before accessing any results

for n,r in results.items():
   print(n, r.get_energy() if r.ok() else 'Failed')

Obviously, runscript.nproc could also be set on a per-job basis. This is useful if some of your jobs do not scale well with the number of CPU cores, or if you have jobs of very different computational cost.

PLAMS scripts under Slurm¶

A PLAMS script can be run under the Slurm batch system and execute jobs within the resource allocation that is created for the script. The script shown in the previous section should work just fine when run under a batch system. The only change you should make is not to set the maximum number of jobs.

config.default_jobrunner = JobRunner(parallel=True)

Furthermore you may need to wrap the call to the PLAMS launch script in a job script, in which we recommend you cd to the directory from which the job was submitted. This makes sure you will find the PLAMS working directory in the normal location. (If $AMSBIN is not already in your environment, this is also the place to set up the AMS environment.)

#!/bin/sh
cd "$SLURM_SUBMIT_DIR"
$AMSBIN/plams myscript.plms

The above job script can then simply be submitted to the batch system:

sbatch [...] myscript.sh

Alternatively you can also skip the job script, and submit the PLAMS launch script itself:

sbatch [...] --chdir=. $AMSBIN/plams myscript.plms