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Table of contents
Introduction
What is PLAMS
What can be done with PLAMS
Simple example
What PLAMS is
not
About this documentation
Getting started
Library contents
Installing PLAMS
Updating PLAMS
Running PLAMS
Defaults file
The launch script
Working folder location
Passing variables
Importing past jobs
Restarting failed script
Multiple input scripts
Components overview
Settings
Tree-like structure
Dot notation
Case sensitivity
Global settings
API
Jobs
Preparing a job
Contents of job settings
Default settings
Running a job
Name conflicts
Prerun and postrun methods
Preview mode
Job API
Single jobs
Subclassing SingleJob
Multijobs
Using MultiJob
Results
Files in the job folder
Synchronization of parallel job executions
Examples
Cleaning job folder
Cleaning for multijobs
API
Job runners
Local job runner
Remote job runner
Job manager
Rerun prevention
Pickling
Restarting scripts
API
Public functions
Logging
Binding decorators
Molecule
Molecule
Atom labeling
Atom
Bond
RDKit interface
ASE interface
Utilities
Periodic Table
Units
Geometry tools
Interfaces
Amsterdam Modeling Suite
AMS driver and engines
Preparing input
Preparing runscript
Molecule handling
AMSJob API
AMSResults API
AMS worker
AMSWorker API
AMSWorkerResults API
AMSWorkerPool API
Analysis tools: Densf, FCF, analysis
KF files
COSMO-RS
Settings
Settings with multiple compound
ADF and CRSJob
COSMO-RS Parameters
Data analyses and plotting
API
ADF (pre-2020 version)
Preparing input
Preparing runscript
API
ReaxFF (pre-2019 version)
Other programs
Dirac
Preparing a calculation
Results extraction
API
Crystal
Preparing a calculation
Molecule parsing
Results extraction
Example
API
DFTB+
Preparing a calculation
Results extraction
Example
API
CP2K
Settings
Molecule parsing
Loading jobs
Molecule loading
API
ORCA
API
MOPAC (standalone program)
Preparing input
API
Examples
Simple examples
Helium dimer dissociation curve
Geometry optimization of water
Many jobs in parallel
Benchmark accuracy of basis sets
Workflow: filtering molecules based on excitation energies
Charge transfer integrals with ADF
Advanced examples
Tuning the range separation
Recipes
ADF and COSMO-RS workflow
ADF fragment job
Reorganization Energy
NBO with ADF
Numerical gradients
Numerical Hessian
ReaxFF molecule gun
Global Minimum Search
Vibrational analysis with ASE
Example
API
Citations
PLAMS
Documentation
/
PLAMS
/
Index
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
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N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
_
__add__() (Molecule method)
__array__() (Molecule method)
__contains__() (KFFile method)
(Settings method)
__delattr__() (Settings method)
__delitem__() (Settings method)
__getattr__() (Settings method)
__getitem__() (KFFile method)
(Molecule method)
(Results method)
(Settings method)
__getstate__() (Job method)
(Molecule method)
__iadd__() (Molecule method)
__init__() (AMSAnalysisJob method)
(Atom method)
(Bond method)
(CRSJob method)
(Cp2kJob method)
(DensfJob method)
(DiracJob method)
(FCFJob method)
(GridRunner method)
(IRJob method)
(Job method)
(JobManager method)
(JobRunner method)
(KFFile method)
(KFHistory method)
(KFReader method)
(Molecule method)
(MultiJob method)
(PeriodicTable method)
(Results method)
(SCMJob method)
(Settings method)
(SingleJob method)
(Units method)
(VibrationsJob method)
__iter__() (Atom method)
(Bond method)
(KFFile method)
(KFReader method)
(Molecule method)
(MultiJob method)
(Settings method)
__len__() (Molecule method)
__missing__() (Settings method)
__new__() (_MetaResults static method)
(_MetaRunner static method)
__repr__() (Settings method)
__round__() (Molecule method)
__setattr__() (Settings method)
__setitem__() (KFFile method)
(Settings method)
__setstate__() (Molecule method)
__str__() (Atom method)
(Bond method)
(Molecule method)
(Settings method)
_atom_symbol() (SCMJob static method)
_atomic_numbers_input_order() (ADFResults method)
(MOPACResults method)
(SCMResults method)
_autodetect() (GridRunner method)
(KFReader method)
_caller_name_and_arg() (in module scm.plams.core.results)
_check_hash() (JobManager method)
_check_queue() (GridRunner method)
_clean() (JobManager method)
(Results method)
_construct_array_dict() (CRSResults method)
_convert_lattice() (ReaxFFJob static method)
_copy_to() (Results method)
_create_index() (KFReader method)
_datablocks() (KFReader static method)
_dict_to_df() (CRSResults static method)
_execute() (Job method)
(MultiJob method)
(SingleJob method)
_export_attribute() (Results method)
(SCMResults method)
_extract_hessian() (ADFResults method)
_finalize() (Job method)
_get_array_dict() (CRSResults method)
_get_data() (KFReader method)
_get_property() (scm.plams.tools.periodic_table.PeriodicTable class method)
_get_ready() (Cp2kJob method)
(DiracJob method)
(Job method)
(MultiJob method)
(ReaxFFJob method)
(SingleJob method)
_get_single_value() (SCMResults method)
_in_thread() (in module scm.plams.core.jobrunner)
_int2inp() (ADFResults method)
(SCMResults method)
_kfpath() (SCMResults method)
_kfpresent() (SCMResults method)
_limit() (in module scm.plams.core.jobrunner)
_log_status() (Job method)
_MetaResults (class in scm.plams.core.results)
_MetaRunner (class in scm.plams.core.jobrunner)
_mol_from_rkf_section() (Molecule static method)
_notify() (MultiJob method)
_parse() (KFReader method)
_prepare() (Job method)
_privileged_access() (in module scm.plams.core.results)
_process_file() (Results method)
_read_block() (KFReader method)
_register() (JobManager method)
_register_name() (JobManager method)
_remove_mol() (AMSAnalysisJob method)
(DensfJob method)
(FCFJob method)
(SCMJob method)
_replace_job_name() (Results static method)
_restrict() (in module scm.plams.core.results)
_result_type (Cp2kJob attribute)
(CRSJob attribute)
_run_job() (JobRunner method)
_serialize_input() (SCMJob method)
_serialize_mol() (AMSAnalysisJob method)
(DensfJob method)
(FCFJob method)
(SCMJob method)
_split() (KFFile static method)
_str() (KFFile static method)
(Settings method)
_write_ffield() (ReaxFFJob method)
_write_geofile() (ReaxFFJob method)
A
add_atom() (Molecule method)
add_bond() (Molecule method)
add_Hs() (in module scm.plams.interfaces.molecule.rdkit)
add_molecule() (Molecule method)
add_to_class() (in module scm.plams.core.functions)
add_to_instance() (in module scm.plams.core.functions)
ADFResults (class in scm.plams.interfaces.adfsuite.adf)
align_lattice() (Molecule method)
AMSAnalysisJob (class in scm.plams.interfaces.adfsuite.amsanalysis)
AMSJob (class in scm.plams.interfaces.adfsuite.ams)
AMSResults (class in scm.plams.interfaces.adfsuite.ams)
AMSWorker (class in scm.plams.interfaces.adfsuite.amsworker)
AMSWorkerPool (class in scm.plams.interfaces.adfsuite.amsworker)
AMSWorkerResults (class in scm.plams.interfaces.adfsuite.amsworker)
angle() (Atom method)
(in module scm.plams.tools.geometry)
apply_reaction_smarts() (in module scm.plams.interfaces.molecule.rdkit)
apply_strain() (Molecule method)
apply_template() (in module scm.plams.interfaces.molecule.rdkit)
as_array() (Molecule method)
as_dict() (Molecule method)
(Settings method)
as_vector() (Bond method)
assign_chirality() (Molecule method)
Atom (class in scm.plams.mol.atom)
awk_file() (Results method)
awk_output() (Results method)
axis_rotation_matrix() (in module scm.plams.tools.geometry)
B
bend() (in module scm.plams.mol.identify)
Bond (class in scm.plams.mol.bond)
bond_matrix() (Molecule method)
C
call() (GridRunner method)
(JobRunner method)
cell_shape() (in module scm.plams.tools.geometry)
check() (AMSAnalysisJob method)
(AMSJob method)
(Cp2kJob method)
(CrystalJob method)
(DFTBPlusJob method)
(DensfJob method)
(DiracJob method)
(Job method)
(MOPACJob method)
(MultiJob method)
(ORCAJob method)
(ReaxFFJob method)
(SCMJob method)
(SingleJob method)
clear() (in module scm.plams.mol.identify)
closest_atom() (Molecule method)
collect() (AMSResults method)
(DiracResults method)
(Results method)
(SCMResults method)
conversion_ratio() (scm.plams.tools.units.Units class method)
convert() (scm.plams.tools.units.Units class method)
copy() (Molecule method)
(Settings method)
cos_to_coskf() (CRSJob static method)
Cp2kJob (class in scm.plams.interfaces.thirdparty.cp2k)
Cp2kResults (class in scm.plams.interfaces.thirdparty.cp2k)
Cp2kSettings2Mol() (in module scm.plams.interfaces.thirdparty.cp2k)
CRSJob (class in scm.plams.interfaces.adfsuite.crs)
CRSResults (class in scm.plams.interfaces.adfsuite.crs)
CrystalJob (class in scm.plams.interfaces.thirdparty.crystal)
D
delete_all_bonds() (Molecule method)
delete_atom() (Molecule method)
delete_bond() (Molecule method)
delete_section() (KFFile method)
DensfJob (class in scm.plams.interfaces.adfsuite.densf)
DFTBPlusJob (class in scm.plams.interfaces.thirdparty.dftbplus)
DFTBPlusResults (class in scm.plams.interfaces.thirdparty.dftbplus)
dihedral() (in module scm.plams.tools.geometry)
DiracJob (class in scm.plams.interfaces.thirdparty.dirac)
DiracResults (class in scm.plams.interfaces.thirdparty.dirac)
distance_array() (in module scm.plams.tools.geometry)
distance_to() (Atom method)
distance_to_mol() (Molecule method)
distance_to_point() (Molecule method)
E
engine_names() (AMSResults method)
F
FCFJob (class in scm.plams.interfaces.adfsuite.fcf)
find_bond() (Molecule method)
find_case() (Settings method)
find_permutation() (in module scm.plams.mol.identify)
finish() (in module scm.plams.core.functions)
flatten() (Settings method)
from_array() (Molecule method)
from_dict() (scm.plams.mol.molecule.Molecule class method)
from_elements() (scm.plams.mol.molecule.Molecule class method)
from_inputfile() (scm.plams.interfaces.adfsuite.ams.AMSJob class method)
(scm.plams.interfaces.adfsuite.scmjob.SCMJob class method)
from_rdmol() (in module scm.plams.interfaces.molecule.rdkit)
from_sequence() (in module scm.plams.interfaces.molecule.rdkit)
from_smarts() (in module scm.plams.interfaces.molecule.rdkit)
from_smiles() (in module scm.plams.interfaces.molecule.rdkit)
fromASE() (in module scm.plams.interfaces.molecule.ase)
full_runscript() (SingleJob method)
G
GeometryOptimization() (AMSWorker method)
GeometryOptimizations() (AMSWorkerPool method)
get_activity_coefficient() (CRSResults method)
get_ASEVib() (VibrationsResults method)
get_atomic_charges() (DFTBPlusResults method)
get_atomic_number() (scm.plams.tools.periodic_table.PeriodicTable class method)
get_backbone_atoms() (in module scm.plams.interfaces.molecule.rdkit)
get_center_of_mass() (Molecule method)
get_charges() (AMSResults method)
(AMSWorkerResults method)
get_chirality() (Molecule method)
get_conformations() (in module scm.plams.interfaces.molecule.rdkit)
get_connectors() (scm.plams.tools.periodic_table.PeriodicTable class method)
get_dipole_vector() (ADFResults method)
get_dipolegradients() (AMSResults method)
(AMSWorkerResults method)
get_dipolemoment() (AMSResults method)
(AMSWorkerResults method)
get_dispersion() (Cp2kResults method)
get_elastictensor() (AMSResults method)
(AMSWorkerResults method)
get_electronegative() (scm.plams.tools.periodic_table.PeriodicTable class method)
get_energy() (ADFResults method)
(AMSResults method)
(AMSWorkerResults method)
(CRSResults method)
(Cp2kResults method)
(DFTBPlusResults method)
get_energy_decomposition() (ADFResults method)
get_engine_properties() (AMSResults method)
get_engine_results() (AMSResults method)
get_errormsg() (AMSJob method)
(AMSResults method)
(AMSWorkerResults method)
get_file_chunk() (Results method)
get_formula() (Molecule method)
get_frequencies() (ADFResults method)
(AMSResults method)
get_gradients() (ADFResults method)
(AMSResults method)
(AMSWorkerResults method)
get_hessian() (ADFResults method)
(AMSResults method)
(AMSWorkerResults method)
get_hirshfeld_charges() (Cp2kResults method)
get_history_molecule() (AMSResults method)
get_history_property() (AMSResults method)
get_history_variables() (AMSResults method)
get_input() (AMSJob method)
(Cp2kJob method)
(CrystalJob method)
(DFTBPlusJob method)
(DiracJob method)
(MOPACJob method)
(ORCAJob method)
(ReaxFFJob method)
(SCMJob method)
(SingleJob method)
get_input_molecule() (ADFResults method)
(AMSResults method)
(AMSWorkerResults method)
get_main_molecule() (ADFResults method)
(AMSResults method)
(AMSWorkerResults method)
get_mass() (Molecule method)
(scm.plams.tools.periodic_table.PeriodicTable class method)
get_metallic() (scm.plams.tools.periodic_table.PeriodicTable class method)
get_molecule() (AMSResults method)
(DFTBPlusResults method)
(SCMResults method)
get_mulliken_charges() (Cp2kResults method)
get_multigrid_info() (Cp2kResults method)
get_nested() (Settings method)
get_output_chunk() (Results method)
get_prop_names() (CRSResults method)
get_properties() (ADFResults method)
(SCMResults method)
get_property_at_step() (AMSResults method)
get_radius() (scm.plams.tools.periodic_table.PeriodicTable class method)
get_results() (CRSResults method)
get_rkf_skeleton() (AMSResults method)
get_runscript() (AMSJob method)
(Cp2kJob method)
(CrystalJob method)
(DFTBPlusJob method)
(DiracJob method)
(MOPACJob method)
(ORCAJob method)
(ReaxFFJob method)
(SCMJob method)
(SingleJob method)
get_runtime() (Cp2kResults method)
get_sigma_potential() (CRSResults method)
get_sigma_profile() (CRSResults method)
get_skeleton() (KFFile method)
get_stresstensor() (AMSResults method)
(AMSWorkerResults method)
get_substructure() (in module scm.plams.interfaces.molecule.rdkit)
get_symbol() (scm.plams.tools.periodic_table.PeriodicTable class method)
get_timings() (ADFResults method)
(AMSResults method)
grep_file() (Results method)
grep_output() (Results method)
GridRunner (class in scm.plams.core.jobrunner)
guess_bonds() (Molecule method)
H
hash() (Job method)
(MultiJob method)
(SingleJob method)
hash_input() (AMSJob method)
(ReaxFFJob method)
(SCMJob method)
(SingleJob method)
hash_runscript() (SingleJob method)
I
in_ring() (Molecule method)
index() (Molecule method)
init() (in module scm.plams.core.functions)
initialize() (in module scm.plams.mol.identify)
IRJob (class in scm.plams.recipes.vibration)
is_aromatic() (Bond method)
iter() (KFHistory method)
iter_optional() (KFHistory method)
iterate() (in module scm.plams.mol.identify)
J
Job (class in scm.plams.core.basejob)
JobManager (class in scm.plams.core.jobmanager)
JobRunner (class in scm.plams.core.jobrunner)
K
KFFile (class in scm.plams.tools.kftools)
KFHistory (class in scm.plams.tools.kftools)
KFReader (class in scm.plams.tools.kftools)
knock() (in module scm.plams.mol.identify)
L
label() (Molecule method)
label_atoms() (in module scm.plams.mol.identify)
length() (Bond method)
load() (in module scm.plams.core.functions)
load_all() (in module scm.plams.core.functions)
load_external() (scm.plams.core.basejob.SingleJob class method)
load_job() (JobManager method)
load_reaxff_control() (in module scm.plams.interfaces.adfsuite.reaxff)
log() (in module scm.plams.core.functions)
M
map_to_central_cell() (Molecule method)
merge() (Settings method)
modify_atom() (in module scm.plams.interfaces.molecule.rdkit)
mol2CrystalConf() (in module scm.plams.interfaces.thirdparty.crystal)
Molecule (class in scm.plams.interfaces.molecule.ase)
(class in scm.plams.mol.molecule)
molecule_name() (in module scm.plams.mol.identify)
MOPACJob (class in scm.plams.interfaces.adfsuite.mopac)
MOPACResults (class in scm.plams.interfaces.adfsuite.mopac)
move_to() (Atom method)
MultiJob (class in scm.plams.core.basejob)
N
name (AMSResults attribute)
(AMSWorkerResults attribute)
neighbors() (Atom method)
(Molecule method)
new_children() (MultiJob method)
(VibrationsJob method)
new_name() (in module scm.plams.mol.identify)
newkf() (SCMResults method)
O
ok() (AMSResults method)
(AMSWorkerResults method)
(Job method)
ORCAJob (class in scm.plams.interfaces.thirdparty.orca)
other_end() (Bond method)
other_jobs() (MultiJob method)
P
partition_protein() (in module scm.plams.interfaces.molecule.rdkit)
PeriodicTable (class in scm.plams.tools.periodic_table)
perturb_atoms() (Molecule method)
perturb_lattice() (Molecule method)
pickle() (Job method)
plot() (CRSResults method)
postrun() (IRJob method)
(Job method)
(VibrationsJob method)
prerun() (Job method)
print_molecule() (ORCAJob method)
R
read() (KFFile method)
(KFReader method)
(Molecule method)
read_all() (KFHistory method)
read_molecules() (in module scm.plams.core.functions)
read_rkf_section() (AMSResults method)
read_section() (KFFile method)
readarray() (SCMResults method)
readase() (Molecule method)
,
[1]
readkf() (SCMResults method)
readpdb() (in module scm.plams.interfaces.molecule.rdkit)
(Molecule method)
readrkf() (AMSResults method)
readxyz() (Molecule method)
ReaxFFJob (class in scm.plams.interfaces.adfsuite.reaxff)
recreate_molecule() (ADFResults method)
(AMSResults method)
(Results method)
recreate_settings() (ADFResults method)
(AMSResults method)
(Cp2kResults method)
(Results method)
refresh() (AMSResults method)
(Results method)
(SCMResults method)
remove_child() (MultiJob method)
remove_job() (JobManager method)
rename() (Results method)
resize() (Bond method)
resize_bond() (Molecule method)
Results (class in scm.plams.core.results)
rkfpath() (AMSResults method)
rotate() (Atom method)
(Bond method)
(Molecule method)
rotate_bond() (Molecule method)
rotate_lattice() (Molecule method)
rotation_matrix() (in module scm.plams.tools.geometry)
round_coords() (Molecule method)
run() (Job method)
run_crs_ams() (in module scm.plams.recipes.ams_crs)
S
save() (KFFile method)
scm.plams.interfaces.molecule.ase (module)
scm.plams.interfaces.molecule.rdkit (module)
scm.plams.tools.geometry (module)
SCMJob (class in scm.plams.interfaces.adfsuite.scmjob)
SCMResults (class in scm.plams.interfaces.adfsuite.scmjob)
sections() (KFFile method)
separate() (Molecule method)
set_atoms_id() (Molecule method)
set_connectors() (scm.plams.tools.periodic_table.PeriodicTable class method)
set_integer_bonds() (Molecule method)
set_mass() (scm.plams.tools.periodic_table.PeriodicTable class method)
set_nested() (Settings method)
set_radius() (scm.plams.tools.periodic_table.PeriodicTable class method)
Settings (class in scm.plams.core.settings)
settings_to_mol() (AMSJob static method)
(SCMJob static method)
SingleJob (class in scm.plams.core.basejob)
SinglePoint() (AMSWorker method)
SinglePoints() (AMSWorkerPool method)
soft_update() (Settings method)
stop() (AMSWorker method)
(AMSWorkerPool method)
str() (Atom method)
substitute() (Molecule method)
supercell() (Molecule method)
suppress_missing() (scm.plams.core.settings.Settings class method)
T
to_input_order() (SCMResults method)
to_rdmol() (in module scm.plams.interfaces.molecule.rdkit)
toASE() (in module scm.plams.interfaces.molecule.ase)
translate() (Atom method)
(Molecule method)
twist() (in module scm.plams.mol.identify)
U
unflatten() (Settings method)
unique_atoms() (in module scm.plams.mol.identify)
unit_cell_volume() (Molecule method)
Units (class in scm.plams.tools.units)
unset_atoms_id() (Molecule method)
update() (Settings method)
V
vector_to() (Atom method)
VibrationsJob (class in scm.plams.recipes.vibration)
VibrationsResults (class in scm.plams.recipes.vibration)
W
wait() (Results method)
wrap() (Molecule method)
write() (KFFile method)
(Molecule method)
writease() (Molecule method)
,
[1]
writepdb() (in module scm.plams.interfaces.molecule.rdkit)