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Table of contents
1. Introduction
1.1. What is PLAMS
1.2. What can be done with PLAMS
1.3. Simple example
1.4. What PLAMS is
not
1.5. About this documentation
2. Getting started
2.1. Library contents
2.2. Installing PLAMS
2.3. Updating PLAMS
2.4. Running PLAMS
2.5. Defaults file
2.6. The launch script
2.6.1. Working folder location
2.6.2. Passing variables
2.6.3. Importing past jobs
2.6.4. Restarting failed script
2.6.5. Multiple input scripts
3. Components overview
3.1. Settings
3.1.1. Tree-like structure
3.1.2. Dot notation
3.1.3. Case sensitivity
3.1.4. Global settings
3.1.5. API
3.2. Jobs
3.2.1. Preparing a job
3.2.1.1. Contents of job settings
3.2.1.2. Default settings
3.2.2. Running a job
3.2.2.1. Name conflicts
3.2.2.2. Prerun and postrun methods
3.2.2.3. Preview mode
3.2.3. Job API
3.2.4. Single jobs
3.2.4.1. Subclassing SingleJob
3.2.5. Multijobs
3.2.5.1. Using MultiJob
3.3. Results
3.3.1. Files in the job folder
3.3.2. Synchronization of parallel job executions
3.3.2.1. Examples
3.3.3. Cleaning job folder
3.3.3.1. Cleaning for multijobs
3.3.4. API
3.4. Job runners
3.4.1. Local job runner
3.4.2. Remote job runner
3.5. Job manager
3.5.1. Rerun prevention
3.5.2. Pickling
3.5.3. Restarting scripts
3.5.4. API
3.6. Public functions
3.6.1. Logging
3.6.2. Binding decorators
3.7. Molecule
3.7.1. Molecule
3.7.1.1. Atom labeling
3.7.2. Atom
3.7.3. Bond
3.7.4. RDKit interface
3.7.5. ASE interface
3.8. Utilities
3.8.1. Periodic Table
3.8.2. Units
3.8.3. Geometry tools
4. Interfaces
4.1. Amsterdam Modeling Suite
4.1.1. AMS driver
4.1.1.1. Preparing input
4.1.1.2. Preparing runscript
4.1.1.3. Molecule handling
4.1.1.4. AMSJob API
4.1.1.5. AMSResults API
4.1.2. ADF
4.1.2.1. Preparing input
4.1.2.2. Preparing runscript
4.1.2.3. API
4.1.3. ReaxFF
4.1.4. Analysis tools: Densf, FCF
4.1.5. KF files
4.1.6. COSMO-RS
4.1.6.1. Settings
4.1.6.2. Settings with multiple compound
4.1.6.3. ADFJob and CRSJob
4.1.6.4. COSMO-RS Parameters
4.1.6.5. Data analyses and plotting
4.1.6.6. API
4.2. Other programs
4.2.1. Dirac
4.2.1.1. Preparing a calculation
4.2.1.2. Results extraction
4.2.1.3. API
4.2.2. Crystal
4.2.2.1. Preparing a calculation
4.2.2.2. Molecule parsing
4.2.2.3. Results extraction
4.2.2.4. Example
4.2.2.5. API
4.2.3. DFTB+
4.2.3.1. Preparing a calculation
4.2.3.2. Results extraction
4.2.3.3. Example
4.2.3.4. API
4.2.4. CP2K
4.2.4.1. Settings
4.2.4.2. Molecule parsing
4.2.4.3. Loading jobs
4.2.4.4. Molecule loading
4.2.4.5. API
4.2.5. ORCA
4.2.5.1. API
4.2.6. MOPAC (standalone program)
4.2.6.1. Preparing input
4.2.6.2. API
5. Examples
5.1. Simple examples
5.1.1. Charge transfer integrals with ADF
5.1.2. Dictionary MultiJob
5.2. Advanced examples
5.2.1. Tuning the range separation
5.3. Recipes
5.3.1. ADF and COSMO-RS workflow
5.3.2. ADF fragment job
5.3.3. NBO with ADF
5.3.4. Numerical gradients
5.3.5. Numerical Hessian
5.3.6. ReaxFF molecule gun
5.3.7. Global Minimum Search
5.3.8. Vibrational analysis with ASE
5.3.8.1. Example
5.3.8.2. API
6. Citations
PLAMS
Documentation
/
PLAMS
/
Index
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
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)
__iadd__() (Molecule method)
__init__() (AMSResults 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)
(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)
__setattr__() (Settings method)
__setitem__() (KFFile method)
(Settings 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)
_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() (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() (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)
AMSJob (class in scm.plams.interfaces.adfsuite.ams)
AMSResults (class in scm.plams.interfaces.adfsuite.ams)
angle() (Atom method)
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)
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)
check() (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_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
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_connectors() (scm.plams.tools.periodic_table.PeriodicTable class method)
get_dipole_vector() (ADFResults method)
get_dispersion() (Cp2kResults method)
get_energy() (ADFResults method)
(AMSResults method)
(CRSResults method)
(Cp2kResults method)
(DFTBPlusResults method)
get_energy_decomposition() (ADFResults method)
get_engine_properties() (AMSResults method)
get_engine_results() (AMSResults method)
get_file_chunk() (Results method)
get_formula() (Molecule method)
get_frequencies() (ADFResults method)
(AMSResults method)
get_gradients() (ADFResults method)
get_hessian() (ADFResults method)
get_hirshfeld_charges() (Cp2kResults method)
get_history_molecule() (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)
get_main_molecule() (ADFResults method)
(AMSResults method)
get_mass() (Molecule method)
(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_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_substructure() (in module scm.plams.interfaces.molecule.rdkit)
get_symbol() (scm.plams.tools.periodic_table.PeriodicTable class method)
get_timings() (ADFResults 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)
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)
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)
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
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
neighbors() (Atom method)
(Molecule method)
new_children() (MultiJob method)
(VibrationsJob method)
new_name() (in module scm.plams.mol.identify)
newkf() (SCMResults method)
O
ok() (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_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_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)
run() (Job method)
run_crs_adf() (in module scm.plams.recipes.adf_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_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)
soft_update() (Settings method)
str() (Atom method)
substitute() (Molecule method)
supercell() (Molecule method)
supress_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)