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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. Running PLAMS
2.4. Defaults file
2.5. Master script
2.5.1. Working folder location
2.5.2. Passing variables
2.5.3. Importing past jobs
2.5.4. Restarting failed script
2.5.5. Multiple input scripts
3. Components overview
3.1. Settings
3.1.1. Tree-like structure
3.1.2. Dot notation
3.1.3. Global settings
3.1.4. API
3.2. Jobs
3.2.1. Preparing a job
3.2.1.1. Contents of job’s 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 crashed 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
3.7.2. Atom
3.7.3. Bond
3.8. Utilities
3.8.1. Periodic Table
3.8.2. Units
3.8.3. Geometry tools
4. Interfaces
4.1. ADF Suite
4.1.1. ADF, BAND and DFTB
4.1.1.1. Preparing input
4.1.1.2. Special atoms in ADF
4.1.1.3. Preparing runscript
4.1.1.4. Results extraction
4.1.1.5. API
4.1.2. Other tools: Densf, FCF
4.1.3. KF files
4.1.3.1. KFFile
4.1.3.2. KFReader
4.2. MOPAC
4.2.1. Preparing input
4.2.2. API
4.3. Dirac
4.3.1. Preparing a calculation
4.3.1.1. Input
4.3.1.2. Runscript
4.3.2. Results extraction
4.3.3. API
PLAMS
Documentation
/
PLAMS
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Index
Index
_
|
A
|
B
|
C
|
D
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
V
|
W
_
__add__() (Molecule method)
__delattr__() (Settings method)
__getattr__() (Settings method)
__getitem__() (KFFile method)
(Molecule method)
(Results method)
__getstate__() (Job method)
__iadd__() (Molecule method)
__iter__() (Atom method)
(Bond method)
(KFFile method)
(KFReader method)
(Molecule method)
(MultiJob method)
(Settings method)
__len__() (Molecule method)
__missing__() (Settings method)
__reduce__() (Settings method)
__setattr__() (Settings method)
__setitem__() (KFFile method)
(Settings method)
__str__() (Atom method)
(Bond method)
(Molecule method)
_atom_symbol() (SCMJob static method)
_atomic_numbers_input_order() (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)
_copy_to() (Results method)
_create_index() (KFReader method)
_datablocks() (KFReader static method)
_execute() (Job method)
(MultiJob method)
(SingleJob method)
_export_attribute() (Results method)
(SCMResults method)
_filename() (SingleJob method)
_finalize() (Job method)
_full_runscript() (SingleJob method)
_get_data() (KFReader method)
_get_property() (scm.plams.tools.periodic_table.PeriodicTable class method)
_get_ready() (DiracJob method)
(Job method)
(MultiJob method)
(SingleJob method)
_get_single_value() (SCMResults method)
_in_thread() (in module scm.plams.core.jobrunner)
_int2inp() (SCMResults method)
_kfpath() (SCMResults method)
_limit() (in module scm.plams.core.jobrunner)
_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)
_reduce() (KFFile method)
(KFReader method)
(SCMJob method)
(SCMResults method)
_register() (JobManager method)
_register_name() (JobManager method)
_remove_mol() (SCMJob method)
_replace_job_name() (Results static method)
_restrict() (in module scm.plams.core.results)
_run_job() (JobRunner method)
_serialize_input() (SCMJob method)
_serialize_mol() (SCMJob method)
_split() (KFFile static method)
_str() (KFFile static method)
(Settings method)
A
add_atom() (Molecule method)
add_bond() (Molecule method)
add_to_class() (in module scm.plams.core.functions)
add_to_instance() (in module scm.plams.core.functions)
align_lattice() (Molecule method)
angle() (Atom method)
apply_strain() (Molecule method)
as_dict() (Molecule method)
(Settings method)
Atom (class in scm.plams.core.basemol)
awk_file() (Results method)
awk_output() (Results method)
B
Bond (class in scm.plams.core.basemol)
C
call() (GridRunner method)
(JobRunner method)
check() (DiracJob method)
(Job method)
(MOPACJob method)
(MultiJob method)
(SCMJob method)
closest_atom() (Molecule method)
collect() (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)
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)
DiracJob (class in scm.plams.interfaces.dirac)
DiracResults (class in scm.plams.interfaces.dirac)
distance_to() (Atom method)
distance_to_mol() (Molecule method)
distance_to_point() (Molecule method)
F
FCFJob (class in scm.plams.interfaces.adfsuite.fcf)
find_bond() (Molecule method)
find_case() (Settings method)
finish() (in module scm.plams.core.functions)
from_dict() (scm.plams.core.basemol.Molecule class method)
G
get_atomic_number() (scm.plams.tools.periodic_table.PeriodicTable class method)
get_center_of_mass() (Molecule method)
get_connectors() (scm.plams.tools.periodic_table.PeriodicTable class method)
get_file_chunk() (Results method)
get_formula() (Molecule method)
get_input() (DiracJob method)
(MOPACJob method)
(SingleJob method)
get_mass() (Molecule method)
(scm.plams.tools.periodic_table.PeriodicTable class method)
get_molecule() (SCMResults method)
get_output_chunk() (Results method)
get_properties() (SCMResults method)
get_radius() (scm.plams.tools.periodic_table.PeriodicTable class method)
get_runscript() (DiracJob method)
(MOPACJob method)
(SCMJob method)
(SingleJob method)
get_symbol() (scm.plams.tools.periodic_table.PeriodicTable class 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() (SCMJob method)
(SingleJob method)
hash_runscript() (SingleJob method)
I
init() (in module scm.plams.core.functions)
is_aromatic() (Bond method)
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)
L
length() (Bond method)
load() (in module scm.plams.core.functions)
load_all() (in module scm.plams.core.functions)
load_job() (JobManager method)
log() (in module scm.plams.core.functions)
M
merge() (Settings method)
Molecule (class in scm.plams.core.basemol)
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() (Molecule method)
new_children() (MultiJob method)
newkf() (SCMResults method)
O
other_end() (Bond method)
P
PeriodicTable (class in scm.plams.tools.periodic_table)
pickle() (Job method)
postrun() (Job method)
prerun() (Job method)
R
read() (KFFile method)
(KFReader method)
(Molecule method)
read_molecules() (in module scm.plams.core.basemol)
readkf() (SCMResults method)
refresh() (Results method)
(SCMResults method)
remove_job() (JobManager method)
rename() (Results method)
resize() (Bond method)
Results (class in scm.plams.core.results)
rotate() (Atom method)
(Molecule method)
rotate_bond() (Molecule method)
rotate_lattice() (Molecule method)
rotation_matrix() (in module scm.plams.tools.geometry)
run() (Job method)
S
save() (KFFile method)
SCMJob (class in scm.plams.interfaces.adfsuite.scmjob)
SCMResults (class in scm.plams.interfaces.adfsuite.scmjob)
separate() (Molecule method)
set_atoms_id() (Molecule method)
Settings (class in scm.plams.core.settings)
SingleJob (class in scm.plams.core.basejob)
soft_update() (Settings method)
str() (Atom method)
T
translate() (Atom method)
(Molecule method)
U
Units (class in scm.plams.tools.units)
unset_atoms_id() (Molecule method)
update() (Settings method)
V
vector_to() (Atom method)
W
wait() (Results method)
wrap() (Molecule method)
write() (KFFile method)
(Molecule method)