Free trial
Toggle navigation
Applications
Products
Support
About us
Search
Search
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. Global settings
3.1.4. 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
3.7.2. 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. Amsterdam Modeling Suite
4.1.1. Disclaimer about AMS2018
4.1.2. AMS driver
4.1.2.1. Preparing input
4.1.2.2. Preparing runscript
4.1.2.3. Molecule handling
4.1.2.4. AMSJob API
4.1.2.5. AMSResults API
4.1.3. ADF
4.1.3.1. Preparing input
4.1.3.2. Preparing runscript
4.1.3.3. API
4.1.4. ReaxFF
4.1.5. MOPAC
4.1.5.1. Preparing input
4.1.5.2. API
4.1.6. Analysis tools: Densf, FCF
4.1.7. KF files
4.1.8. Legacy: BAND, DFTB, UFF
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
4.3. Molecule interfaces
4.3.1. RDKit
4.3.2. ASE
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 fragment job
5.3.2. NBO with ADF
5.3.3. Numerical gradients
5.3.4. Numerical Hessian
5.3.5. ReaxFF molecule gun
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)
__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)
__setattr__() (Settings method)
__setitem__() (KFFile method)
(Settings method)
__str__() (Atom method)
(Bond method)
(Molecule method)
_atomic_numbers_input_order() (ADFResults 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)
_finalize() (Job 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)
_in_thread() (in module scm.plams.core.jobrunner)
_int2inp() (ADFResults 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)
_replace_job_name() (Results static method)
_restrict() (in module scm.plams.core.results)
_run_job() (JobRunner 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)
ADFJob (class in scm.plams.interfaces.adfsuite.adf)
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_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() (AMSJob method)
(CrystalJob method)
(DFTBPlusJob method)
(DiracJob method)
(Job method)
(MOPACJob method)
(MultiJob method)
(SingleJob method)
closest_atom() (Molecule method)
collect() (AMSResults method)
(DiracResults method)
(Results method)
conversion_ratio() (scm.plams.tools.units.Units class method)
convert() (scm.plams.tools.units.Units class method)
copy() (Molecule method)
(Settings method)
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)
DiracJob (class in scm.plams.interfaces.thirdparty.dirac)
DiracResults (class in scm.plams.interfaces.thirdparty.dirac)
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)
finish() (in module scm.plams.core.functions)
from_dict() (scm.plams.core.basemol.Molecule class method)
full_runscript() (SingleJob method)
G
get_atomic_charges() (DFTBPlusResults method)
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_dipole_vector() (ADFResults method)
get_energy() (ADFResults 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_gradients() (ADFResults method)
get_input() (AMSJob method)
(CrystalJob method)
(DFTBPlusJob method)
(DiracJob method)
(MOPACJob 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)
get_output_chunk() (Results method)
get_properties() (ADFResults method)
get_radius() (scm.plams.tools.periodic_table.PeriodicTable class method)
get_rkf_skeleton() (AMSResults method)
get_runscript() (AMSJob method)
(CrystalJob method)
(DFTBPlusJob method)
(DiracJob method)
(MOPACJob method)
(SingleJob method)
get_skeleton() (KFFile method)
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)
(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_external() (scm.plams.core.basejob.SingleJob class method)
load_job() (JobManager method)
log() (in module scm.plams.core.functions)
M
merge() (Settings method)
mol2CrystalConf() (in module scm.plams.interfaces.thirdparty.crystal)
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)
O
ok() (Job method)
other_end() (Bond method)
other_jobs() (MultiJob 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.functions)
read_rkf_section() (AMSResults method)
read_section() (KFFile method)
readrkf() (AMSResults method)
recreate_molecule() (ADFResults method)
(AMSResults method)
(Results method)
recreate_settings() (ADFResults method)
(AMSResults method)
(Results method)
refresh() (AMSResults method)
(Results method)
remove_job() (JobManager method)
rename() (Results method)
resize() (Bond method)
Results (class in scm.plams.core.results)
rkfpath() (AMSResults method)
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)
sections() (KFFile method)
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)