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Table of contents
1. Introduction
1.1. Parameter Fitting: A Lennard-Jones Example
1.2. General Application
2. Getting Started
2.1. Installation
2.2. Unit Tests
2.3. First Steps with ParAMS
3. Components
3.1. Architecture Quick Reference
3.2. Collections
3.2.1. Job Collection
3.2.1.1. Adding Jobs
3.2.1.2. Working with the Collection
3.2.1.3. I/O
3.2.1.4. Generating AMSJobs
3.2.1.5. Running Collection Jobs
3.2.2. Engine Collection
3.2.3. Collections API
3.2.3.1. JCEntry
3.2.3.2. JobCollection
3.2.3.3. Engine
3.2.3.4. EngineCollection
3.2.3.5. Collection Base Class
3.3. Data Set
3.3.1. Adding Entries
3.3.2. Accessing Entries
3.3.3. Removing Entries
3.3.4. Adding External Reference Data
3.3.5. Calculating and Adding Reference Data with AMS
3.3.6. Storage and I/O
3.3.7. Calculating the Loss Function Value
3.3.8. Checking for Consistency with a given Job Collection
3.3.9. Splitting into Subsets
3.3.10. Data Set Entry API
3.3.11. Data Set API
3.4. Extractors and Comparators
3.4.1. Supported Data Structures
3.4.2. Custom Comparators
3.4.3. Available Extractors
3.4.3.1. Distance
3.4.3.2. Angles
3.4.3.3. Dihedral
3.4.3.4. RMSD
3.4.3.5. Energy
3.4.3.6. Forces
3.4.3.7. Hessian
3.4.3.8. Stress Tensor
3.4.3.9. Charges
3.4.3.10. Vibrational Frequencies
3.4.3.11. PES
3.5. Parameter Interfaces
3.5.1. Available Parameter Interfaces
3.5.1.1. xTB
3.5.1.2. ReaxFF
3.5.1.3. Lennard Jones
3.5.2. Parameter Interface Basics
3.5.3. Working with Parameters
3.5.4. The Active Parameters Subset
3.5.5. Storage
3.5.5.1. Lossless Storage
3.5.6. Relation to PLAMS Settings
3.5.7. Parameter API
3.5.8. Interface Base Class API
3.6. Optimizers
3.6.1. CMA-ES
3.6.1.1. List of valid
cmasettings
3.6.1.2. References
3.6.2. Scipy
3.6.3. Nevergrad
3.6.4. Adaptive Rate MC
3.6.5. Simple Grid Optimizer
3.6.6. Optimizer Base Class
3.6.6.1. BaseOptimizer API
3.6.6.2. MinimizeResult API
3.7. Optimization
3.7.1. Optimization Setup
3.7.2. Optimization API
3.8. Parallelization
3.9. Constraints
3.10. Callbacks
3.10.1. Logger
3.10.2. Timeout
3.10.3. Target Value
3.10.4. Maximum Iterations
3.10.5. Early Stopping
3.10.6. Stopfile
3.10.7. Time per Evaluation
3.10.8. Load Average
3.10.9. User-Defined Callbacks
3.10.10. Callback API
3.11. Loss Functions
3.11.1. Least Absolute Error
3.11.2. Mean Absolute Error
3.11.3. Root-Mean-Square Error
3.11.4. Sum of Squares Error
3.11.5. Loss Function API
3.12. Utilities
3.12.1. Optimization History
3.12.2. Active Parameter Search
3.12.3. Data Set Sensitivity
3.12.4. Plotting Funcitons
3.12.5. ReaxFF Conversion
4. ParAMS Main Script
4.1. The Configuration File
5. Examples
5.1. Parameterization of a Lennard-Jones Engine for Argon
5.1.1. Understanding and running the example
5.1.2. Evaluating the Optimization
5.1.3. Modifying the example
5.2. Parameterization of a Water Force Field with ReaxFF
5.2.1. Complete Example Script
5.2.2. Changing the Example Script
5.3. Refitting HF Charges with the ACKS2 Model
5.3.1. The Config File
5.3.2. Preparing the YAML Files from Input
5.3.3. Running the Optimization
5.3.4. Comparing the new parameters
5.3.5. Playing with the example
6. Changelog
ParAMS
Documentation
/
ParAMS
/
Index
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
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V
|
W
|
X
_
__add__() (BaseCollection method)
(DataSet method)
__call__() (BaseCollection method)
(BaseParameters method)
(Callback method)
(DataSet method)
(Loss method)
__contains__() (BaseCollection method)
(DataSet method)
__delitem__() (BaseCollection method)
(DataSet method)
__eq__() (BaseCollection method)
(BaseParameters method)
(DataSet method)
__getitem__() (BaseCollection method)
(BaseParameters method)
(DataSet method)
(History method)
__init__() (ActiveParameterSearch method)
(ARMCOptimizer method)
(BaseCollection method)
(BaseParameters method)
(CMAOptimizer method)
(DataSet method)
(Engine method)
(JCEntry method)
(LennardJonesParams method)
(Loss method)
(Nevergrad method)
(Optimization method)
(ReaxParams method)
(Scipy method)
(SimpleGridOptimizer method)
(SubsetScan method)
(XTBParams method)
__iter__() (BaseCollection method)
(BaseParameters method)
(DataSet method)
(History method)
__len__() (BaseCollection method)
(BaseParameters method)
(DataSet method)
(History method)
__ne__() (BaseCollection method)
(DataSet method)
__repr__() (Loss method)
__setitem__() (BaseCollection method)
__str__() (BaseCollection method)
(DataSet method)
(Engine method)
(JCEntry method)
(Optimization method)
__sub__() (DataSet method)
_check_entry() (BaseCollection method)
_inner() (ARMCOptimizer method)
A
active (BaseParameters attribute)
ActiveParameterSearch (class in scm.params.common.parametersearch)
add() (History method)
add_entry() (BaseCollection method)
(DataSet method)
ARMCOptimizer (class in scm.params.optimizers.armc)
B
BaseCollection (class in scm.params.core.basecollection)
BaseOptimizer (class in scm.params.optimizers.base)
BaseParameters (class in scm.params.parameterinterfaces.base)
bounds (ARMCOptimizer attribute)
C
calculate_reference() (DataSet method)
Callback (class in scm.params.core.callbacks)
callstop() (ARMCOptimizer static method)
check_consistency() (DataSet method)
CMAOptimizer (class in scm.params.optimizers.cma)
copy() (DataSet method)
(Engine method)
(JCEntry method)
D
DataSet (class in scm.params.core.dataset)
DataSetEntry (class in scm.params.core.dataset)
delete() (Optimization method)
duplicate_entry() (JobCollection method)
E
EarlyStopping (class in scm.params.core.callbacks)
Engine (class in scm.params.core.engines)
EngineCollection (class in scm.params.core.engines)
evaluate() (DataSet method)
extract() (in module scm.params.extractors.angles)
(in module scm.params.extractors.charges)
(in module scm.params.extractors.dihedral)
(in module scm.params.extractors.distance)
(in module scm.params.extractors.energy)
(in module scm.params.extractors.forces)
(in module scm.params.extractors.hessian)
(in module scm.params.extractors.pes)
(in module scm.params.extractors.rmsd)
(in module scm.params.extractors.stresstensor)
(in module scm.params.extractors.vibfreq)
F
from_jobids() (DataSet method)
(JobCollection method)
fx (History attribute)
G
geo_to_params() (in module scm.params.common.reaxff_converter)
get() (DataSet method)
get_engine() (BaseParameters method)
(LennardJonesParams method)
(ReaxParams method)
(XTBParams method)
get_is_active() (ActiveParameterSearch method)
H
History (class in scm.params.common.history)
I
index() (BaseParameters method)
(DataSet method)
is_active (BaseParameters attribute)
is_pipeable() (JCEntry method)
items() (BaseCollection method)
J
JCEntry (class in scm.params.core.jobcollection)
JobCollection (class in scm.params.core.jobcollection)
jobids (DataSet attribute)
K
keys() (BaseCollection method)
L
LAE (class in scm.params.core.lossfunctions)
LennardJonesParams (class in scm.params.parameterinterfaces.lennardjones)
load() (ActiveParameterSearch static method)
(BaseCollection method)
(DataSet method)
(EngineCollection method)
(History method)
(JobCollection method)
load_yaml() (JobCollection method)
LoadAvg (class in scm.params.core.callbacks)
Logger (class in scm.params.core.callbacks)
Loss (class in scm.params.core.lossfunctions)
M
MAE (class in scm.params.core.lossfunctions)
makesteps_exp() (SubsetScan method)
max() (History method)
MaxIter (class in scm.params.core.callbacks)
maxjobs() (DataSet method)
min() (History method)
minimize() (ARMCOptimizer method)
(BaseOptimizer method)
(SimpleGridOptimizer method)
MinimizeResult (class in scm.params.optimizers.base)
move() (ARMCOptimizer method)
N
names (BaseParameters attribute)
Nevergrad (class in scm.params.optimizers.ng)
O
on_end() (Callback method)
Optimization (class in scm.params.core.parameteroptimization)
optimize() (Optimization method)
P
ParallelLevels (class in scm.params.common.parallellevels)
Parameter (class in scm.params.parameterinterfaces.base)
phi_apply() (ARMCOptimizer method)
phi_update() (ARMCOptimizer method)
pickle_dump() (BaseParameters method)
(DataSet method)
(JobCollection method)
pickle_load() (DataSet method)
(JobCollection method)
(scm.params.parameterinterfaces.base.BaseParameters class method)
plot_contributions() (in module scm.params.common.plotting)
plot_history() (in module scm.params.common.plotting)
plot_residuals() (in module scm.params.common.plotting)
plotscan() (SubsetScan method)
predictions_from_residuals() (DataSet method)
print_contributions() (DataSet method)
print_residuals() (DataSet method)
R
random() (DataSet method)
range (BaseParameters attribute)
ReaxParams (class in scm.params.parameterinterfaces.reaxff)
remove() (DataSet method)
remove_entry() (BaseCollection method)
rename_entry() (BaseCollection method)
reset() (Callback method)
RMSE (class in scm.params.core.lossfunctions)
run() (JobCollection method)
S
save() (ActiveParameterSearch method)
scan() (ActiveParameterSearch method)
(SubsetScan method)
Scipy (class in scm.params.optimizers.scipy)
scm.params.common.reaxff_converter (module)
SimpleGridOptimizer (class in scm.params.optimizers.simplegrid)
split() (DataSet method)
SSE (class in scm.params.core.lossfunctions)
Stopfile (class in scm.params.core.callbacks)
store() (BaseCollection method)
(DataSet method)
(EngineCollection method)
(JobCollection method)
SubsetScan (class in scm.params.common.subsetscan)
summary() (Optimization method)
T
TargetValue (class in scm.params.core.callbacks)
Timeout (class in scm.params.core.callbacks)
TimePerEval (class in scm.params.core.callbacks)
to_amsjobs() (JobCollection method)
trainset_to_params() (in module scm.params.common.reaxff_converter)
V
values() (BaseCollection method)
W
write() (BaseParameters method)
(History method)
(LennardJonesParams method)
(ReaxParams method)
(XTBParams method)
X
x (BaseParameters attribute)
(History attribute)
XTBParams (class in scm.params.parameterinterfaces.xtb)