gridmaker
latest
Overview:
General Workflow
Parameter-search Grid
Interaction Parameters
Systems and Topologies
Coordinates
Protocols
Properties
Surrogate Model
Score
Grid Shifting
Program Usage:
Command-line
Customization API
Input File
Output Files
Post-processing
Restarting a run
Validation mode
Example Applications:
Tutorial
gridmaker
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Index
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Index
A
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C
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D
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F
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G
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I
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L
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M
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N
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P
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S
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T
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U
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V
A
add_custom_component_property() (in module gmak.api)
add_custom_composite_property() (in module gmak.api)
add_custom_gridshifter() (in module gmak.api)
add_custom_protocol() (in module gmak.api)
add_custom_score() (in module gmak.api)
add_custom_surrogate_model() (in module gmak.api)
add_custom_system() (in module gmak.api)
add_gmx_custom_parameter_writer() (in module gmak.api)
C
calc_extend() (in module gmak.api_signatures)
calc_initial_len() (in module gmak.api_signatures)
calc_score() (in module gmak.api_signatures)
calc_score_err() (in module gmak.api_signatures)
calculator() (in module gmak.api_signatures)
component_calculator() (in module gmak.api_signatures)
composite_calculator() (in module gmak.api_signatures)
compute() (in module gmak.api_signatures)
compute_pareto() (gmak.post_processing.GmakOutput method)
CustomParameter (gmak.interaction_parameter.InteractionParameterType attribute)
D
derives_from_atom() (gmak.interaction_parameter.InteractionPair method)
F
flat2tuple() (in module gmak.cartesiangrid)
from_gmak_bin() (gmak.post_processing.GmakOutput class method)
G
get_dataframe() (gmak.post_processing.GmakOutput method)
get_last_frame() (in module gmak.api_signatures)
globalLogger (in module gmak.logger)
GmakOutput (class in gmak.post_processing)
gmx_custom_parameter_writer() (in module gmak.api_signatures)
GmxTopologyOutput (class in gmak.gmx_system)
groupby_X() (gmak.post_processing.GmakOutput method)
I
indent() (gmak.logger.Logger method)
InputParameters (class in gmak.custom_attributes.CustomizableAttributesMixin)
InteractionAtom (class in gmak.interaction_parameter)
InteractionPair (class in gmak.interaction_parameter)
InteractionParameter (class in gmak.interaction_parameter)
InteractionParameterType (class in gmak.interaction_parameter)
L
LJ_14_V (gmak.interaction_parameter.InteractionParameterType attribute)
LJ_14_W (gmak.interaction_parameter.InteractionParameterType attribute)
LJ_V (gmak.interaction_parameter.InteractionParameterType attribute)
LJ_W (gmak.interaction_parameter.InteractionParameterType attribute)
Logger (class in gmak.logger)
M
MacroParameter (gmak.interaction_parameter.InteractionParameterType attribute)
N
name (gmak.interaction_parameter.InteractionAtom property)
(gmak.interaction_parameter.InteractionParameter property)
name_i (gmak.interaction_parameter.InteractionPair property)
name_j (gmak.interaction_parameter.InteractionPair property)
P
pairs_exclude (gmak.interaction_parameter.InteractionAtom property)
pairs_include (gmak.interaction_parameter.InteractionAtom property)
particles (gmak.interaction_parameter.InteractionParameter property)
path (gmak.gmx_system.GmxTopologyOutput property)
putMessage() (gmak.logger.Logger method)
S
simulator() (in module gmak.api_signatures)
T
to_tuple() (gmak.interaction_parameter.InteractionPair method)
topo_out_creator() (in module gmak.api_signatures)
topo_out_writer() (in module gmak.api_signatures)
TopologyOutput (class in gmak.systems)
type (gmak.interaction_parameter.InteractionParameter property)
U
unindent() (gmak.logger.Logger method)
V
value (gmak.interaction_parameter.InteractionParameter property)