MODOI
The Algorithm
Tutorial
Butane Simulation
Configuring MODOI for Butane
Running the Simulation
Implementations
Local_Simulation Script
Components
SimulationClient Package
SimulationClient.SimulationClient Module
SimulationClient.CustomBFGS Module
SimulationClient.Geometric Module
SimulationClient.LinearAlgebra Module
SimulationClient.MetricValues Module
SimulationPotential Module
SimulationServer Module
SimulationUtilities Package
SimulationUtilities.Communication_Codes Module
SimulationUtilities.Configuration_Processing Module
SimulationUtilities.Curve Module
SimulationUtilities.Extract_States_PDB Module
SimulationUtilities.Visualize Module
MODOI
Docs
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Index
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A
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C
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D
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E
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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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O
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P
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R
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S
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T
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W
_
__init__() (SimulationClient.SimulationClient.SimulationClient method)
(SimulationPotential.SimulationPotential.SimulationPotential method)
(SimulationServer.SimulationServer.SimulationServer method)
A
ADDRESS (SimulationPotential.SimulationPotential.SimulationPotential attribute)
(SimulationServer.SimulationServer.SimulationServer attribute)
all_nodes_moved() (SimulationUtilities.Curve.Curve method)
AUTHKEY (SimulationClient.SimulationClient.SimulationClient attribute)
(SimulationPotential.SimulationPotential.SimulationPotential attribute)
(SimulationServer.SimulationServer.SimulationServer attribute)
C
comm_code() (in module SimulationUtilities.Communication_Codes)
CONFIGURATION (SimulationClient.SimulationClient.SimulationClient attribute)
(SimulationPotential.SimulationPotential.SimulationPotential attribute)
(SimulationServer.SimulationServer.SimulationServer attribute)
configuration (SimulationUtilities.Curve.Curve attribute)
convert_atoms_to_vector() (in module SimulationUtilities.Configuration_Processing)
convert_vector_to_atoms() (in module SimulationUtilities.Configuration_Processing)
Curve (class in SimulationUtilities.Curve)
CURVE (SimulationServer.SimulationServer.SimulationServer attribute)
CURVE_ADDRESS (SimulationClient.SimulationClient.SimulationClient attribute)
D
default_initial_state (SimulationUtilities.Curve.Curve attribute)
DELAY (SimulationClient.SimulationClient.SimulationClient attribute)
E
end_point (SimulationUtilities.Curve.Curve attribute)
extract_states_pdb() (in module SimulationUtilities.Extract_States_PDB)
F
find_geodesic_midpoint() (in module SimulationClient.CustomBFGS)
FINISHED (SimulationServer.SimulationServer.SimulationServer attribute)
G
get_curve() (SimulationServer.SimulationServer.SimulationServer method)
get_metric() (in module SimulationClient.MetricValues)
get_points() (SimulationUtilities.Curve.Curve method)
GradLength() (in module SimulationClient.Geometric)
I
ID (SimulationClient.SimulationClient.SimulationClient attribute)
L
Length() (in module SimulationClient.Geometric)
M
MASS_MATRIX (SimulationClient.SimulationClient.SimulationClient attribute)
mass_norm() (in module SimulationClient.LinearAlgebra)
METRIC_SERVERS (SimulationClient.SimulationClient.SimulationClient attribute)
movement (SimulationUtilities.Curve.Curve attribute)
N
next_movable_node() (SimulationUtilities.Curve.Curve method)
node_movable (SimulationUtilities.Curve.Curve attribute)
nodes_moved (SimulationUtilities.Curve.Curve attribute)
norm() (in module SimulationClient.Geometric)
norm_gradient() (in module SimulationClient.Geometric)
number_of_distinct_nodes_moved (SimulationUtilities.Curve.Curve attribute)
number_of_nodes (SimulationUtilities.Curve.Curve attribute)
O
orthonormal_tangent_basis() (in module SimulationClient.LinearAlgebra)
OUTPUT_FILENAME (SimulationServer.SimulationServer.SimulationServer attribute)
P
points (SimulationUtilities.Curve.Curve attribute)
R
read_configuration_file() (in module SimulationUtilities.Configuration_Processing)
run_potential_server() (SimulationPotential.SimulationPotential.SimulationPotential method)
run_simulation() (SimulationServer.SimulationServer.SimulationServer method)
S
save_simulation() (SimulationServer.SimulationServer.SimulationServer method)
set_node_movable() (SimulationUtilities.Curve.Curve method)
set_node_position() (SimulationUtilities.Curve.Curve method)
set_output_file() (SimulationServer.SimulationServer.SimulationServer method)
shifts_to_curve() (in module SimulationClient.LinearAlgebra)
shutdown_metric() (in module SimulationClient.MetricValues)
SimulationClient (class in SimulationClient.SimulationClient)
SimulationClient.CustomBFGS (module)
SimulationClient.Geometric (module)
SimulationClient.LinearAlgebra (module)
SimulationClient.MetricValues (module)
SimulationClient.SimulationClient (module)
SimulationPotential (class in SimulationPotential.SimulationPotential)
SimulationPotential.SimulationPotential (module)
SimulationServer (class in SimulationServer.SimulationServer)
SimulationServer.SimulationServer (module)
SimulationUtilities.Communication_Codes (module)
SimulationUtilities.Configuration_Processing (module)
SimulationUtilities.Curve (module)
SimulationUtilities.Extract_States_PDB (module)
SimulationUtilities.Visualize (module)
start_client() (SimulationClient.SimulationClient.SimulationClient method)
start_point (SimulationUtilities.Curve.Curve attribute)
T
tangent (SimulationUtilities.Curve.Curve attribute)
total_number_of_nodes (SimulationUtilities.Curve.Curve attribute)
W
write_xyz_animation() (in module SimulationUtilities.Visualize)