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github.com/Colvars/colvars
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Functions
1,368 in github.com/Colvars/colvars
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Functions
1,368
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Types & classes
209
Method
isRecvSpanningTreeOn
namd/src/SimParameters.h:1078
Method
isRecvSpanningTreeUnset
namd/src/SimParameters.h:1079
Method
isSendSpanningTreeOn
namd/src/SimParameters.h:1076
Method
isSendSpanningTreeUnset
namd/src/SimParameters.h:1077
Method
is_dynamic
src/colvardeps.h:125
Method
is_not_set
src/colvardeps.h:132
Method
is_scalar
Whether this variable is a real number
src/colvarvalue.h:267
Method
is_static
src/colvardeps.h:126
Method
is_static
src/colvardeps.h:134
Method
is_user
src/colvardeps.h:127
Method
is_user
src/colvardeps.h:135
Function
issetinparseopts
namd/src/SimParameters.C:109
Function
istrueinparseopts
namd/src/SimParameters.C:104
Method
key_already_set
src/colvarparse.cpp:540
Method
l2norm
src/colvargrid.cpp:850
Method
linearCombination
src/colvarcomp.h:1609
Method
linearCombination
src/colvarcomp_gpath.cpp:408
Method
list2str
Utility function to serialize a list into a string
colvartools/colvars_grid.py:263
Function
load_atoms
namd/src/colvarproxy_namd.C:961
Method
load_atoms
gromacs/src/colvarproxy_gromacs.cpp:296
Method
load_atoms
src/colvarproxy.cpp:212
Method
load_atoms
src/colvarmodule.cpp:1868
Function
load_coords
namd/src/colvarproxy_namd.C:849
Method
load_coords
gromacs/src/colvarproxy_gromacs.cpp:305
Method
load_coords
src/colvarproxy.cpp:223
Method
load_coords
src/colvarmodule.cpp:1877
Method
log
gromacs/src/colvarproxy_gromacs.cpp:275
Method
log
lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:310
Method
log_default_params
Level at which a keyword's default value is logged
src/colvarmodule.h:666
Method
log_init_messages
Level at which initialization messages are logged
src/colvarmodule.h:654
Method
log_input_files
Level at which input-file operations (configuration, state) are logged
src/colvarmodule.h:678
Method
log_level
Level of logging requested by the user
src/colvarmodule.h:648
Method
log_output_files
Level at which output-file operations are logged
src/colvarmodule.h:672
Method
log_user_params
Level at which a keyword's user-provided value is logged
src/colvarmodule.h:660
Method
logn
Reimplemented to work around MS compiler issues. Note: log() is currently defined as the text logging function, but this can be changed at a later ti
src/colvarmodule.h:174
Method
main
src/colvarmodule.cpp:92
Method
main_loop
src/colvarcomp_coordnums.cpp:192
Method
map_total
src/colvarcomp_volmaps.cpp:18
Method
mark_key_set_default
src/colvarparse.cpp:132
Method
mark_key_set_user
src/colvarparse.cpp:119
Method
matrix
Return the associated 3x3 matrix
src/colvartypes.h:1430
Method
matrix2d
Default constructor
src/colvartypes.h:462
Method
memory_usage
---------------------------------------------------------------------- */ local memory usage. approximately. */
lammps/src/USER-COLVARS/fix_colvars.cpp:1003
Method
meshgrid
Returns a mesh grid suitable for plotting the data
colvartools/colvars_grid.py:65
Method
min_post_force
---------------------------------------------------------------------- */
lammps/src/USER-COLVARS/fix_colvars.cpp:861
Method
min_setup
lammps/src/USER-COLVARS/fix_colvars.h:53
Method
modify_param
lammps/src/USER-COLVARS/fix_colvars.cpp:498
Method
n_matrix
src/colvar_UIestimator.h:35
Method
n_vector
src/colvar_UIestimator.h:142
Function
namdPython_clear
namd/src/ScriptTcl.C:269
Function
namdPython_traverse
namd/src/ScriptTcl.C:264
Function
nonbonded_select
namd/src/SimParameters.C:392
Method
norm
src/colvartypes.h:220
Method
norm
Norm of the quaternion
src/colvartypes.h:1115
Method
nr_linbcg_sym
b : RHS of equation x : initial guess for the solution; output is solution itol : convergence criterion
src/colvargrid.cpp:797
Method
num_biases
src/colvarmodule.cpp:521
Method
num_cvcs
\brief Number of CVC objects defined
src/colvar.h:394
Method
num_df
src/colvarvalue.cpp:68
Method
num_dimensions
Dimensionality of the collective variable (d)
colvartools/plot_colvars_traj.py:74
Method
num_dimensions
\brief Number of dimensions of the value of this colvar
src/colvar.h:388
Method
num_dimensions
src/colvarvalue.cpp:91
Method
num_frames
Number of trajectory frames loaded (n)
colvartools/plot_colvars_traj.py:83
Method
num_frames
Number of trajectory frames loaded
colvartools/plot_colvars_traj.py:137
Function
num_replicas
namd/src/colvarproxy_namd.C:1399
Method
num_replicas
lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:367
Method
num_variables
How many variables are defined for this bias
src/colvarbias.h:39
Method
num_variables
Return the number of colvar objects
src/colvargrid.h:100
Method
num_variables_feature
src/colvarmodule.cpp:507
Method
one_time_init
lammps/src/USER-COLVARS/fix_colvars.cpp:423
Method
open_traj_file
src/colvarmodule.cpp:1583
Function
operator *
src/colvartypes.h:962
Function
operator *
src/colvarvalue.cpp:481
Method
operator *
src/colvartypes.h:172
Method
operator *
src/colvartypes.h:598
Method
operator *
src/colvartypes.h:843
Method
operator *
src/colvartypes.h:1180
Method
operator *=
src/colvartypes.h:132
Method
operator *=
src/colvartypes.h:558
Method
operator *=
src/colvartypes.h:782
Method
operator *=
src/colvartypes.h:1126
Method
operator *=
src/colvarvalue.h:593
Function
operator +
src/colvarvalue.cpp:425
Method
operator +
src/colvartypes.h:148
Method
operator +
src/colvartypes.h:574
Method
operator +
src/colvartypes.h:831
Method
operator +
src/colvartypes.h:1166
Method
operator +=
src/colvartypes.h:114
Method
operator +=
src/colvartypes.h:540
Method
operator +=
src/colvartypes.h:768
Method
operator +=
src/colvartypes.h:1145
Method
operator +=
src/colvarvalue.h:539
Function
operator -
src/colvarvalue.cpp:452
Method
operator -
src/colvartypes.h:160
Method
operator -
src/colvartypes.h:586
Method
operator -
src/colvartypes.h:826
Method
operator -
src/colvartypes.h:1172
Method
operator -=
src/colvartypes.h:123
Method
operator -=
src/colvartypes.h:549
Method
operator -=
src/colvartypes.h:775
Method
operator -=
src/colvartypes.h:1149
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