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Functions1,368 in github.com/Colvars/colvars

Methodrequest_total_force
src/colvarmodule.cpp:1994
Methodrequest_total_force
lammps/src/USER-COLVARS/colvarproxy_lammps.h:102
Methodrequire_feature_alt
src/colvardeps.cpp:407
Methodrequire_feature_children
src/colvardeps.cpp:402
Methodrequire_feature_self
Shorthand functions for describing dependencies
src/colvardeps.cpp:390
Methodreset
src/colvarproxy_volmaps.cpp:26
Methodreset
\brief Reset data (in case the grid is being reused)
src/colvargrid.h:191
Methodreset
Set all elements to zero
src/colvartypes.h:78
Methodreset
Set all elements to zero
src/colvartypes.h:451
Methodreset
\brief Set all components to zero
src/colvartypes.h:715
Methodreset
\brief Set all components to zero (null quaternion)
src/colvartypes.h:1036
Methodreset
src/colvarmodule.cpp:1155
Methodreset
src/colvarvalue.cpp:113
Methodreset_index_groups
src/colvarmodule.cpp:1855
Methodreset_pbc_lattice
src/colvarproxy.cpp:96
Methodreset_rotation
\brief Set the q0 component to 1 and the others to 0 (quaternion representing no rotation)
src/colvartypes.h:1043
Methodrestart
lammps/src/USER-COLVARS/fix_colvars.cpp:975
Methodrestart_frequency
gromacs/src/colvarproxy_gromacs.cpp:236
Methodrestore_children_deps
re-enable children features (and increase ref count accordingly) So free_children_deps() can be called whenever an object becomes inactive
src/colvardeps.cpp:73
Methodrestraint_convert_k
src/colvarbias_alb.cpp:419
Methodrestraint_force
src/colvarbias_restraint.cpp:770
Methodrestraint_force
src/colvarbias_alb.cpp:411
Methodrestraint_potential
src/colvarbias_restraint.cpp:763
Methodrestraint_potential
src/colvarbias_alb.cpp:403
Methodrmatrix
Default constructor
src/colvartypes.h:916
Methodrmsd
src/colvarcomp_distances.cpp:953
Methodrotate
\brief Rotate v through this quaternion (put it in the rotated reference frame)
src/colvartypes.h:1208
Methodrotation
Default constructor
src/colvartypes.h:1392
Methodround
src/colvar_UIestimator.h:132
Methodrow
src/colvartypes.h:371
Functionrun_colvar_callback
vmd/src/colvarproxy_vmd.C:405
Functionrun_colvar_callback
namd/src/colvarproxy_namd.C:578
Functionrun_colvar_gradient_callback
vmd/src/colvarproxy_vmd.C:413
Functionrun_colvar_gradient_callback
namd/src/colvarproxy_namd.C:586
Functionrun_colvarscript_command
src/colvarscript.cpp:457
Functionrun_force_callback
vmd/src/colvarproxy_vmd.C:395
Functionrun_force_callback
namd/src/colvarproxy_namd.C:573
Methodrvector
src/colvartypes.h:709
Methodscalable_group_coms
namd/src/colvarproxy_namd.h:208
Methodscale
Scale the weight with this factor (by default 1.0 is used)
src/colvarbias_meta.h:345
FunctionscriptSet
namd/src/SimParameters.C:169
Functionscript_obj_to_str
vmd/src/colvarproxy_vmd.C:424
Functionscript_obj_to_str
namd/src/colvarproxy_namd.C:1087
Methodscripted_forces
src/colvarmodule.h:783
Methodselect_closest_image
The position to look for the closest periodic image ref_pos The reference position
gromacs/src/colvarproxy_gromacs.cpp:258
Methodselfcoordnum
src/colvarcomp_coordnums.cpp:395
Functionsend_SimParameters
namd/src/SimParameters.C:6983
Methodset
src/colvartypes.h:384
Methodset
\brief Set all components to a scalar
src/colvartypes.h:1030
FunctionsetParameter
namd/src/ScriptTcl.C:118
Methodset_cvc_param
src/colvar.cpp:2031
Methodset_dummy
src/colvaratoms.cpp:181
Methodset_dummy_pos
src/colvaratoms.cpp:193
Methodset_elem
src/colvarvalue.cpp:315
Methodset_error_bits
src/colvarmodule.cpp:1724
Methodset_from_euler_angles
"Constructor" after Euler angles (in radians) http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles
src/colvartypes.h:1006
Methodset_param
src/colvarparams.cpp:102
Methodset_positive
src/colvartypes.h:1136
Methodset_sizes
Set the sizes in each direction
src/colvargrid.h:123
Methodset_state_params
src/colvarbias_restraint.cpp:73
Methodset_state_params
src/colvarbias_alb.cpp:247
Methodset_state_params
src/colvarbias_meta.cpp:1276
Methodset_state_params
src/colvarbias.cpp:430
Functionset_unit_system
vmd/src/colvarproxy_vmd.C:195
Functionset_unit_system
namd/src/colvarproxy_namd.C:1228
Methodset_unit_system
lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:331
Methodset_value
src/colvar_UIestimator.h:171
Methodsetmask
lammps/src/USER-COLVARS/fix_colvars.cpp:389
Methodsetup
src/colvarproxy.cpp:645
Methodsetup
src/colvarcomp.cpp:289
Methodsetup
src/colvaratoms.cpp:287
Methodsetup
lammps/src/USER-COLVARS/fix_colvars.cpp:531
Methodsetup
re-initialize data where needed
lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:189
Methodsetup_output
(Re)initialize the output files (does not write them yet)
src/colvarbias.h:180
Methodsetup_output
src/colvarbias_meta.cpp:1585
Methodsin
Reimplemented to work around MS compiler issues
src/colvarmodule.h:142
Functionsmp_biases_loop
namd/src/colvarproxy_namd.C:1351
Functionsmp_biases_script_loop
namd/src/colvarproxy_namd.C:1372
Functionsmp_colvars_loop
namd/src/colvarproxy_namd.C:1321
Methodsmp_enabled
namd/src/colvarproxy_namd.h:121
Methodsmp_lock
namd/src/colvarproxy_namd.h:155
Methodsmp_stream_error
src/colvarproxy.cpp:707
Methodsmp_trylock
namd/src/colvarproxy_namd.h:161
Methodsmp_trylock
src/colvarproxy.cpp:443
Methodsmp_unlock
namd/src/colvarproxy_namd.h:166
Methodspin_angle
\brief Return the spin angle (in degrees) with respect to the provided axis (which MUST be normalized)
src/colvartypes.h:1438
Methodsplit_string
src/colvarparse.cpp:922
Methodstate_file_prefix
src/colvarmodule.cpp:1286
Methodstep_absolute
Return the current step number from the beginning of the whole calculation
src/colvarmodule.h:237
Methodstep_relative
Return the current step number from the beginning of this run
src/colvarmodule.h:230
Methodsteps
The array of step numbers, with shape = (n,)
colvartools/plot_colvars_traj.py:88
Methodstring const &cmd_key))
Get a pointer to the implementation of the given command
src/colvarscript.h:234
Methodstrip_values
src/colvarparse.cpp:552
Methodsum
src/colvartypes.h:225
Methodsummary
Print a short summary of the contents of the object
colvartools/colvars_grid.py:50
Methodswitching_function
src/colvarcomp_coordnums.cpp:20
Functiontcl_colvars
vmd/src/colvarproxy_vmd.C:39
Methodtcl_get_str
src/colvarproxy_tcl.cpp:42
Methodtcl_run_colvar_callback
src/colvarproxy_tcl.cpp:72
Methodtcl_run_colvar_gradient_callback
src/colvarproxy_tcl.cpp:111
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