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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
request_total_force
src/colvarmodule.cpp:1994
Method
request_total_force
lammps/src/USER-COLVARS/colvarproxy_lammps.h:102
Method
require_feature_alt
src/colvardeps.cpp:407
Method
require_feature_children
src/colvardeps.cpp:402
Method
require_feature_self
Shorthand functions for describing dependencies
src/colvardeps.cpp:390
Method
reset
src/colvarproxy_volmaps.cpp:26
Method
reset
\brief Reset data (in case the grid is being reused)
src/colvargrid.h:191
Method
reset
Set all elements to zero
src/colvartypes.h:78
Method
reset
Set all elements to zero
src/colvartypes.h:451
Method
reset
\brief Set all components to zero
src/colvartypes.h:715
Method
reset
\brief Set all components to zero (null quaternion)
src/colvartypes.h:1036
Method
reset
src/colvarmodule.cpp:1155
Method
reset
src/colvarvalue.cpp:113
Method
reset_index_groups
src/colvarmodule.cpp:1855
Method
reset_pbc_lattice
src/colvarproxy.cpp:96
Method
reset_rotation
\brief Set the q0 component to 1 and the others to 0 (quaternion representing no rotation)
src/colvartypes.h:1043
Method
restart
lammps/src/USER-COLVARS/fix_colvars.cpp:975
Method
restart_frequency
gromacs/src/colvarproxy_gromacs.cpp:236
Method
restore_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
Method
restraint_convert_k
src/colvarbias_alb.cpp:419
Method
restraint_force
src/colvarbias_restraint.cpp:770
Method
restraint_force
src/colvarbias_alb.cpp:411
Method
restraint_potential
src/colvarbias_restraint.cpp:763
Method
restraint_potential
src/colvarbias_alb.cpp:403
Method
rmatrix
Default constructor
src/colvartypes.h:916
Method
rmsd
src/colvarcomp_distances.cpp:953
Method
rotate
\brief Rotate v through this quaternion (put it in the rotated reference frame)
src/colvartypes.h:1208
Method
rotation
Default constructor
src/colvartypes.h:1392
Method
round
src/colvar_UIestimator.h:132
Method
row
src/colvartypes.h:371
Function
run_colvar_callback
vmd/src/colvarproxy_vmd.C:405
Function
run_colvar_callback
namd/src/colvarproxy_namd.C:578
Function
run_colvar_gradient_callback
vmd/src/colvarproxy_vmd.C:413
Function
run_colvar_gradient_callback
namd/src/colvarproxy_namd.C:586
Function
run_colvarscript_command
src/colvarscript.cpp:457
Function
run_force_callback
vmd/src/colvarproxy_vmd.C:395
Function
run_force_callback
namd/src/colvarproxy_namd.C:573
Method
rvector
src/colvartypes.h:709
Method
scalable_group_coms
namd/src/colvarproxy_namd.h:208
Method
scale
Scale the weight with this factor (by default 1.0 is used)
src/colvarbias_meta.h:345
Function
scriptSet
namd/src/SimParameters.C:169
Function
script_obj_to_str
vmd/src/colvarproxy_vmd.C:424
Function
script_obj_to_str
namd/src/colvarproxy_namd.C:1087
Method
scripted_forces
src/colvarmodule.h:783
Method
select_closest_image
The position to look for the closest periodic image ref_pos The reference position
gromacs/src/colvarproxy_gromacs.cpp:258
Method
selfcoordnum
src/colvarcomp_coordnums.cpp:395
Function
send_SimParameters
namd/src/SimParameters.C:6983
Method
set
src/colvartypes.h:384
Method
set
\brief Set all components to a scalar
src/colvartypes.h:1030
Function
setParameter
namd/src/ScriptTcl.C:118
Method
set_cvc_param
src/colvar.cpp:2031
Method
set_dummy
src/colvaratoms.cpp:181
Method
set_dummy_pos
src/colvaratoms.cpp:193
Method
set_elem
src/colvarvalue.cpp:315
Method
set_error_bits
src/colvarmodule.cpp:1724
Method
set_from_euler_angles
"Constructor" after Euler angles (in radians) http://en.wikipedia.org/wiki/Conversion_between_quaternions_and_Euler_angles
src/colvartypes.h:1006
Method
set_param
src/colvarparams.cpp:102
Method
set_positive
src/colvartypes.h:1136
Method
set_sizes
Set the sizes in each direction
src/colvargrid.h:123
Method
set_state_params
src/colvarbias_restraint.cpp:73
Method
set_state_params
src/colvarbias_alb.cpp:247
Method
set_state_params
src/colvarbias_meta.cpp:1276
Method
set_state_params
src/colvarbias.cpp:430
Function
set_unit_system
vmd/src/colvarproxy_vmd.C:195
Function
set_unit_system
namd/src/colvarproxy_namd.C:1228
Method
set_unit_system
lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:331
Method
set_value
src/colvar_UIestimator.h:171
Method
setmask
lammps/src/USER-COLVARS/fix_colvars.cpp:389
Method
setup
src/colvarproxy.cpp:645
Method
setup
src/colvarcomp.cpp:289
Method
setup
src/colvaratoms.cpp:287
Method
setup
lammps/src/USER-COLVARS/fix_colvars.cpp:531
Method
setup
re-initialize data where needed
lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:189
Method
setup_output
(Re)initialize the output files (does not write them yet)
src/colvarbias.h:180
Method
setup_output
src/colvarbias_meta.cpp:1585
Method
sin
Reimplemented to work around MS compiler issues
src/colvarmodule.h:142
Function
smp_biases_loop
namd/src/colvarproxy_namd.C:1351
Function
smp_biases_script_loop
namd/src/colvarproxy_namd.C:1372
Function
smp_colvars_loop
namd/src/colvarproxy_namd.C:1321
Method
smp_enabled
namd/src/colvarproxy_namd.h:121
Method
smp_lock
namd/src/colvarproxy_namd.h:155
Method
smp_stream_error
src/colvarproxy.cpp:707
Method
smp_trylock
namd/src/colvarproxy_namd.h:161
Method
smp_trylock
src/colvarproxy.cpp:443
Method
smp_unlock
namd/src/colvarproxy_namd.h:166
Method
spin_angle
\brief Return the spin angle (in degrees) with respect to the provided axis (which MUST be normalized)
src/colvartypes.h:1438
Method
split_string
src/colvarparse.cpp:922
Method
state_file_prefix
src/colvarmodule.cpp:1286
Method
step_absolute
Return the current step number from the beginning of the whole calculation
src/colvarmodule.h:237
Method
step_relative
Return the current step number from the beginning of this run
src/colvarmodule.h:230
Method
steps
The array of step numbers, with shape = (n,)
colvartools/plot_colvars_traj.py:88
Method
string const &cmd_key))
Get a pointer to the implementation of the given command
src/colvarscript.h:234
Method
strip_values
src/colvarparse.cpp:552
Method
sum
src/colvartypes.h:225
Method
summary
Print a short summary of the contents of the object
colvartools/colvars_grid.py:50
Method
switching_function
src/colvarcomp_coordnums.cpp:20
Function
tcl_colvars
vmd/src/colvarproxy_vmd.C:39
Method
tcl_get_str
src/colvarproxy_tcl.cpp:42
Method
tcl_run_colvar_callback
src/colvarproxy_tcl.cpp:72
Method
tcl_run_colvar_gradient_callback
src/colvarproxy_tcl.cpp:111
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