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Functions1,368 in github.com/Colvars/colvars

Functioncompare
Compare two cvcs using their names Used to sort CVC array in scripted coordinates
src/colvar.cpp:46
FunctioncompareColvarComponent
src/colvarcomp_gpath.cpp:26
MethodcomponentDisabled
src/colvarcomp.h:1414
Methodcompute
src/colvar_geometricpath.h:157
Methodcompute
src/colvar_arithmeticpath.h:96
MethodcomputeDerivatives
src/colvar_geometricpath.h:227
MethodcomputeDerivatives
src/colvar_arithmeticpath.h:102
MethodcomputeDistanceBetweenReferenceFrames
src/colvarcomp_gpath.cpp:606
MethodcomputeDistanceToReferenceFrames
src/colvarcomp_gpath.cpp:125
MethodcomputeValue
src/colvar_geometricpath.h:189
MethodcomputeValue
src/colvar_arithmeticpath.h:70
Methodcompute_coordnum
src/colvarcomp_coordnums.cpp:219
Methodcompute_overlap_matrix
src/colvartypes.cpp:271
Methodcompute_scalar
lammps/src/USER-COLVARS/fix_colvars.cpp:996
Methodcompute_selfcoordnum
src/colvarcomp_coordnums.cpp:447
Methodconvergence
Calculate the rmsd of data from a reference (by default, the final data)
colvartools/colvars_grid.py:346
Methodconvert_x
src/colvar_UIestimator.h:92
Methodconvert_x
src/colvar_UIestimator.h:190
Methodconvert_y
src/colvar_UIestimator.h:114
Methodcoordnum
src/colvarcomp_coordnums.cpp:93
Methodcos
Reimplemented to work around MS compiler issues
src/colvarmodule.h:148
Methodcurrent_bin
Calculate the bin index for a given bias.
src/colvarbias_abf.cpp:674
Methodcurrent_bin_scalar_bound
\brief Report the bin corresponding to the current value of variable i and assign first or last bin if out of boundaries
src/colvargrid.h:401
Methodcvc
src/colvarcomp.cpp:19
Methodcvc_param_exists
src/colvar.cpp:1988
Methodd_restraint_potential_dk
src/colvarbias_restraint.cpp:777
Methoddebug
\brief Whether debug output should be enabled (compile-time option)
src/colvarmodule.h:322
Methoddecrease_depth
src/colvarmodule.cpp:1696
Methoddelete_features
src/colvarbias.h:220
Methoddelete_features
src/colvar.h:103
Methoddelete_features
src/colvarcomp.h:153
Methoddelete_features
src/colvaratoms.h:233
Methoddelete_hill
src/colvarbias_meta.cpp:397
Methoddeterminant
Return the determinant
src/colvartypes.h:942
MethoddetermineClosestFrames
src/colvar_geometricpath.h:163
Methoddiagonalize_matrix
src/colvartypes.cpp:294
MethoddihedPC
src/colvarcomp_protein.cpp:294
Methoddihedral
src/colvarcomp_angles.cpp:251
Methoddipole_angle
src/colvarcomp_angles.cpp:140
Methoddipole_magnitude
src/colvarcomp_distances.cpp:743
Methoddist2
src/colvarcomp.cpp:602
Methoddist2
\brief Square distance from another quaternion on the 4-dimensional unit sphere: returns the square of the angle along the shorter of the two geodesic
src/colvartypes.h:1260
Methoddist2
src/colvarvalue.h:719
Methoddist2
src/colvarcomp_rotations.cpp:141
Methoddist2
src/colvarcomp_distances.cpp:149
Methoddist2
src/colvarcomp_angles.cpp:475
Methoddist2_grad
Gradient of the square distance: returns a 4-vector equivalent to that provided by slerp
src/colvartypes.h:1277
Methoddist2_lgrad
src/colvarcomp.cpp:609
Methoddist2_lgrad
src/colvarcomp_rotations.cpp:148
Methoddist2_lgrad
src/colvarcomp_distances.cpp:156
Methoddist2_lgrad
src/colvarcomp_angles.cpp:484
Methoddist2_rgrad
src/colvarcomp.cpp:616
Methoddist2_rgrad
src/colvarcomp_rotations.cpp:155
Methoddist2_rgrad
src/colvarcomp_distances.cpp:163
Methoddist2_rgrad
src/colvarcomp_angles.cpp:493
Methoddistance
src/colvarcomp_distances.cpp:20
Methoddistance_dir
src/colvarcomp_distances.cpp:481
Methoddistance_inv
src/colvarcomp_distances.cpp:559
Methoddistance_pairs
src/colvarcomp_distances.cpp:658
Methoddistance_vec
src/colvarcomp_distances.cpp:101
Methoddistance_xy
src/colvarcomp_distances.cpp:368
Methoddistance_z
src/colvarcomp_distances.cpp:171
MethoddoCallback
namd/src/ScriptTcl.h:114
MethoddoCompareFrameDistance
src/colvar_geometricpath.h:28
Methoddo_feature_side_effects
src/colvar.cpp:902
Methoddo_feature_side_effects
Implements possible actions to be carried out when a given feature is enabled Base function does nothing, can be overloaded
src/colvardeps.h:222
Methoddo_feature_side_effects
src/colvaratoms.cpp:877
Methoddt
namd/src/colvarproxy_namd.h:115
Methoddt
Time step of the simulation (fs) GROMACS uses picoseconds.
gromacs/src/colvarproxy_gromacs.cpp:226
Methoddt
src/colvarmodule.cpp:1988
Methoddt
lammps/src/USER-COLVARS/colvarproxy_lammps.h:99
Methodeigenvector
src/colvarcomp_distances.cpp:1217
Methodend_of_step
src/colvar.cpp:1800
Methodend_of_step
src/colvarmodule.cpp:1097
Methodend_of_step
src/colvarbias.cpp:376
Methodend_of_step
---------------------------------------------------------------------- */
lammps/src/USER-COLVARS/fix_colvars.cpp:875
Methodenergy_difference
src/colvarbias_restraint.cpp:841
Methodenergy_difference
src/colvarmodule.cpp:677
Methodenergy_difference
Calculate change in energy from using alternate configuration
src/colvarbias_restraint.h:32
Methodentropy
Calculate the Shannon entropy of scalar data, interpreted as unnormalized distribution and the volume (number) of sampled bins
colvartools/colvars_grid.py:318
Methoderror
gromacs/src/colvarproxy_gromacs.cpp:279
Methoderror
src/colvarmodule.cpp:1751
Methoderror
lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:323
Methoderror_key_required
src/colvarparse.cpp:144
Methodexclude_feature_self
Ensure that exclusions are symmetric
src/colvardeps.cpp:396
Methodexec_command
Execute a script command
src/colvarscript.h:197
Methodfabs
Reimplemented to work around MS compiler issues
src/colvarmodule.h:130
Methodfatal_error
gromacs/src/colvarproxy_gromacs.cpp:284
Methodfatal_error
src/colvarmodule.cpp:1759
Methodfdiff_velocity
src/colvar.h:157
Methodfeature
src/colvardeps.h:102
Methodfeature_state
src/colvardeps.h:47
Methodfloor
Reimplemented to work around MS compiler issues
src/colvarmodule.h:124
Functionflush_output_stream
namd/src/colvarproxy_namd.C:1043
Methodfree_children_deps
src/colvardeps.cpp:43
Methodfrom_simple_string
src/colvartypes.h:326
Methodfrom_simple_string
src/colvartypes.h:686
Methodfrom_simple_string
src/colvarvalue.cpp:678
FunctiongetBondLambda
namd/src/SimParameters.C:7217
FunctiongetCurrentLambda
fepb BKR
namd/src/SimParameters.C:7138
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