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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
Function
compare
Compare two cvcs using their names Used to sort CVC array in scripted coordinates
src/colvar.cpp:46
Function
compareColvarComponent
src/colvarcomp_gpath.cpp:26
Method
componentDisabled
src/colvarcomp.h:1414
Method
compute
src/colvar_geometricpath.h:157
Method
compute
src/colvar_arithmeticpath.h:96
Method
computeDerivatives
src/colvar_geometricpath.h:227
Method
computeDerivatives
src/colvar_arithmeticpath.h:102
Method
computeDistanceBetweenReferenceFrames
src/colvarcomp_gpath.cpp:606
Method
computeDistanceToReferenceFrames
src/colvarcomp_gpath.cpp:125
Method
computeValue
src/colvar_geometricpath.h:189
Method
computeValue
src/colvar_arithmeticpath.h:70
Method
compute_coordnum
src/colvarcomp_coordnums.cpp:219
Method
compute_overlap_matrix
src/colvartypes.cpp:271
Method
compute_scalar
lammps/src/USER-COLVARS/fix_colvars.cpp:996
Method
compute_selfcoordnum
src/colvarcomp_coordnums.cpp:447
Method
convergence
Calculate the rmsd of data from a reference (by default, the final data)
colvartools/colvars_grid.py:346
Method
convert_x
src/colvar_UIestimator.h:92
Method
convert_x
src/colvar_UIestimator.h:190
Method
convert_y
src/colvar_UIestimator.h:114
Method
coordnum
src/colvarcomp_coordnums.cpp:93
Method
cos
Reimplemented to work around MS compiler issues
src/colvarmodule.h:148
Method
current_bin
Calculate the bin index for a given bias.
src/colvarbias_abf.cpp:674
Method
current_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
Method
cvc
src/colvarcomp.cpp:19
Method
cvc_param_exists
src/colvar.cpp:1988
Method
d_restraint_potential_dk
src/colvarbias_restraint.cpp:777
Method
debug
\brief Whether debug output should be enabled (compile-time option)
src/colvarmodule.h:322
Method
decrease_depth
src/colvarmodule.cpp:1696
Method
delete_features
src/colvarbias.h:220
Method
delete_features
src/colvar.h:103
Method
delete_features
src/colvarcomp.h:153
Method
delete_features
src/colvaratoms.h:233
Method
delete_hill
src/colvarbias_meta.cpp:397
Method
determinant
Return the determinant
src/colvartypes.h:942
Method
determineClosestFrames
src/colvar_geometricpath.h:163
Method
diagonalize_matrix
src/colvartypes.cpp:294
Method
dihedPC
src/colvarcomp_protein.cpp:294
Method
dihedral
src/colvarcomp_angles.cpp:251
Method
dipole_angle
src/colvarcomp_angles.cpp:140
Method
dipole_magnitude
src/colvarcomp_distances.cpp:743
Method
dist2
src/colvarcomp.cpp:602
Method
dist2
\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
Method
dist2
src/colvarvalue.h:719
Method
dist2
src/colvarcomp_rotations.cpp:141
Method
dist2
src/colvarcomp_distances.cpp:149
Method
dist2
src/colvarcomp_angles.cpp:475
Method
dist2_grad
Gradient of the square distance: returns a 4-vector equivalent to that provided by slerp
src/colvartypes.h:1277
Method
dist2_lgrad
src/colvarcomp.cpp:609
Method
dist2_lgrad
src/colvarcomp_rotations.cpp:148
Method
dist2_lgrad
src/colvarcomp_distances.cpp:156
Method
dist2_lgrad
src/colvarcomp_angles.cpp:484
Method
dist2_rgrad
src/colvarcomp.cpp:616
Method
dist2_rgrad
src/colvarcomp_rotations.cpp:155
Method
dist2_rgrad
src/colvarcomp_distances.cpp:163
Method
dist2_rgrad
src/colvarcomp_angles.cpp:493
Method
distance
src/colvarcomp_distances.cpp:20
Method
distance_dir
src/colvarcomp_distances.cpp:481
Method
distance_inv
src/colvarcomp_distances.cpp:559
Method
distance_pairs
src/colvarcomp_distances.cpp:658
Method
distance_vec
src/colvarcomp_distances.cpp:101
Method
distance_xy
src/colvarcomp_distances.cpp:368
Method
distance_z
src/colvarcomp_distances.cpp:171
Method
doCallback
namd/src/ScriptTcl.h:114
Method
doCompareFrameDistance
src/colvar_geometricpath.h:28
Method
do_feature_side_effects
src/colvar.cpp:902
Method
do_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
Method
do_feature_side_effects
src/colvaratoms.cpp:877
Method
dt
namd/src/colvarproxy_namd.h:115
Method
dt
Time step of the simulation (fs) GROMACS uses picoseconds.
gromacs/src/colvarproxy_gromacs.cpp:226
Method
dt
src/colvarmodule.cpp:1988
Method
dt
lammps/src/USER-COLVARS/colvarproxy_lammps.h:99
Method
eigenvector
src/colvarcomp_distances.cpp:1217
Method
end_of_step
src/colvar.cpp:1800
Method
end_of_step
src/colvarmodule.cpp:1097
Method
end_of_step
src/colvarbias.cpp:376
Method
end_of_step
---------------------------------------------------------------------- */
lammps/src/USER-COLVARS/fix_colvars.cpp:875
Method
energy_difference
src/colvarbias_restraint.cpp:841
Method
energy_difference
src/colvarmodule.cpp:677
Method
energy_difference
Calculate change in energy from using alternate configuration
src/colvarbias_restraint.h:32
Method
entropy
Calculate the Shannon entropy of scalar data, interpreted as unnormalized distribution and the volume (number) of sampled bins
colvartools/colvars_grid.py:318
Method
error
gromacs/src/colvarproxy_gromacs.cpp:279
Method
error
src/colvarmodule.cpp:1751
Method
error
lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:323
Method
error_key_required
src/colvarparse.cpp:144
Method
exclude_feature_self
Ensure that exclusions are symmetric
src/colvardeps.cpp:396
Method
exec_command
Execute a script command
src/colvarscript.h:197
Method
fabs
Reimplemented to work around MS compiler issues
src/colvarmodule.h:130
Method
fatal_error
gromacs/src/colvarproxy_gromacs.cpp:284
Method
fatal_error
src/colvarmodule.cpp:1759
Method
fdiff_velocity
src/colvar.h:157
Method
feature
src/colvardeps.h:102
Method
feature_state
src/colvardeps.h:47
Method
floor
Reimplemented to work around MS compiler issues
src/colvarmodule.h:124
Function
flush_output_stream
namd/src/colvarproxy_namd.C:1043
Method
free_children_deps
src/colvardeps.cpp:43
Method
from_simple_string
src/colvartypes.h:326
Method
from_simple_string
src/colvartypes.h:686
Method
from_simple_string
src/colvarvalue.cpp:678
Function
getBondLambda
namd/src/SimParameters.C:7217
Function
getCurrentLambda
fepb BKR
namd/src/SimParameters.C:7138
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