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Functions1,368 in github.com/Colvars/colvars

⨍ Functions 1,368◇ Types & classes 209

↓ 2 callersMethodconjugate

Return the conjugate quaternion

src/colvartypes.h:1121

↓ 2 callersMethodcurrent_bin

src/colvarbias.cpp:404

↓ 2 callersMethoddecr_ref_count

src/colvardeps.cpp:357

↓ 2 callersMethoddelete_requested

Whether deallocation was requested

src/colvarproxy.h:687

↓ 2 callersMethoddelta_grid

\brief Get the change from this to other_grid and store the result in this. this_grid := other_grid - this_grid Grids must have the same dimensions.

src/colvargrid.h:487

↓ 2 callersMethoddipole

\brief Return the (previously calculated) dipole of the atom group

src/colvaratoms.h:488

↓ 2 callersMethodexp

Reimplemented to work around MS compiler issues

src/colvarmodule.h:166

↓ 2 callersMethodget_param

src/colvarparams.cpp:94

↓ 2 callersMethodget_tcl_interp

Get a pointer to the Tcl interpreter

src/colvarproxy_tcl.h:49

↓ 2 callersMethodget_version_from_string

src/colvarproxy.cpp:697

↓ 2 callersMethodinit_atom

src/colvarproxy.cpp:181

↓ 2 callersFunctioninthash_init

* inthash_init() - Initialize a new hash table. * * tptr: Pointer to the hash table to initialize * buckets: The number of initial buckets to cr

lammps/src/USER-COLVARS/fix_colvars.cpp:160

↓ 2 callersMethodmodify_atom_ids

src/colvarproxy.h:265

↓ 2 callersMethodmodify_atom_total_forces

src/colvarproxy.h:289

↓ 2 callersFunctionmy_backup_file

safely move filename to filename.extension

lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:34

↓ 2 callersMethodname

The name of the collective variable

colvartools/plot_colvars_traj.py:69

↓ 2 callersMethodnum_biases_feature

src/colvarmodule.cpp:527

↓ 2 callersMethodoutput_traj

src/colvarbias_meta.cpp:1904

↓ 2 callersFunctionpdb_field_str2enum

vmd/src/colvarproxy_vmd.C:472

↓ 2 callersFunctionpdb_field_str2enum

namd/src/colvarproxy_namd.C:811

↓ 2 callersMethodperiodic_boundaries

src/colvar.cpp:2045

↓ 2 callersMethodpositions

src/colvaratoms.cpp:1219

↓ 2 callersMethodprint_state

src/colvardeps.cpp:431

↓ 2 callersFunctionpython_tcl_convert

namd/src/ScriptTcl.C:161

↓ 2 callersMethodread_config_string

src/colvarmodule.cpp:163

↓ 2 callersMethodread_files

Read a series of colvars.traj files. filenames : list of strings list of file names to read from list_variables :

colvartools/plot_colvars_traj.py:182

↓ 2 callersMethodread_total_force

Get the total force

src/colvaratoms.h:131

↓ 2 callersMethodread_velocity

Get the current velocity

src/colvaratoms.h:125

↓ 2 callersMethodremove_file

src/colvarproxy.cpp:540

↓ 2 callersMethodremove_small_values

\brief Assign values that are smaller than scalar constant the latter value (fast loop)

src/colvargrid.h:578

↓ 2 callersMethodreplica_comm_recv

src/colvarproxy_replicas.cpp:41

↓ 2 callersMethodreplica_comm_send

src/colvarproxy_replicas.cpp:49

↓ 2 callersMethodreset

colvartools/colvars_grid.py:36

↓ 2 callersMethodreset_data

Set mutable data (everything except id and mass) to zero

src/colvaratoms.h:94

↓ 2 callersMethodrun

src/colvarscript.cpp:245

↓ 2 callersMethodset_temper

gromacs/src/colvarproxy_gromacs.cpp:207

↓ 2 callersMethodset_unit_system

gromacs/src/colvarproxy_gromacs.cpp:315

↓ 2 callersFunctionsetupIDWS

Return true if IDWS is active, else return false. */

namd/src/SimParameters.C:7110

↓ 2 callersMethodslice

src/colvartypes.h:236

↓ 2 callersMethodsmp_num_threads

src/colvarproxy.cpp:424

↓ 2 callersMethodsqrt

Reimplemented to work around MS compiler issues

src/colvarmodule.h:136

↓ 2 callersFunctionsuspend

namd/src/ScriptTcl.C:70

↓ 2 callersFunctiontcl_python_convert

namd/src/ScriptTcl.C:191

↓ 2 callersMethodupdate_forces_energy

src/colvar.cpp:1672

↓ 2 callersFunctionupdate_group_properties

namd/src/colvarproxy_namd.C:1201

↓ 2 callersMethodvalue_output

\brief Return the value suitable for output purposes (so that it may be rescaled or manipulated without changing it permanently)

src/colvargrid.h:716

↓ 2 callersMethodvariables_active_smp_items

src/colvarmodule.cpp:116

↓ 2 callersMethodwrite_field

colvartools/abf_data.cpp:326

↓ 2 callersMethodwrite_output_files

src/colvarmodule.cpp:1458

↓ 2 callersMethodwrite_restart_file

src/colvarmodule.cpp:1002

↓ 2 callersMethodwrite_state_to_replicas

src/colvarbias_meta.cpp:1746

↓ 1 callersMethod_parse_comment_line

Read in a comment line from a colvars.traj file and update the names of collective variables according to the contents of the comment

colvartools/plot_colvars_traj.py:146

↓ 1 callersMethod_parse_line

Read in a data line from a colvars.traj file

colvartools/plot_colvars_traj.py:161

↓ 1 callersMethod_resize

Change the number of records in the trajectory

colvartools/plot_colvars_traj.py:60

↓ 1 callersMethod_set_num_dimensions

Set the number of components of the collective variable

colvartools/plot_colvars_traj.py:49

↓ 1 callersMethodadd_atom_id

src/colvaratoms.cpp:140

↓ 1 callersMethodadd_bias_force_actual_value

src/colvar.h:704

↓ 1 callersMethodadd_config_file

lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:163

↓ 1 callersMethodadd_config_string

lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:168

↓ 1 callersMethodappend_new_config

src/colvarmodule.cpp:258

↓ 1 callersMethodapplied_force

Get the current applied force

src/colvar.h:320

↓ 1 callersMethodapply_atom_force

Request that this force is applied to the given atom

src/colvarproxy.h:251

↓ 1 callersMethodapply_volmap_force

Request that this force is applied to the given volumetric map

src/colvarproxy_volmaps.h:52

↓ 1 callersMethodaxes

Returns the axes as a list of 1d meshes

colvartools/colvars_grid.py:60

↓ 1 callersMethodbin_count

src/colvarbias.cpp:409

↓ 1 callersMethodbin_num

So far, these are only implemented in colvarbias_abf

src/colvarbias.cpp:399

↓ 1 callersMethodcalc

src/colvarmodule.cpp:694

↓ 1 callersMethodcalc_Jacobian_derivative

src/colvarcomp.cpp:467

↓ 1 callersMethodcalc_fit_gradients

src/colvarcomp.cpp:475

↓ 1 callersMethodcalc_force_invgrads

src/colvarcomp.cpp:459

↓ 1 callersMethodcalc_gradients

src/colvarcomp_apath.cpp:65

↓ 1 callersMethodcalc_pmf

calculate gradients from the internal variables

src/colvar_UIestimator.h:380

↓ 1 callersMethodcalc_value

src/colvarcomp_gpath.cpp:245

↓ 1 callersMethodcalculate

trigger colvars computation

gromacs/src/colvarproxy_gromacs.cpp:340

↓ 1 callersMethodchange_configuration

src/colvarbias.cpp:382

↓ 1 callersMethodcheck_consistency

\brief Check that the grid information inside (boundaries, widths, ...) is consistent with the current setting of the colvars

src/colvargrid.h:894

↓ 1 callersMethodclear_atom

src/colvarproxy.cpp:200

↓ 1 callersMethodclear_atom_group

src/colvarproxy.cpp:286

↓ 1 callersMethodclear_error_msgs

src/colvarproxy.cpp:685

↓ 1 callersMethodclear_keyword_registry

src/colvarparse.cpp:575

↓ 1 callersFunctionclear_volmap

namd/src/colvarproxy_namd.C:1290

↓ 1 callersMethodcollect_cvc_data

src/colvar.cpp:1310

↓ 1 callersMethodcollect_gradients

src/colvarcomp.cpp:417

↓ 1 callersMethodcompute

trigger colvars computation

lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:196

↓ 1 callersFunctionconfig_parser

namd/src/SimParameters.C:406

↓ 1 callersFunctionconfig_parser_basic

namd/src/SimParameters.C:444

↓ 1 callersFunctionconfig_parser_boundary

namd/src/SimParameters.C:1995

↓ 1 callersFunctionconfig_parser_constorque

namd/src/SimParameters.C:1975

↓ 1 callersFunctionconfig_parser_constraints

namd/src/SimParameters.C:1537

↓ 1 callersFunctionconfig_parser_fileio

namd/src/SimParameters.C:673

↓ 1 callersFunctionconfig_parser_fullelect

namd/src/SimParameters.C:822

↓ 1 callersFunctionconfig_parser_gridforce

namd/src/SimParameters.C:1910

↓ 1 callersFunctionconfig_parser_methods

namd/src/SimParameters.C:999

↓ 1 callersFunctionconfig_parser_mgridforce

namd/src/SimParameters.C:1881

↓ 1 callersFunctionconfig_parser_misc

namd/src/SimParameters.C:2107

↓ 1 callersFunctionconfig_parser_movdrag

namd/src/SimParameters.C:1941

↓ 1 callersFunctionconfig_parser_openatom

namd/src/SimParameters.C:1871

↓ 1 callersFunctionconfig_parser_rotdrag

namd/src/SimParameters.C:1955

↓ 1 callersMethodcos_theta

\brief Return the projection of the orientation vector onto a predefined axis

src/colvartypes.h:1473

↓ 1 callersMethodcurrent_bin_scalar_fraction

\brief Report the fraction of bin beyond current_bin_scalar()

src/colvargrid.h:422

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