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Functions1,368 in github.com/Colvars/colvars

⨍ Functions 1,368◇ Types & classes 209

↓ 1 callersFunctioncvscript_command_names

src/colvarscript_commands.cpp:29

↓ 1 callersFunctioncvscript_n_commands

src/colvarscript_commands.cpp:22

↓ 1 callersMethoddcos_theta_dq

Return the derivative of the tilt wrt the quaternion

src/colvartypes.h:1488

↓ 1 callersMethoddebug_gradients

src/colvarcomp.cpp:483

↓ 1 callersMethoddefault_restart_frequency

Default restart frequency (as set by the simulation engine)

src/colvarproxy.h:619

↓ 1 callersMethoddeserialize_status

set status from string

lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:285

↓ 1 callersMethoddist2_rgrad

src/colvar.cpp:2094

↓ 1 callersMethoddspin_angle_dq

\brief Return the derivative of the spin angle with respect to the quaternion

src/colvartypes.h:1449

↓ 1 callersFunctioneigsrt

src/colvartypes.cpp:641

↓ 1 callersMethodenergy

src/colvarbias_meta.h:315

↓ 1 callersMethodenergy_difference

src/colvarbias.cpp:390

↓ 1 callersMethodentropy

src/colvargrid.cpp:108

↓ 1 callersMethodflush_output_streams

src/colvarproxy.cpp:775

↓ 1 callersFunctionfmax

src/colvarbias_alb.cpp:19

↓ 1 callersFunctionfmin

src/colvarbias_alb.cpp:20

↓ 1 callersFunctiongetLambdaDelta

namd/src/SimParameters.C:7174

↓ 1 callersMethodget_atom_charge

Get the charge of the given atom

src/colvarproxy.h:233

↓ 1 callersMethodget_atom_group_charge

Get the charge of the given atom group

src/colvarproxy.h:376

↓ 1 callersMethodget_atom_group_com

Read the current position of the center of mass given atom group

src/colvarproxy.h:382

↓ 1 callersMethodget_atom_group_mass

Get the mass of the given atom group

src/colvarproxy.h:370

↓ 1 callersMethodget_atom_group_total_force

Read the current total force of the given atom group

src/colvarproxy.h:388

↓ 1 callersMethodget_atom_lists

src/colvar.cpp:1185

↓ 1 callersMethodget_atom_mass

Get the mass of the given atom

src/colvarproxy.h:227

↓ 1 callersMethodget_atom_position

Read the current position of the given atom

src/colvarproxy.h:239

↓ 1 callersMethodget_atom_total_force

Read the current total force of the given atom

src/colvarproxy.h:245

↓ 1 callersMethodget_atom_velocity

Read the current velocity of the given atom

src/colvarproxy.h:257

↓ 1 callersMethodget_command_names

Get names of all commands

src/colvarscript.h:147

↓ 1 callersMethodget_elem

src/colvarvalue.cpp:303

↓ 1 callersMethodget_molid

src/colvarproxy.cpp:134

↓ 1 callersMethodget_param_grad

src/colvarcomp.cpp:343

↓ 1 callersMethodget_volmap_value

Read the current value of the volumetric map

src/colvarproxy_volmaps.h:46

↓ 1 callersMethodinit

Colvars Initialization

gromacs/src/colvarproxy_gromacs.cpp:109

↓ 1 callersMethodinit

lammps/src/USER-COLVARS/fix_colvars.cpp:405

↓ 1 callersFunctioninit_atom

vmd/src/colvarproxy_vmd.C:724

↓ 1 callersMethodinit_atom_group

src/colvarproxy.cpp:277

↓ 1 callersMethodinit_from_boundaries

src/colvargrid.h:324

↓ 1 callersMethodinit_gromacs_atom

gromacs/src/colvarproxy_gromacs.cpp:415

↓ 1 callersFunctioninit_tcl_pointers

namd/src/colvarproxy_namd.C:565

↓ 1 callersFunctioninit_volmap

namd/src/colvarproxy_namd.C:1240

↓ 1 callersMethodinit_volmap

src/colvarproxy_volmaps.cpp:49

↓ 1 callersFunctioninitialize_config_data

namd/src/SimParameters.C:127

↓ 1 callersMethodintegral

src/colvargrid.cpp:94

↓ 1 callersFunctioninthash_destroy

* inthash_destroy() - Delete the entire table, and all remaining entries. * */

lammps/src/USER-COLVARS/fix_colvars.cpp:246

↓ 1 callersFunctioninthash_insert

* inthash_insert() - Insert an entry into the hash table. If the entry already * exists return a pointer to it, otherwise return HASH_FAIL. * *

lammps/src/USER-COLVARS/fix_colvars.cpp:217

↓ 1 callersMethodis_available

Checks whether given feature is available Defaults to querying f_*_active

src/colvardeps.h:173

↓ 1 callersMethodis_dynamic

src/colvardeps.h:133

↓ 1 callersFunctionjacobi

src/colvartypes.cpp:559

↓ 1 callersFunctionload_atoms

vmd/src/colvarproxy_vmd.C:636

↓ 1 callersMethodload_coords_xyz

src/colvarmodule.cpp:1917

↓ 1 callersMethodlog_gradient_finite_diff

\brief Return the log-gradient from finite differences on the *same* grid for dimension n

src/colvargrid.h:1255

↓ 1 callersMethodmatch

\brief Choose the closest between Q2 and -Q2 and save it back. Not required for dist2() and dist2_grad()

src/colvartypes.h:1305

↓ 1 callersMethodminimum_pos_value

src/colvargrid.cpp:78

↓ 1 callersMethodminimum_value

src/colvargrid.cpp:69

↓ 1 callersMethodmodify_atom_charges

src/colvarproxy.h:277

↓ 1 callersMethodmodify_atom_masses

src/colvarproxy.h:270

↓ 1 callersMethodmodify_atom_new_colvar_forces

src/colvarproxy.h:294

↓ 1 callersMethodmodify_atom_types

lammps/src/USER-COLVARS/colvarproxy_lammps.h:117

↓ 1 callersFunctionmy_backup_file

Taken from colvarproxy_lammps. safely move filename to filename.extension

gromacs/src/colvarproxy_gromacs.cpp:77

↓ 1 callersFunctionnamd_python_initialize

namd/src/ScriptTcl.C:319

↓ 1 callersMethodnorm

src/colvartypes.h:801

↓ 1 callersMethodnorm2

src/colvartypes.h:210

↓ 1 callersMethodnorm2

src/colvartypes.h:796

↓ 1 callersMethodnorm2

Square norm of the quaternion

src/colvartypes.h:1109

↓ 1 callersMethodnum_active_cvcs

\brief number of CVC objects with an active flag (as set by update_cvc_flags)

src/colvar.h:401

↓ 1 callersMethodnum_biases_type

src/colvarmodule.cpp:541

↓ 1 callersMethodnum_variables

src/colvarmodule.cpp:501

↓ 1 callersMethodparam_exists

src/colvarparams.cpp:42

↓ 1 callersFunctionparse_cl

colvartools/abf_integrate.cpp:311

↓ 1 callersFunctionparse_mgrid_params

/ / FUNCTION parse_mgrid_params */ / / /

namd/src/SimParameters.C:6487

↓ 1 callersMethodparse_params

Read a grid definition from a config string

src/colvargrid.h:818

↓ 1 callersMethodposition_derivative_inner

src/colvartypes.cpp:178

↓ 1 callersFunctionprint_config

namd/src/SimParameters.C:4432

↓ 1 callersFunctionprint_mgrid_params

namd/src/SimParameters.C:6925

↓ 1 callersMethodprint_properties

src/colvaratoms.cpp:341

↓ 1 callersMethodproject_hills

src/colvarbias_meta.cpp:873

↓ 1 callersMethodprovide

src/colvardeps.cpp:93

↓ 1 callersMethodraw_data_num

\brief Size of the data as they are represented in memory.

src/colvargrid.h:545

↓ 1 callersMethodread

Read data from a Colvars multicolumn file

colvartools/colvars_grid.py:103

↓ 1 callersFunctionreadExtendedSystem

namd/src/SimParameters.C:2322

↓ 1 callersMethodread_colvar

src/colvarmodule.cpp:661

↓ 1 callersMethodread_data

src/colvarcomp.cpp:377

↓ 1 callersMethodread_position

Get the current position

src/colvaratoms.h:119

↓ 1 callersMethodread_state_file

lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:173

↓ 1 callersMethodread_state_prefix

src/colvarbias.cpp:562

↓ 1 callersMethodread_state_string

src/colvarbias.cpp:578

↓ 1 callersFunctionrebuild_table_int

* rebuild_table_int() - Create new hash table when old one fills up. * * tptr: Pointer to a hash table */

lammps/src/USER-COLVARS/fix_colvars.cpp:127

↓ 1 callersMethodregister_named_atom_group

src/colvarmodule.cpp:625

↓ 1 callersMethodremove_all_children

src/colvardeps.cpp:500

↓ 1 callersMethodrename_file

src/colvarproxy.cpp:573

↓ 1 callersMethodreplica_comm_barrier

src/colvarproxy_replicas.cpp:38

↓ 1 callersFunctionreplica_enabled

namd/src/colvarproxy_namd.C:1385

↓ 1 callersMethodreplica_share

src/colvarbias.cpp:414

↓ 1 callersMethodrequest_deletion

src/colvarproxy.cpp:637

↓ 1 callersFunctionrequest_total_force

vmd/src/colvarproxy_vmd.C:328

↓ 1 callersMethodreset_atoms_data

Call reset_data() for each atom

src/colvaratoms.h:408

↓ 1 callersMethodreset_bias_force

src/colvar.h:713

↓ 1 callersMethodrotation_matrix

Return the 3x3 matrix associated to this quaternion

src/colvartypes.h:1222

↓ 1 callersFunctionrunController

namd/src/ScriptTcl.C:107

↓ 1 callersMethodrun_colvar_callback

src/colvarproxy.cpp:495

↓ 1 callersMethodrun_colvar_gradient_callback

src/colvarproxy.cpp:503

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