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Functions1,368 in github.com/Colvars/colvars

⨍ Functions 1,368◇ Types & classes 209

↓ 5 callersMethodget_colvar_cmd_arg

src/colvarscript.h:286

↓ 5 callersMethodincr

\brief Increment the index, in a way that will make it loop over the whole nd-dimensional array

src/colvargrid.h:763

↓ 5 callersMethodincrease_value

src/colvar_UIestimator.h:74

↓ 5 callersFunctioninthash_lookup

* inthash_lookup() - Lookup an entry in the hash table and return a pointer to * it or HASH_FAIL if it wasn't found. * * tptr: Pointer to the

lammps/src/USER-COLVARS/fix_colvars.cpp:192

↓ 5 callersMethodnew_index

\brief Get the index corresponding to the "first" bin, to be used as the initial value for an index in looping

src/colvargrid.h:745

↓ 5 callersMethodoffset

colvartools/abf_data.cpp:197

↓ 5 callersMethodpositions_shifted

src/colvaratoms.cpp:1240

↓ 5 callersMethodread_config_file

src/colvarmodule.cpp:134

↓ 5 callersMethodrequest_group2_gradients

Allocate space for the derivatives of the rotation

src/colvartypes.h:1371

↓ 5 callersFunctionsetup

vmd/src/colvarproxy_vmd.C:145

↓ 5 callersMethodsmp_enabled

src/colvarproxy.cpp:325

↓ 5 callersMethodvariables_active_smp

src/colvarmodule.cpp:110

↓ 4 callersMethodadd_grid

\brief Add data from another grid of the same type, AND identical definition (boundaries, widths)

src/colvargrid.h:694

↓ 4 callersFunctionatobool

namd/src/SimParameters.C:163

↓ 4 callersMethodcalc_required_properties

src/colvaratoms.cpp:967

↓ 4 callersMethodcenter_ref_pos

src/colvaratoms.cpp:940

↓ 4 callersMethodcheck_atom_id

src/colvarproxy.cpp:191

↓ 4 callersMethodcopy_grid

\brief Copy data from another grid of the same type, AND identical definition (boundaries, widths) Added for shared ABF.

src/colvargrid.h:511

↓ 4 callersMethodcosine

\brief Return the cosine between the orientation frame associated to this quaternion and another

src/colvartypes.h:1251

↓ 4 callersMethodfrom_simple_string

src/colvartypes.cpp:46

↓ 4 callersMethodget_bias_cmd_arg

src/colvarscript.h:293

↓ 4 callersMethodget_output_stream

src/colvarproxy.cpp:740

↓ 4 callersMethodget_time_step_factor

\brief returns time_step_factor

src/colvardeps.h:92

↓ 4 callersFunctionhistory_add_value

src/colvar.cpp:2439

↓ 4 callersMethodinit

src/colvar.cpp:53

↓ 4 callersMethodis_derivative

src/colvarvalue.cpp:202

↓ 4 callersMethodkey_lookup

src/colvarparse.cpp:656

↓ 4 callersMethodlog

src/colvarmodule.cpp:1677

↓ 4 callersMethodmap_grid

\brief Add data from another grid of the same type Note: this function maps other_grid inside this one regardless of whether it fits or not.

src/colvargrid.h:651

↓ 4 callersMethodnum_replicas

src/colvarproxy_replicas.cpp:32

↓ 4 callersMethodoutput_width

src/colvarvalue.cpp:780

↓ 4 callersMethodproc_features

src/colvarscript.cpp:349

↓ 4 callersMethodraw_data_in

\brief Input the data as they are represented in memory.

src/colvargrid.h:539

↓ 4 callersMethodraw_data_out

\brief Extract the grid data as they are represented in memory. Put the results in "out_data".

src/colvargrid.h:534

↓ 4 callersMethodresize

Allocation routine, used by all constructors

src/colvartypes.h:402

↓ 4 callersMethodset_div

src/colvargrid.cpp:259

↓ 4 callersMethodset_value

Set the value at the point with index ix

src/colvargrid.h:469

↓ 4 callersMethodsetup

\brief Allocate data

src/colvargrid.h:144

↓ 4 callersMethodsmp_thread_id

src/colvarproxy.cpp:414

↓ 4 callersFunctionupdate_atom_properties

namd/src/colvarproxy_namd.C:766

↓ 4 callersMethodweight

src/colvarbias_meta.h:339

↓ 3 callersMethodacc_force

\brief Accumulate the gradient based on the force (i.e. sums the opposite of the force)

src/colvargrid.h:1562

↓ 3 callersMethodaddress

Get the low-level index corresponding to an index

src/colvargrid.h:58

↓ 3 callersMethodas_vector

src/colvarvalue.h:639

↓ 3 callersMethodbackup_file

src/colvarproxy.cpp:533

↓ 3 callersFunctionbarrier

namd/src/ScriptTcl.C:74

↓ 3 callersMethodbin_distance_from_boundaries

\brief Get the minimal distance (in number of bins) from the boundaries; a negative number is returned if the given point is off-grid

src/colvargrid.h:621

↓ 3 callersMethodcalc_value

src/colvarcomp_apath.cpp:60

↓ 3 callersFunctioncheck_atom_id

vmd/src/colvarproxy_vmd.C:705

↓ 3 callersFunctioncolvarscript_obj

Get a pointer to the main colvarscript object

src/colvarscript.h:248

↓ 3 callersFunctioncompute_deviation

colvartools/abf_integrate.cpp:218

↓ 3 callersMethodcreate_sorted_ids

src/colvaratoms.cpp:892

↓ 3 callersMethodget_atom_id

Get the numeric ID of the given atom (for the program)

src/colvarproxy.h:221

↓ 3 callersMethodget_command_cmdline_help

src/colvarscript.cpp:230

↓ 3 callersMethodget_energy

src/colvarbias.h:203

↓ 3 callersMethodget_param_ptr

src/colvarparams.cpp:73

↓ 3 callersFunctionhistory_incr

src/colvar.cpp:2449

↓ 3 callersFunctionif

namd/src/SimParameters.C:5985

↓ 3 callersMethodincr_count

Increment the counter at given position

src/colvargrid.h:1221

↓ 3 callersMethodinit_from_colvars

src/colvargrid.h:253

↓ 3 callersMethodintegrate

src/colvargrid.cpp:221

↓ 3 callersFunctioninthash

inthash() - Hash function returns a hash number for a given key. * tptr: Pointer to a hash table, key: The key to create a hash number for */

lammps/src/USER-COLVARS/fix_colvars.cpp:111

↓ 3 callersMethodmaximum_value

src/colvargrid.cpp:59

↓ 3 callersMethodmodify_atom_positions

src/colvarproxy.h:284

↓ 3 callersMethodparse

src/colvaratoms.cpp:354

↓ 3 callersMethodreplica_enabled

src/colvarproxy_replicas.cpp:20

↓ 3 callersMethodreplica_index

src/colvarproxy_replicas.cpp:26

↓ 3 callersMethodrequest_actual_value

\brief Request grid to use actual values of extended coords

src/colvargrid.h:135

↓ 3 callersFunctionround_to_integer

src/colvarproxy.cpp:64

↓ 3 callersMethodrun

python/colvars.py:7

↓ 3 callersFunctionset_bool

Avoid having to put the bool assignment in the template :-(

src/colvarparse.cpp:26

↓ 3 callersMethodset_temperature

lammps/src/USER-COLVARS/colvarproxy_lammps.h:69

↓ 3 callersMethodset_zero_minimum

\brief Add constant to potential so that its minimum value is zero Useful e.g. for output

src/colvargrid.h:1676

↓ 3 callersMethodsmp_lock

src/colvarproxy.cpp:434

↓ 3 callersMethodsmp_num_threads

namd/src/colvarproxy_namd.h:144

↓ 3 callersMethodsmp_thread_id

namd/src/colvarproxy_namd.h:139

↓ 3 callersMethodsmp_unlock

src/colvarproxy.cpp:454

↓ 3 callersFunctionupdate_atoms_map

namd/src/colvarproxy_namd.C:165

↓ 3 callersMethodupdated_charges

Record whether masses have been updated

src/colvarproxy.h:306

↓ 3 callersMethodupdated_masses

Record whether masses have been updated

src/colvarproxy.h:300

↓ 3 callersMethodwrap

colvartools/abf_data.h:74

↓ 3 callersMethodwrite_output_files

src/colvar.cpp:2397

↓ 3 callersMethodwrite_restart

lammps/src/USER-COLVARS/fix_colvars.cpp:960

↓ 2 callersMethod_append_data

Read data from given file, appending frames to the time series if already present

colvartools/colvars_grid.py:162

↓ 2 callersMethodadd_bias_force

src/colvar.h:693

↓ 2 callersMethodadd_constant

\brief Add a constant to all elements (fast loop)

src/colvargrid.h:563

↓ 2 callersMethodadd_energy

src/colvarproxy.cpp:41

↓ 2 callersMethodapply_atom_group_force

Request that this force is applied to the given atom group

src/colvarproxy.h:394

↓ 2 callersMethodapply_translation

src/colvaratoms.cpp:1044

↓ 2 callersMethodaverage

Compute and return average value for a 1D gradient grid

src/colvargrid.h:1618

↓ 2 callersMethodbackup_file

src/colvarmodule.cpp:1452

↓ 2 callersMethodbin_to_value_scalar

\brief Use the two boundaries and the width to report the central value corresponding to a bin index

src/colvargrid.h:455

↓ 2 callersMethodcalc_center_of_geometry

src/colvaratoms.cpp:1103

↓ 2 callersMethodcalc_cvcs

src/colvar.cpp:1276

↓ 2 callersMethodcalc_dipole

src/colvaratoms.cpp:1138

↓ 2 callersMethodcalc_scripted_forces

src/colvarmodule.cpp:984

↓ 2 callersFunctioncheck_atom_id

namd/src/colvarproxy_namd.C:652

↓ 2 callersMethodclear

Deallocation routine

src/colvartypes.h:445

↓ 2 callersMethodcommunicate_forces

src/colvar.cpp:1819

↓ 2 callersMethodconfig_changed

src/colvarmodule.cpp:265

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