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Functions1,368 in github.com/Colvars/colvars

⨍ Functions 1,368◇ Types & classes 209

Methodtcl_run_force_callback

src/colvarproxy_tcl.cpp:52

Methodtemperature

namd/src/colvarproxy_namd.h:105

Methodtemperature

Temperature of the simulation (K)

gromacs/src/colvarproxy_gromacs.cpp:220

Methodtemperature

src/colvarmodule.cpp:1982

Methodtemperature

lammps/src/USER-COLVARS/colvarproxy_lammps.h:98

src/colvarcomp_rotations.cpp:267

Methodto_lower_cppstr

\brief Return a lowercased copy of the string

src/colvarparse.h:257

Methodto_simple_string

src/colvartypes.h:312

Methodto_simple_string

src/colvartypes.h:672

Methodto_simple_string

src/colvarvalue.cpp:651

src/colvarmodule.cpp:2051

Methodtotal_forces

src/colvaratoms.cpp:1282

Methodtotal_forces_enabled

namd/src/colvarproxy_namd.h:82

Methodtotal_forces_same_step

lammps/src/USER-COLVARS/colvarproxy_lammps.h:71

Methodtranspose

src/colvartypes.h:950

Methodtype_checking

\brief Whether or not the type check is enforced

src/colvarvalue.h:99

Methodtype_keyword

src/colvarvalue.cpp:44

Methodunsupported_op

src/colvarscript.cpp:420

src/colvarbias_histogram.cpp:114

src/colvarbias_restraint.cpp:38

src/colvarbias_alb.cpp:139

src/colvarbias_abf.cpp:336

src/colvarbias_meta.cpp:431

called from MD engine every step

src/colvar_UIestimator.h:304

src/colvarbias_restraint.h:107

MethodupdateDistanceToReferenceFrames

src/colvarcomp_apath.cpp:43

MethodupdateDistanceToReferenceFrames

src/colvarcomp_gpath.cpp:159

Methodupdate_acc_work

src/colvarbias_restraint.cpp:390

Methodupdate_active_cvc_square_norm

src/colvar.cpp:1918

Methodupdate_bias

src/colvarbias_meta.cpp:566

Methodupdate_centers

src/colvarbias_restraint.cpp:313

Methodupdate_colvar_forces

src/colvarmodule.cpp:917

Methodupdate_div_local

src/colvargrid.cpp:329

Methodupdate_grid_data

src/colvarbias_meta.cpp:630

Methodupdate_grid_params

src/colvarbias_meta.cpp:461

Methodupdate_pbc_lattice

src/colvarproxy.cpp:70

Methodupdate_replicas_registry

src/colvarbias_meta.cpp:1019

Methodupdate_system_force

src/colvarbias_abf.h:116

Methodupdate_system_forces

src/colvarbias.cpp:752

Methodupdate_total_charge

src/colvaratoms.cpp:323

Methodupdate_total_mass

src/colvaratoms.cpp:305

Methodvalue_input

\brief Get the value from a formatted output and transform it into the internal representation (the two may be different, e.g. when using colvar_grid_

src/colvargrid.h:725

Methodvalue_input

\brief Get the value from a formatted output and transform it into the internal representation (it may have been rescaled or manipulated)

src/colvargrid.h:1236

Methodvalue_input

\brief Get the value from a formatted output and transform it into the internal representation (it may have been rescaled or manipulated)

src/colvargrid.h:1459

Methodvalue_input

\brief Get the value from a formatted output and transform it into the internal representation (it may have been rescaled or manipulated)

src/colvargrid.h:1597

Methodvalue_output

\brief Return the value of the function at ix divided by its number of samples (if the count grid is defined)

src/colvargrid.h:1439

Methodvalue_output

\brief Return the value of the function at ix divided by its number of samples (if the count grid is defined)

src/colvargrid.h:1583

Methodvalue_to_bin_scalar

\brief Use the lower boundary and the width to report which bin the provided value is in

src/colvargrid.h:416

Methodvalue_to_bin_scalar_bound

\brief Use the lower boundary and the width to report which bin the provided value is in and assign first or last bin if out of boundaries

src/colvargrid.h:437

Methodvalue_to_bin_scalar_fraction

\brief Use the lower boundary and the width to report the fraction of bin beyond value_to_bin_scalar() that the provided value is in

src/colvargrid.h:429

The array of collective variable values, with shape = (n, d)

colvartools/plot_colvars_traj.py:93

Methodvariables

Names of variables defined

colvartools/plot_colvars_traj.py:142

Methodvariables

Access the variables vector

src/colvarbias.h:45

Methodvariables_active

src/colvarmodule.cpp:104

Default constructor

src/colvartypes.h:39

Methodvelocities

src/colvaratoms.cpp:1261

Methodversion_number

Get the version number (higher = more recent)

src/colvarmodule.h:85

Methodversion_number

Get the version number (higher = more recent)

src/colvarproxy.h:745

Methodvolmaps_available

src/colvarproxy_volmaps.cpp:20

src/colvarcomp.cpp:623

Wrap an index vector around periodic boundary conditions also checks validity of non-periodic indices

src/colvargrid.h:363

Methodwrap_string

src/colvarmodule.cpp:2176

Methodwrite_1D_pmf

src/colvar_UIestimator.h:510

Methodwrite_acf

src/colvar.cpp:2619

Write data to a dx file

colvartools/colvars_grid.py:268

Methodwrite_gradients_samples

src/colvarbias_abf.cpp:625

Methodwrite_grid_to_file

src/colvarbias_abf.cpp:586

Methodwrite_interal_data

write interal data, used for testing

src/colvar_UIestimator.h:539

Methodwrite_output_files

src/colvarbias_histogram.cpp:174

Methodwrite_output_files

src/colvarbias_restraint.cpp:1484

Methodwrite_output_files

Write any output files that this bias may have (e.g. PMF files)

src/colvarbias.h:189

Methodwrite_output_files

src/colvarbias_abf.cpp:809

Methodwrite_output_files

src/colvarbias_meta.cpp:1761

Methodwrite_output_files

src/colvarbias.cpp:857

Methodwrite_pmf

src/colvarbias_meta.cpp:1771

Methodwrite_replica_state_file

src/colvarbias_meta.cpp:1858

Methodwrite_state_to_replicas

If this bias is communicating with other replicas through files, send it to them

src/colvarbias.h:198

Methodwrite_traj_files

src/colvarmodule.cpp:1032

Methodwritehead

write heads of the output files

src/colvar_UIestimator.h:530

colvartools/abf_data.cpp:182

Method~ArithmeticPathBase

src/colvar_arithmeticpath.h:21

Method~CVBasedPath

src/colvarcomp_gpath.cpp:630

Method~CartesianBasedPath

src/colvarcomp_gpath.cpp:115

Method~FixColvars

* Clean up on deleting the fix. * *********************************/

lammps/src/USER-COLVARS/fix_colvars.cpp:366

Method~GeometricPathBase

src/colvar_geometricpath.h:69

Method~SimParameters

namd/src/SimParameters.h:1056

Method~UIestimator

src/colvar_UIestimator.h:301

Method~alpha_angles

src/colvarcomp_protein.cpp:128

src/colvarcomp.h:772

Method~aspathCV

src/colvarcomp_apath.cpp:101

gromacs/src/colvarproxy_gromacs.cpp:529

src/colvaratoms.cpp:69

Method~atom_group

src/colvaratoms.cpp:99

Method~azpathCV

src/colvarcomp_apath.cpp:190

Method~cartesian

src/colvarcomp.h:1402

src/colvar.cpp:1196

Method~colvar_grid

src/colvargrid.h:206

Method~colvar_grid_count

src/colvargrid.h:1208

Method~colvar_grid_gradient

src/colvargrid.h:1519

Method~colvar_grid_scalar

src/colvargrid.cpp:55

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