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Functions1,368 in github.com/Colvars/colvars

⨍ Functions 1,368◇ Types & classes 209

↓ 855 callersMethodsize

src/colvarvalue.h:366

↓ 490 callersFunctionlog

vmd/src/colvarproxy_vmd.C:339

↓ 406 callersFunctionerror

vmd/src/colvarproxy_vmd.C:349

↓ 200 callersMethodbegin

src/colvaratoms.h:273

↓ 190 callersMethodend

src/colvaratoms.h:283

↓ 143 callersMethodtype

src/colvarvalue.cpp:172

↓ 140 callersMethodvalue

Set the hill value as specified

src/colvarbias_meta.h:333

↓ 124 callersMethodclear

src/colvarbias.cpp:227

↓ 92 callersMethodresize

src/colvartypes.h:88

↓ 88 callersMethodis_enabled

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

src/colvardeps.h:167

↓ 66 callersMethodcenter_of_mass

\brief Return the center of mass (COM) of the atomic positions

src/colvaratoms.h:459

↓ 63 callersMethodsize

src/colvartypes.h:83

↓ 54 callersMethodreset

src/colvarbias.cpp:206

↓ 53 callersMethodsize

src/colvarmodule.cpp:128

↓ 48 callersFunctionmain

colvartools/abf_integrate.cpp:29

↓ 47 callersMethodapply_colvar_force

src/colvaratoms.cpp:1324

↓ 43 callersMethodget_value

src/colvar_UIestimator.h:66

↓ 39 callersMethodset

\brief Set all components to a scalar

src/colvartypes.h:736

↓ 39 callersMethodset_result_str

src/colvarscript.cpp:427

↓ 30 callersMethodnorm

Norm of this colvarvalue

src/colvarvalue.h:185

↓ 29 callersMethodappend

Append time frames from a Colvars multicolumn file with same data shape Can be used to load history files from consecutive runs.

colvartools/colvars_grid.py:128

↓ 29 callersMethodnorm2

src/colvarvalue.h:664

↓ 26 callersMethodoutput_stream

src/colvarproxy.cpp:715

↓ 26 callersMethodset_weighted_gradient

src/colvaratoms.cpp:1152

↓ 25 callersMethodclose_output_stream

src/colvarproxy.cpp:788

↓ 25 callersMethodunit

src/colvartypes.h:806

↓ 23 callersMethodtotal_force

TODO make this an accessor

src/colvaratoms.cpp:1305

↓ 21 callersMethoddist2

src/colvar.cpp:2074

↓ 19 callersFunctionexit

namd/src/colvarproxy_namd.C:645

↓ 19 callersMethodobj_to_str

Use scripting language to get the string representation of an object

src/colvarscript.h:141

↓ 19 callersMethodtype

Get the current type

src/colvarvalue.h:166

↓ 18 callersMethodatom

src/colvaratoms.cpp:20

↓ 17 callersMethodadd_error_msg

src/colvarproxy.cpp:675

↓ 17 callersMethodget_frame

src/colvarproxy.cpp:521

↓ 17 callersMethodmodule

Pointer to the Colvars main object

src/colvarscript.h:174

↓ 16 callersMethodget_keyval

src/colvarparse.cpp:360

↓ 16 callersMethodindex_ok

\brief Check that the index is within range in each of the dimensions

src/colvargrid.h:752

↓ 16 callersFunctionlog

namd/src/colvarproxy_namd.C:614

↓ 16 callersMethodrotate

Return the rotated vector

src/colvartypes.h:1418

↓ 16 callersMethodwrite

Write data (final, not history) to a Colvars multicolumn file (2d only)

colvartools/colvars_grid.py:224

↓ 15 callersMethodcalc_optimal_rotation

src/colvartypes.cpp:333

↓ 15 callersMethoddist2_lgrad

src/colvar.cpp:2084

↓ 14 callersMethodenable

src/colvardeps.cpp:125

↓ 14 callersMethodread_total_forces

TODO make this a calc function

src/colvaratoms.cpp:1083

↓ 14 callersFunctionreset

namd/src/colvarproxy_namd.C:258

↓ 13 callersMethodundef_op

src/colvarvalue.cpp:416

↓ 12 callersFunctionerror

namd/src/colvarproxy_namd.C:624

↓ 11 callersMethodget_module_cmd_arg

src/colvarscript.h:279

↓ 11 callersMethodtotal_forces_same_step

src/colvarproxy.cpp:58

↓ 11 callersMethodwrap

src/colvar.cpp:2105

↓ 10 callersMethodget_colvars_index

\brief Get the bin indices corresponding to the provided values of the colvars

src/colvargrid.h:587

↓ 10 callersMethodproxy

Pointer to the colvarproxy object (interface with host engine)

src/colvarscript.h:180

↓ 10 callersMethodset_value

src/colvar_UIestimator.h:70

↓ 10 callersMethodsum

src/colvarvalue.h:696

↓ 9 callersMethodapply_constraints

src/colvarvalue.cpp:138

↓ 9 callersFunctionbackup_file

namd/src/colvarproxy_namd.C:1076

↓ 9 callersMethodbiases_active

src/colvarmodule.cpp:122

↓ 9 callersMethodcenter_of_geometry

\brief Return the center of geometry of the atomic positions

src/colvaratoms.h:437

↓ 9 callersMethodcheck_keywords

src/colvarparse.cpp:584

↓ 9 callersMethodclear

src/colvartypes.h:93

↓ 9 callersMethoddisable

src/colvardeps.cpp:294

↓ 9 callersMethodflush_output_stream

src/colvarproxy.cpp:757

↓ 9 callersMethodmultiplicity

Return the multiplicity of the type used

src/colvargrid.h:129

↓ 9 callersMethodxx

Return the xx element

src/colvartypes.h:897

↓ 9 callersMethodyy

Return the yy element

src/colvartypes.h:905

↓ 9 callersMethodzz

Return the zz element

src/colvartypes.h:913

↓ 8 callersMethodcurrent_bin_scalar

\brief Report the bin corresponding to the current value of variable i

src/colvargrid.h:394

↓ 8 callersMethodinner

\brief Inner product (as a 4-d vector) with Q2; requires match() if the largest overlap is looked for

src/colvartypes.h:1314

↓ 8 callersMethodmultiply_constant

\brief Multiply all elements by a scalar constant (fast loop)

src/colvargrid.h:571

↓ 8 callersMethodsetup_input

src/colvarmodule.cpp:1187

↓ 8 callersMethodto_simple_string

src/colvartypes.cpp:36

↓ 7 callersMethodapply_force

src/colvaratoms.cpp:1370

↓ 7 callersMethoddist2_grad

src/colvarvalue.cpp:567

↓ 7 callersFunctionload_coords

vmd/src/colvarproxy_vmd.C:510

↓ 7 callersMethodsetup

src/colvar.cpp:1171

↓ 7 callersMethodupdate

src/colvarbias.cpp:301

↓ 7 callersMethodvariables

src/colvarmodule.cpp:98

↓ 7 callersMethodxy

Return the xy element

src/colvartypes.h:899

↓ 7 callersMethodxz

Return the xz element

src/colvartypes.h:901

↓ 7 callersMethodyx

Return the yx element

src/colvartypes.h:903

↓ 7 callersMethodyz

Return the yz element

src/colvartypes.h:907

↓ 7 callersMethodzx

Return the zx element

src/colvartypes.h:909

↓ 7 callersMethodzy

Return the zy element

src/colvartypes.h:911

↓ 6 callersMethodacc_value

Accumulate the value

src/colvargrid.h:1373

↓ 6 callersMethodadd_atom

src/colvaratoms.cpp:115

↓ 6 callersMethodangstrom_to_internal

\brief Convert a length from Angstrom to internal

src/colvarproxy.h:77

↓ 6 callersMethodc_array

Return a pointer to the data location

src/colvartypes.h:57

↓ 6 callersMethodexit

gromacs/src/colvarproxy_gromacs.cpp:292

↓ 6 callersMethodget_vector

Return the vector component

src/colvartypes.h:1160

↓ 6 callersMethodinverse

Return the inverse of this rotation

src/colvartypes.h:1424

↓ 6 callersMethodnumber_of_points

Return the number of points in the i-th direction, if provided, or the total number

src/colvargrid.h:107

↓ 6 callersMethodread_positions

src/colvaratoms.cpp:954

↓ 6 callersMethodrequest_group1_gradients

Allocate space for the derivatives of the rotation

src/colvartypes.h:1363

↓ 6 callersMethodreset

src/colvarproxy.cpp:155

↓ 6 callersMethodsetup_output

src/colvarmodule.cpp:1240

↓ 6 callersMethodsimulation_running

Whether a simulation is running (warn against irrecovarable errors)

src/colvarproxy.h:725

↓ 6 callersMethodwrite_multicol

\brief Write the grid in a format which is both human readable and suitable for visualization e.g. with gnuplot

src/colvargrid.h:1014

↓ 5 callersMethodallowed

colvartools/abf_data.h:99

↓ 5 callersMethodcalc

Default schedule (everything is serialized)

src/colvar.cpp:1261

↓ 5 callersMethodget_cmdline_help_summary

src/colvarscript.cpp:198

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