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Functions1,368 in github.com/Colvars/colvars

⨍ Functions 1,368◇ Types & classes 209

Function_to_str

src/colvarmodule.cpp:2013

Function_to_str_vector

src/colvarmodule.cpp:2027

Methodacc_force_weighted

\brief Accumulate the gradient based on the force (i.e. sums the opposite of the force) with a non-integer weight

src/colvargrid.h:1572

Methodacc_value

\brief Accumulate the value

src/colvargrid.h:1552

Reimplemented to work around MS compiler issues

src/colvarmodule.h:154

Methodadd_atom_group_slot

src/colvarproxy.cpp:258

Methodadd_atom_name_residue_range

src/colvaratoms.cpp:705

Methodadd_atom_numbers

src/colvaratoms.cpp:591

Methodadd_atom_numbers_range

src/colvaratoms.cpp:670

Methodadd_atom_slot

src/colvarproxy.cpp:168

Methodadd_atoms_of_group

src/colvaratoms.cpp:560

Methodadd_child

src/colvardeps.cpp:448

Methodadd_colvar

src/colvarbias.cpp:269

src/colvarvalue.cpp:287

Functionadd_energy

vmd/src/colvarproxy_vmd.C:294

Functionadd_energy

namd/src/colvarproxy_namd.C:596

Methodadd_energy

Pass restraint energy value for current timestep to MD engine

gromacs/src/colvarproxy_gromacs.cpp:407

Methodadd_energy

lammps/src/USER-COLVARS/colvarproxy_lammps.h:101

Methodadd_error_msg

src/colvarscript.cpp:439

src/colvarbias_meta.cpp:364

Methodadd_index_group

src/colvaratoms.cpp:629

Methodadd_keyword

src/colvarparse.cpp:526

Methodadd_volmap_slot

src/colvarproxy_volmaps.cpp:39

Methodalpha_angles

src/colvarcomp_protein.cpp:23

Perform analysis tasks

src/colvarbias.h:99

src/colvar.cpp:2423

src/colvarmodule.cpp:1069

src/colvarcomp_angles.cpp:15

Methodapply_force

gromacs/src/colvarproxy_gromacs.cpp:557

Methodapply_force

src/colvarcomp_protein.cpp:250

Methodapply_force

src/colvarcomp.h:1420

Methodapply_force

src/colvarcomp_coordnums.cpp:285

Methodapply_force

src/colvarcomp_apath.cpp:84

Methodapply_force

src/colvarcomp_volmaps.cpp:57

Methodapply_force

src/colvarcomp_rotations.cpp:127

Methodapply_force

src/colvarcomp_distances.cpp:87

Methodapply_force

src/colvarcomp_angles.cpp:123

Methodapply_force

src/colvarcomp_gpath.cpp:271

Methodapply_force

\brief Apply a force to the atom Note: the force is not applied instantly, but will be used later by the MD integrator (the colvars module does not i

src/colvaratoms.h:145

Methodas_vector

src/colvartypes.h:759

Methodas_vector

src/colvartypes.h:1098

src/colvarcomp.h:1658

src/colvarcomp_apath.cpp:15

Reimplemented to work around MS compiler issues

src/colvarmodule.h:160

Multiplication by sparse matrix representing Laplacian NOTE: Laplacian must be symmetric for solving with CG

src/colvargrid.cpp:381

gromacs/src/colvarproxy_gromacs.cpp:490

Methodatom_group

src/colvaratoms.cpp:78

Methodatom_group_by_name

src/colvarmodule.cpp:611

src/colvarcomp.h:1665

src/colvarcomp_apath.cpp:103

Methodbackend_angstrom_value

namd/src/colvarproxy_namd.h:95

Methodbackend_angstrom_value

GROMACS uses nanometers and kJ/mol internally

gromacs/src/colvarproxy_gromacs.cpp:212

Methodbackend_angstrom_value

lammps/src/USER-COLVARS/colvarproxy_lammps.h:95

Methodbackup_file

gromacs/src/colvarproxy_gromacs.cpp:324

Methodbackup_file

\brief Rename the given file, before overwriting it

src/colvarproxy.h:576

Methodbackup_file

lammps/src/USER-COLVARS/colvarproxy_lammps.cpp:342

Methodbias_by_name

src/colvarmodule.cpp:583

Methodbin_count

Give the count at a given bin index.

src/colvarbias_abf.cpp:678

For Tcl implementation of selection rules. Give the total number of bins for a given bias.

src/colvarbias_abf.cpp:670

Methodboltzmann

namd/src/colvarproxy_namd.h:100

Methodboltzmann

From Gnu units $ units -ts 'k' 'kJ/mol/K/avogadro' 0.0083144599 with v2.16 (older value 0.0083144621)

gromacs/src/colvarproxy_gromacs.cpp:217

Methodboltzmann

src/colvarmodule.cpp:1976

Methodboltzmann

lammps/src/USER-COLVARS/colvarproxy_lammps.h:97

Methodbuild_atom_list

src/colvar.cpp:917

Methodbuild_correlation_matrix

src/colvartypes.cpp:251

Return the 2-d C array

src/colvartypes.h:519

Methodcalc_1D_pmf

calculate 1D pmf

src/colvar_UIestimator.h:478

Methodcalc_Jacobian_derivative

src/colvarcomp_distances.cpp:81

Methodcalc_Jacobian_derivative

src/colvarcomp_angles.cpp:114

src/colvar.cpp:2457

Methodcalc_apply_roto_translation

src/colvaratoms.cpp:996

Methodcalc_biases

src/colvarmodule.cpp:853

Methodcalc_center_of_mass

src/colvaratoms.cpp:1118

Methodcalc_colvar_properties

src/colvar.cpp:1606

Methodcalc_colvars

src/colvarmodule.cpp:761

Functioncalc_colvars_items_smp

namd/src/colvarproxy_namd.C:1300

Methodcalc_coor_acf

src/colvar.cpp:2577

Functioncalc_cv_biases_smp

namd/src/colvarproxy_namd.C:1331

Functioncalc_cv_scripted_forces

namd/src/colvarproxy_namd.C:1360

Methodcalc_cvc_Jacobians

src/colvar.cpp:1564

Methodcalc_cvc_gradients

src/colvar.cpp:1453

Methodcalc_cvc_total_force

src/colvar.cpp:1505

Methodcalc_cvc_values

src/colvar.cpp:1350

Methodcalc_energy

src/colvarbias_abf.cpp:836

Methodcalc_energy

src/colvarbias_meta.cpp:655

Methodcalc_energy

src/colvarbias.cpp:334

Methodcalc_fit_gradients

src/colvaratoms.cpp:1166

Methodcalc_force_invgrads

src/colvarcomp_distances.cpp:69

Methodcalc_force_invgrads

src/colvarcomp_angles.cpp:91

Methodcalc_forces

src/colvarbias_meta.cpp:707

Methodcalc_forces

src/colvarbias.cpp:341

Methodcalc_gradients

src/colvarcomp_protein.cpp:187

Methodcalc_gradients

\brief Calculate the atomic gradients, to be reused later in order to apply forces

src/colvarcomp.h:171

Methodcalc_gradients

src/colvarcomp.h:1419

Methodcalc_gradients

src/colvarcomp_coordnums.cpp:279

Methodcalc_gradients

src/colvarcomp_volmaps.cpp:51

Methodcalc_gradients

src/colvarcomp_rotations.cpp:118

Methodcalc_gradients

src/colvarcomp_distances.cpp:61

Methodcalc_gradients

src/colvarcomp_angles.cpp:74

Methodcalc_gradients

src/colvarcomp_gpath.cpp:250

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