Support dynamic communication of atom buffers #789
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -202,6 +202,10 @@ int colvarproxy_namd::update_atoms_map(AtomIDList::const_iterator begin, | |
| init_atoms_map(); | ||
| } | ||
|
|
||
| if (cvm::debug()) { | ||
| cvm::log("Updating atoms_map for "+cvm::to_str(begin - end)+" atoms.\n"); | ||
| } | ||
|
|
||
| for (AtomIDList::const_iterator a_i = begin; a_i != end; a_i++) { | ||
|
|
||
| if (atoms_map[*a_i] >= 0) continue; | ||
|
|
@@ -215,7 +219,7 @@ int colvarproxy_namd::update_atoms_map(AtomIDList::const_iterator begin, | |
|
|
||
| if (atoms_map[*a_i] < 0) { | ||
| // this atom is probably managed by another GlobalMaster: | ||
| // add it here anyway so that Colvars can ensure it is requested | ||
| int const index = add_atom_slot(*a_i); | ||
| atoms_map[*a_i] = index; | ||
| modifyRequestedAtoms().add(*a_i); | ||
|
|
@@ -566,11 +570,14 @@ void colvarproxy_namd::calculate() | |
| print_output_atomic_data(); | ||
| } | ||
|
|
||
| // communicate all forces to NAMD | ||
| for (size_t i = 0; i < atoms_ids.size(); i++) { | ||
| if (atoms_refcount[i] > 0) { | ||
| // Add a force only if the atom is currently used | ||
| cvm::rvector const &f = atoms_new_colvar_forces[i]; | ||
| modifyForcedAtoms().add(atoms_ids[i]); | ||
| modifyAppliedForces().add(Vector(f.x, f.y, f.z)); | ||
| } | ||
| } | ||
|
|
||
| if (atom_groups_new_colvar_forces.size() > 0) { | ||
|
|
@@ -612,13 +619,48 @@ void colvarproxy_namd::calculate() | |
| #endif | ||
| #endif | ||
|
|
||
| if (atom_list_frequency() > 0) { | ||
| if (((cvm::step_relative()+1) % atom_list_frequency()) == 0) { | ||
| // Before all-atom evaluation | ||
| update_requested_atoms(); | ||
| } | ||
| if ((cvm::step_relative() % atom_list_frequency()) == 0) { | ||
| // After all-atom computation | ||
|
Member
There was a problem hiding this comment. I may need to implement this in #783 as well. Why is
Member
Author
There was a problem hiding this comment. Those two requests happen at consecutive steps, first to recall all atoms that have positive refcount, then at the next step to prune those that don't. |
||
| update_requested_atoms(); | ||
| } | ||
| } | ||
|
|
||
| // NAMD does not destruct GlobalMaster objects, so we must remember | ||
| // to write all output files at the end of a run | ||
| if (step == simparams->N) { | ||
| post_run(); | ||
| } | ||
| } | ||
|
|
||
|
|
||
| int colvarproxy_namd::update_requested_atoms() | ||
| { | ||
| int error_code = COLVARS_OK; | ||
| if (cvm::debug()) { | ||
| cvm::log("Updating list of requested atoms from NAMD.\n"); | ||
| cvm::log("Before: "+cvm::to_str(modifyRequestedAtoms().size())+ | ||
| " elements.\n"); | ||
| } | ||
| modifyRequestedAtoms().clear(); | ||
| for (size_t i = 0; i < atoms_ids.size(); i++) { | ||
| if (atoms_refcount[i] > 0) { | ||
| modifyRequestedAtoms().add(atoms_ids[i]); | ||
| } | ||
| } | ||
| if (cvm::debug()) { | ||
| cvm::log("After: "+cvm::to_str(modifyRequestedAtoms().size())+ | ||
| " elements.\n"); | ||
| } | ||
|
|
||
| return COLVARS_OK; | ||
| } | ||
|
|
||
|
|
||
| void colvarproxy_namd::update_accelMD_info() { | ||
| // This aMD factor is from previous step! | ||
| amd_weight_factor = std::exp(controller->accelMDdV / (target_temperature() * boltzmann())); | ||
|
|
@@ -836,10 +878,20 @@ int colvarproxy_namd::init_atom(cvm::residue_id const &residue, | |
| } | ||
|
|
||
|
|
||
| int colvarproxy_namd::clear_atom(int index) | ||
| { | ||
| int error_code = colvarproxy::clear_atom(index); | ||
| if (error_code == COLVARS_OK) { | ||
| if (atoms_refcount[index] == 0) { | ||
| // Clear this atom entry from the requested atoms | ||
| int aid = atoms_ids[index]; | ||
| int const aid_index_in_gm = modifyRequestedAtoms().find(aid); | ||
| if (aid_index_in_gm >= 0) { | ||
| modifyRequestedAtoms().del(aid_index_in_gm, 1); | ||
| } | ||
| } | ||
| } | ||
| return error_code; | ||
| } | ||
|
|
||
|
|
||
|
|
@@ -1435,18 +1487,39 @@ void colvarproxy_namd::GridForceGridLoop(T const *g, | |
| cvm::atom_iter atom_begin, | ||
| cvm::atom_iter atom_end, | ||
| cvm::real *value, | ||
| cvm::real *atom_field, | ||
| int *inside) | ||
| { | ||
| float V = 0.0f; | ||
| Vector dV(0.0); | ||
| int i = 0, status = -1; | ||
| cvm::atom_iter ai = atom_begin; | ||
| for ( ; ai != atom_end; ai++, i++) { | ||
|
|
||
| if ((flags & volmap_flag_use_atomlist) && | ||
| !(flags & volmap_flag_rebuild_atomlist)) { | ||
| if (inside[i] == 0) { | ||
| // Skip atom according to precomputed list | ||
| continue; | ||
| } | ||
| } | ||
|
|
||
| // TODO look into compute_V() to skip gradient computation | ||
|
|
||
| if (g->compute_VdV(Position(ai->pos.x, ai->pos.y, ai->pos.z), V, dV)) { | ||
| // out-of-bounds atom | ||
| if (flags & volmap_flag_rebuild_atomlist) { | ||
| inside[i] = 0; | ||
| decrease_refcount(ai->array_index()); | ||
| } | ||
| V = 0.0f; | ||
| dV = 0.0; | ||
| } else { | ||
|
|
||
| if (flags & volmap_flag_rebuild_atomlist) { | ||
| inside[i] = 1; | ||
| } | ||
|
|
||
| if (flags & volmap_flag_use_atom_field) { | ||
| *value += V * atom_field[i]; | ||
| if (flags & volmap_flag_gradients) { | ||
|
|
@@ -1469,16 +1542,47 @@ void colvarproxy_namd::getGridForceGridValue(int flags, | |
| cvm::atom_iter atom_begin, | ||
| cvm::atom_iter atom_end, | ||
| cvm::real *value, | ||
| cvm::real *atom_field, | ||
| int *inside) | ||
| { | ||
| if (atom_field) { | ||
|
|
||
| if (flags & volmap_flag_use_atomlist) { | ||
| if (flags & volmap_flag_rebuild_atomlist) { | ||
| int const new_flags = volmap_flag_use_atom_field | | ||
| volmap_flag_use_atomlist | volmap_flag_rebuild_atomlist; | ||
| GridForceGridLoop<T, new_flags>(g, atom_begin, atom_end, | ||
| value, atom_field, inside); | ||
| } else { | ||
| int const new_flags = volmap_flag_use_atom_field | | ||
| volmap_flag_use_atomlist; | ||
| GridForceGridLoop<T, new_flags>(g, atom_begin, atom_end, | ||
| value, atom_field, inside); | ||
| } | ||
| } else { | ||
| int const new_flags = volmap_flag_use_atom_field; | ||
| GridForceGridLoop<T, new_flags>(g, atom_begin, atom_end, | ||
| value, atom_field, inside); | ||
| } | ||
|
|
||
| } else { | ||
|
|
||
| if (flags & volmap_flag_use_atomlist) { | ||
| if (flags & volmap_flag_rebuild_atomlist) { | ||
| int const new_flags = volmap_flag_use_atomlist | | ||
| volmap_flag_rebuild_atomlist; | ||
| GridForceGridLoop<T, new_flags>(g, atom_begin, atom_end, | ||
| value, atom_field, inside); | ||
| } else { | ||
| int const new_flags = volmap_flag_use_atomlist; | ||
| GridForceGridLoop<T, new_flags>(g, atom_begin, atom_end, | ||
| value, atom_field, inside); | ||
| } | ||
| } else { | ||
| int const new_flags = volmap_flag_null; | ||
| GridForceGridLoop<T, new_flags>(g, atom_begin, atom_end, | ||
| value, atom_field, inside); | ||
| } | ||
| } | ||
| } | ||
|
|
||
|
|
@@ -1488,19 +1592,20 @@ int colvarproxy_namd::compute_volmap(int flags, | |
| cvm::atom_iter atom_begin, | ||
| cvm::atom_iter atom_end, | ||
| cvm::real *value, | ||
| cvm::real *atom_field, | ||
| int *inside) | ||
| { | ||
| Molecule *mol = Node::Object()->molecule; | ||
| GridforceGrid *grid = mol->get_gridfrc_grid(volmap_id); | ||
| // Inheritance is not possible with GridForceGrid's design | ||
| if (grid->get_grid_type() == GridforceGrid::GridforceGridTypeFull) { | ||
| GridforceFullMainGrid *g = dynamic_cast<GridforceFullMainGrid *>(grid); | ||
| getGridForceGridValue<GridforceFullMainGrid>(flags, g, atom_begin, atom_end, | ||
| value, atom_field, inside); | ||
| } else if (grid->get_grid_type() == GridforceGrid::GridforceGridTypeLite) { | ||
| GridforceLiteGrid *g = dynamic_cast<GridforceLiteGrid *>(grid); | ||
| getGridForceGridValue<GridforceLiteGrid>(flags, g, atom_begin, atom_end, | ||
| value, atom_field, inside); | ||
| } | ||
| return COLVARS_OK; | ||
| } | ||
|
|
||
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
It may work well in the GlobalMaster interface. However, the CudaGlobalMaster interface regards
atoms_idsas the atoms requested. What should I do to #783?There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I'm commenting here only on this issue, since your other comments seem to connect to it.
The crux of the problem appears to be that classic GlobalMaster has its own list of currently requested atoms, which is dynamic and distinct from
colvarproxy::atoms_ids, which is a static list. Instead, CUDAGlobalMaster uses directlyatoms_ids.I guess this could be addressed by hosting both lists (static and dynamic) within the proxy object, so that the different implementations can just use the one that they support.