From d3e69170f08e57bf0221d39a87bc349648590fa7 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Sat, 2 Jul 2022 12:18:56 -0400 Subject: [PATCH 01/72] bugfix: specials update corner case --- src/REACTION/fix_bond_react.cpp | 88 +++++++++++++++++++-------------- 1 file changed, 50 insertions(+), 38 deletions(-) diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index 6efb9630a2..9e2f07ba4a 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -2904,6 +2904,11 @@ void FixBondReact::update_everything() int nmark = nlocal; memory->create(mark,nmark,"bond/react:mark"); for (int i = 0; i < nmark; i++) mark[i] = 0; + + // flag used to delete special interactions + int *delflag; + memory->create(delflag,atom->maxspecial,"bond/react:delflag"); + tagint *tag = atom->tag; AtomVec *avec = atom->avec; @@ -3029,62 +3034,68 @@ void FixBondReact::update_everything() // very nice and easy to completely overwrite special bond info for landlocked atoms for (int i = 0; i < update_num_mega; i++) { rxnID = update_mega_glove[0][i]; + onemol = atom->molecules[unreacted_mol[rxnID]]; twomol = atom->molecules[reacted_mol[rxnID]]; for (int j = 0; j < twomol->natoms; j++) { int jj = equivalences[j][1][rxnID]-1; - if (atom->map(update_mega_glove[jj+1][i]) < nlocal && atom->map(update_mega_glove[jj+1][i]) >= 0) { + int ilocal = atom->map(update_mega_glove[jj+1][i]); + if (ilocal < nlocal && ilocal >= 0) { if (landlocked_atoms[j][rxnID] == 1) { for (int k = 0; k < 3; k++) { - nspecial[atom->map(update_mega_glove[jj+1][i])][k] = twomol->nspecial[j][k]; + nspecial[ilocal][k] = twomol->nspecial[j][k]; } for (int p = 0; p < twomol->nspecial[j][2]; p++) { - special[atom->map(update_mega_glove[jj+1][i])][p] = update_mega_glove[equivalences[twomol->special[j][p]-1][1][rxnID]][i]; + special[ilocal][p] = update_mega_glove[equivalences[twomol->special[j][p]-1][1][rxnID]][i]; } } // now delete and replace landlocked atoms from non-landlocked atoms' special info + // delete 1-2, 1-3, 1-4 specials individually. only delete if special exists in pre-reaction template if (landlocked_atoms[j][rxnID] == 0) { - for (int k = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; k > -1; k--) { - for (int p = 0; p < twomol->natoms; p++) { - int pp = equivalences[p][1][rxnID]-1; - if (p!=j && special[atom->map(update_mega_glove[jj+1][i])][k] == update_mega_glove[pp+1][i] - && landlocked_atoms[p][rxnID] == 1) { - for (int n = k; n < nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n++) { - special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n+1]; + int ispec, fspec, imolspec, fmolspec, nspecdel[3]; + for (int k = 0; k < 3; k++) nspecdel[k] = 0; + for (int k = 0; k < atom->maxspecial; k++) delflag[k] = 0; + for (int specn = 0; specn < 3; specn++) { + if (specn == 0) { + imolspec = 0; + ispec = 0; + } else { + imolspec = onemol->nspecial[jj][specn-1]; + ispec = nspecial[ilocal][specn-1]; + } + fmolspec = onemol->nspecial[jj][specn]; + fspec = nspecial[ilocal][specn]; + for (int k = ispec; k < fspec; k++) { + for (int p = imolspec; p < fmolspec; p++) { + if (update_mega_glove[onemol->special[jj][p]][i] == special[ilocal][k]) { + delflag[k] = 1; + for (int m = 2; m >= specn; m--) nspecdel[m]++; + break; } - if (k+1 > nspecial[atom->map(update_mega_glove[jj+1][i])][1]) { - nspecial[atom->map(update_mega_glove[jj+1][i])][2]--; - } else if (k+1 > nspecial[atom->map(update_mega_glove[jj+1][i])][0]) { - nspecial[atom->map(update_mega_glove[jj+1][i])][1]--; - nspecial[atom->map(update_mega_glove[jj+1][i])][2]--; - } else { - nspecial[atom->map(update_mega_glove[jj+1][i])][0]--; - nspecial[atom->map(update_mega_glove[jj+1][i])][1]--; - nspecial[atom->map(update_mega_glove[jj+1][i])][2]--; - } - break; } } } + int incr = 0; + for (int k = 0; k < nspecial[ilocal][2]; k++) + if (delflag[k] == 0) special[ilocal][incr++] = special[ilocal][k]; + for (int m = 0; m < 3; m++) nspecial[ilocal][m] -= nspecdel[m]; // now reassign from reacted template for (int k = 0; k < twomol->nspecial[j][2]; k++) { - if (landlocked_atoms[twomol->special[j][k]-1][rxnID] == 1) { - if (k > twomol->nspecial[j][1] - 1) { - insert_num = nspecial[atom->map(update_mega_glove[jj+1][i])][2]++; - } else if (k > twomol->nspecial[j][0] - 1) { - insert_num = nspecial[atom->map(update_mega_glove[jj+1][i])][1]++; - nspecial[atom->map(update_mega_glove[jj+1][i])][2]++; - } else { - insert_num = nspecial[atom->map(update_mega_glove[jj+1][i])][0]++; - nspecial[atom->map(update_mega_glove[jj+1][i])][1]++; - nspecial[atom->map(update_mega_glove[jj+1][i])][2]++; - } - if (nspecial[atom->map(update_mega_glove[jj+1][i])][2] > atom->maxspecial) - error->one(FLERR,"Bond/react special bond generation overflow"); - for (int n = nspecial[atom->map(update_mega_glove[jj+1][i])][2]-1; n > insert_num; n--) { - special[atom->map(update_mega_glove[jj+1][i])][n] = special[atom->map(update_mega_glove[jj+1][i])][n-1]; - } - special[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->special[j][k]-1][1][rxnID]][i]; + if (k > twomol->nspecial[j][1] - 1) { + insert_num = nspecial[ilocal][2]++; + } else if (k > twomol->nspecial[j][0] - 1) { + insert_num = nspecial[ilocal][1]++; + nspecial[ilocal][2]++; + } else { + insert_num = nspecial[ilocal][0]++; + nspecial[ilocal][1]++; + nspecial[ilocal][2]++; } + if (nspecial[ilocal][2] > atom->maxspecial) + error->one(FLERR,"Bond/react special bond generation overflow"); + for (int n = nspecial[ilocal][2]-1; n > insert_num; n--) { + special[ilocal][n] = special[ilocal][n-1]; + } + special[ilocal][insert_num] = update_mega_glove[equivalences[twomol->special[j][k]-1][1][rxnID]][i]; } } } @@ -3480,6 +3491,7 @@ void FixBondReact::update_everything() } } memory->destroy(mark); + memory->destroy(delflag); MPI_Allreduce(&ndelone,&ndel,1,MPI_INT,MPI_SUM,world); From ab6a658dee455f081898c670b11c87c547ee8f37 Mon Sep 17 00:00:00 2001 From: jrgissing Date: Sat, 2 Jul 2022 16:17:35 -0400 Subject: [PATCH 02/72] very-small-templates bugfix --- src/REACTION/fix_bond_react.cpp | 39 +++++++++++++++++++-------------- 1 file changed, 23 insertions(+), 16 deletions(-) diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index 9e2f07ba4a..7bfa2db866 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -1724,17 +1724,7 @@ void FixBondReact::inner_crosscheck_loop() int num_choices = 0; for (int i = 0; i < nfirst_neighs; i++) { - - int already_assigned = 0; - for (int j = 0; j < onemol->natoms; j++) { - if (glove[j][1] == xspecial[atom->map(glove[pion][1])][i]) { - already_assigned = 1; - break; - } - } - - if (already_assigned == 0 && - type[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol_xspecial[pion][neigh]-1]) { + if (type[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] == onemol->type[(int)onemol_xspecial[pion][neigh]-1]) { if (num_choices > 5) { // here failed because too many identical first neighbors. but really no limit if situation arises status = GUESSFAIL; return; @@ -1748,11 +1738,28 @@ void FixBondReact::inner_crosscheck_loop() // ...actually, avail_guesses should never be zero here anyway if (guess_branch[avail_guesses-1] == 0) guess_branch[avail_guesses-1] = num_choices; - //std::size_t size = sizeof(tag_choices) / sizeof(tag_choices[0]); - std::sort(tag_choices, tag_choices + num_choices); //, std::greater()); - glove[onemol_xspecial[pion][neigh]-1][0] = onemol_xspecial[pion][neigh]; - glove[onemol_xspecial[pion][neigh]-1][1] = tag_choices[guess_branch[avail_guesses-1]-1]; - guess_branch[avail_guesses-1]--; + std::sort(tag_choices, tag_choices + num_choices); + for (int i = guess_branch[avail_guesses-1]-1; i >= 0; i--) { + int already_assigned = 0; + for (int j = 0; j < onemol->natoms; j++) { + if (glove[j][1] == tag_choices[i]) { + already_assigned = 1; + break; + } + } + if (already_assigned == 1) { + guess_branch[avail_guesses-1]--; + if (guess_branch[avail_guesses-1] == 0) { + status = REJECT; + return; + } + } else { + glove[onemol_xspecial[pion][neigh]-1][0] = onemol_xspecial[pion][neigh]; + glove[onemol_xspecial[pion][neigh]-1][1] = tag_choices[i]; + guess_branch[avail_guesses-1]--; + break; + } + } //another check for ghost atoms. perhaps remove the one in make_a_guess if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { From bc542a86732037e359d2087012421b85b5404513 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 2 Jul 2022 19:38:37 -0400 Subject: [PATCH 03/72] cosmetic changes, silence warnings, avoid temporary char buffers --- src/REACTION/fix_bond_react.cpp | 182 +++++++++++++++----------------- 1 file changed, 85 insertions(+), 97 deletions(-) diff --git a/src/REACTION/fix_bond_react.cpp b/src/REACTION/fix_bond_react.cpp index 7bfa2db866..0405971bdd 100644 --- a/src/REACTION/fix_bond_react.cpp +++ b/src/REACTION/fix_bond_react.cpp @@ -289,9 +289,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : char *str = utils::strdup(&arg[iarg][2]); var_id[NEVERY][rxn] = input->variable->find(str); if (var_id[NEVERY][rxn] < 0) - error->all(FLERR,"Bond/react: Variable name does not exist"); + error->all(FLERR,"Fix bond/react: Variable name does not exist"); if (!input->variable->equalstyle(var_id[NEVERY][rxn])) - error->all(FLERR,"Bond/react: Variable is not equal-style"); + error->all(FLERR,"Fix bond/react: Variable is not equal-style"); var_flag[NEVERY][rxn] = 1; delete [] str; } else { @@ -305,9 +305,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : char *str = utils::strdup(&arg[iarg][2]); var_id[RMIN][rxn] = input->variable->find(str); if (var_id[RMIN][rxn] < 0) - error->all(FLERR,"Bond/react: Variable name does not exist"); + error->all(FLERR,"Fix bond/react: Variable name does not exist"); if (!input->variable->equalstyle(var_id[RMIN][rxn])) - error->all(FLERR,"Bond/react: Variable is not equal-style"); + error->all(FLERR,"Fix bond/react: Variable is not equal-style"); double cutoff = input->variable->compute_equal(var_id[RMIN][rxn]); cutsq[rxn][0] = cutoff*cutoff; var_flag[RMIN][rxn] = 1; @@ -324,9 +324,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : char *str = utils::strdup(&arg[iarg][2]); var_id[RMAX][rxn] = input->variable->find(str); if (var_id[RMAX][rxn] < 0) - error->all(FLERR,"Bond/react: Variable name does not exist"); + error->all(FLERR,"Fix bond/react: Variable name does not exist"); if (!input->variable->equalstyle(var_id[RMAX][rxn])) - error->all(FLERR,"Bond/react: Variable is not equal-style"); + error->all(FLERR,"Fix bond/react: Variable is not equal-style"); double cutoff = input->variable->compute_equal(var_id[RMAX][rxn]); cutsq[rxn][1] = cutoff*cutoff; var_flag[RMAX][rxn] = 1; @@ -359,9 +359,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : char *str = utils::strdup(&arg[iarg+1][2]); var_id[PROB][rxn] = input->variable->find(str); if (var_id[PROB][rxn] < 0) - error->all(FLERR,"Bond/react: Variable name does not exist"); + error->all(FLERR,"Fix bond/react: Variable name does not exist"); if (!input->variable->equalstyle(var_id[PROB][rxn])) - error->all(FLERR,"Bond/react: Variable is not equal-style"); + error->all(FLERR,"Fix bond/react: Variable is not equal-style"); fraction[rxn] = input->variable->compute_equal(var_id[PROB][rxn]); var_flag[PROB][rxn] = 1; delete [] str; @@ -397,7 +397,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[iarg+1],"no") == 0) custom_charges_fragid[rxn] = -1; //default else { custom_charges_fragid[rxn] = atom->molecules[unreacted_mol[rxn]]->findfragment(arg[iarg+1]); - if (custom_charges_fragid[rxn] < 0) error->one(FLERR,"Bond/react: Molecule fragment for " + if (custom_charges_fragid[rxn] < 0) error->one(FLERR,"Fix bond/react: Molecule fragment for " "'custom_charges' keyword does not exist"); } iarg += 2; @@ -407,7 +407,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[iarg+1],"off") == 0) molecule_keyword[rxn] = OFF; //default else if (strcmp(arg[iarg+1],"inter") == 0) molecule_keyword[rxn] = INTER; else if (strcmp(arg[iarg+1],"intra") == 0) molecule_keyword[rxn] = INTRA; - else error->one(FLERR,"Bond/react: Illegal option for 'molecule' keyword"); + else error->one(FLERR,"Fix bond/react: Illegal option for 'molecule' keyword"); iarg += 2; } else if (strcmp(arg[iarg],"modify_create") == 0) { if (iarg++ > narg) error->all(FLERR,"Illegal fix bond/react command: " @@ -419,7 +419,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : if (strcmp(arg[iarg+1],"all") == 0) modify_create_fragid[rxn] = -1; //default else { modify_create_fragid[rxn] = atom->molecules[reacted_mol[rxn]]->findfragment(arg[iarg+1]); - if (modify_create_fragid[rxn] < 0) error->one(FLERR,"Bond/react: Molecule fragment for " + if (modify_create_fragid[rxn] < 0) error->one(FLERR,"Fix bond/react: Molecule fragment for " "'modify_create' keyword does not exist"); } iarg += 2; @@ -477,9 +477,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : read(i); fclose(fp); if (ncreate == 0 && onemol->natoms != twomol->natoms) - error->all(FLERR,"Bond/react: Reaction templates must contain the same number of atoms"); + error->all(FLERR,"Fix bond/react: Reaction templates must contain the same number of atoms"); else if (ncreate > 0 && onemol->natoms + ncreate != twomol->natoms) - error->all(FLERR,"Bond/react: Incorrect number of created atoms"); + error->all(FLERR,"Fix bond/react: Incorrect number of created atoms"); iatomtype[i] = onemol->type[ibonding[i]-1]; jatomtype[i] = onemol->type[jbonding[i]-1]; find_landlocked_atoms(i); @@ -507,7 +507,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : delete [] files; if (atom->molecular != Atom::MOLECULAR) - error->all(FLERR,"Bond/react: Cannot use fix bond/react with non-molecular systems"); + error->all(FLERR,"Fix bond/react: Cannot use fix bond/react with non-molecular systems"); // check if bonding atoms are 1-2, 1-3, or 1-4 bonded neighbors // if so, we don't need non-bonded neighbor list @@ -799,7 +799,7 @@ void FixBondReact::init() for (int i = 0; i < nreacts; i++) { if (!utils::strmatch(force->pair_style,"^hybrid")) if (force->pair == nullptr || cutsq[i][1] > force->pair->cutsq[iatomtype[i]][jatomtype[i]]) - error->all(FLERR,"Bond/react: Fix bond/react cutoff is longer than pairwise cutoff"); + error->all(FLERR,"Fix bond/react: Fix bond/react cutoff is longer than pairwise cutoff"); } // need a half neighbor list, built every Nevery steps @@ -1357,7 +1357,7 @@ void FixBondReact::superimpose_algorithm() // let's go ahead and catch the simplest of hangs //if (hang_catch > onemol->natoms*4) if (hang_catch > atom->nlocal*30) { - error->one(FLERR,"Bond/react: Excessive iteration of superimpose algorithm. " + error->one(FLERR,"Fix bond/react: Excessive iteration of superimpose algorithm. " "Please check that all pre-reaction template atoms are linked to an initiator atom, " "via at least one path that does not involve edge atoms."); } @@ -1482,7 +1482,7 @@ void FixBondReact::make_a_guess() for (int i = 0; i < nxspecial[atom->map(glove[pion][1])][0]; i++) { if (atom->map(xspecial[atom->map(glove[pion][1])][i]) < 0) { - error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); // parallel issues. + error->one(FLERR,"Fix bond/react: Fix bond/react needs ghost atoms from further away"); // parallel issues. } if (i_limit_tags[(int)atom->map(xspecial[atom->map(glove[pion][1])][i])] != 0) { status = GUESSFAIL; @@ -1593,7 +1593,7 @@ void FixBondReact::check_a_neighbor() //another check for ghost atoms. perhaps remove the one in make_a_guess if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { - error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); + error->one(FLERR,"Fix bond/react: Fix bond/react needs ghost atoms from further away"); } for (int j = 0; j < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; j++) { @@ -1645,7 +1645,7 @@ void FixBondReact::check_a_neighbor() //another check for ghost atoms. perhaps remove the one in make_a_guess if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { - error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); + error->one(FLERR,"Fix bond/react: Fix bond/react needs ghost atoms from further away"); } for (int ii = 0; ii < onemol_nxspecial[onemol_xspecial[pion][neigh]-1][0]; ii++) { @@ -1687,7 +1687,7 @@ void FixBondReact::crosscheck_the_neighbor() glove[onemol_xspecial[pion][trace]-1][0] == 0) { if (avail_guesses == MAXGUESS) { - error->warning(FLERR,"Bond/react: Fix bond/react failed because MAXGUESS set too small. ask developer for info"); + error->warning(FLERR,"Fix bond/react: Fix bond/react failed because MAXGUESS set too small. ask developer for info"); status = GUESSFAIL; return; } @@ -1763,7 +1763,7 @@ void FixBondReact::inner_crosscheck_loop() //another check for ghost atoms. perhaps remove the one in make_a_guess if (atom->map(glove[(int)onemol_xspecial[pion][neigh]-1][1]) < 0) { - error->one(FLERR,"Bond/react: Fix bond/react needs ghost atoms from further away"); + error->one(FLERR,"Fix bond/react: Fix bond/react needs ghost atoms from further away"); } if (guess_branch[avail_guesses-1] == 0) avail_guesses--; @@ -2117,7 +2117,8 @@ get per-atom variable names used by custom constraint void FixBondReact::customvarnames() { - int pos,pos1,pos2,pos3,prev3; + std::size_t pos,pos1,pos2,pos3; + int prev3; std::string varstr,argstr,varid; // search all constraints' varstr for special 'rxn' functions @@ -2131,19 +2132,19 @@ void FixBondReact::customvarnames() prev3 = -1; while (true) { // find next reaction special function occurrence - pos1 = INT_MAX; + pos1 = std::string::npos; for (int i = 0; i < nrxnfunction; i++) { pos = varstr.find(rxnfunclist[i],prev3+1); if (pos == std::string::npos) continue; if (pos < pos1) pos1 = pos; } - if (pos1 == INT_MAX) break; + if (pos1 == std::string::npos) break; pos2 = varstr.find("(",pos1); pos3 = varstr.find(")",pos2); if (pos2 == std::string::npos || pos3 == std::string::npos) - error->all(FLERR,"Bond/react: Illegal rxn function syntax\n"); - prev3 = pos3; + error->all(FLERR,"Fix bond/react: Illegal rxn function syntax\n"); + prev3 = (int)pos3; argstr = varstr.substr(pos2+1,pos3-pos2-1); argstr.erase(remove_if(argstr.begin(), argstr.end(), isspace), argstr.end()); // remove whitespace pos2 = argstr.find(","); @@ -2188,15 +2189,15 @@ void FixBondReact::get_customvars() } for (int i = 0; i < ncustomvars; i++) { varid = customvarstrs[i]; - if (varid.substr(0,2) != "v_") error->all(FLERR,"Bond/react: Reaction special function variable " + if (varid.substr(0,2) != "v_") error->all(FLERR,"Fix bond/react: Reaction special function variable " "name should begin with 'v_'"); varid = varid.substr(2); int ivar = input->variable->find(varid.c_str()); if (ivar < 0) - error->all(FLERR,"Bond/react: Reaction special function variable " + error->all(FLERR,"Fix bond/react: Reaction special function variable " "name does not exist"); if (!input->variable->atomstyle(ivar)) - error->all(FLERR,"Bond/react: Reaction special function must " + error->all(FLERR,"Fix bond/react: Reaction special function must " "reference an atom-style variable"); input->variable->compute_atom(ivar,igroup,tempvvec,1,0); @@ -2211,7 +2212,8 @@ evaulate expression for variable constraint double FixBondReact::custom_constraint(const std::string& varstr) { - int pos,pos1,pos2,pos3,irxnfunc; + std::size_t pos,pos1,pos2,pos3; + int irxnfunc; int prev3 = -1; double val; std::string argstr,varid,fragid,evlcat; @@ -2220,7 +2222,7 @@ double FixBondReact::custom_constraint(const std::string& varstr) // search varstr for special 'rxn' functions while (true) { // find next reaction special function occurrence - pos1 = INT_MAX; + pos1 = std::string::npos; for (int i = 0; i < nrxnfunction; i++) { pos = varstr.find(rxnfunclist[i],prev3+1); if (pos == std::string::npos) continue; @@ -2229,13 +2231,13 @@ double FixBondReact::custom_constraint(const std::string& varstr) irxnfunc = i; } } - if (pos1 == INT_MAX) break; + if (pos1 == std::string::npos) break; fragid = "all"; // operate over entire reaction site by default pos2 = varstr.find("(",pos1); pos3 = varstr.find(")",pos2); if (pos2 == std::string::npos || pos3 == std::string::npos) - error->one(FLERR,"Bond/react: Illegal rxn function syntax\n"); + error->one(FLERR,"Fix bond/react: Illegal rxn function syntax\n"); evlstr.push_back(varstr.substr(prev3+1,pos1-(prev3+1))); prev3 = pos3; argstr = varstr.substr(pos2+1,pos3-pos2-1); @@ -2274,13 +2276,13 @@ double FixBondReact::rxnfunction(const std::string& rxnfunc, const std::string& // variable name should always be found, at this point // however, let's double check for completeness if (ivar < 0) - error->one(FLERR,"Bond/react: Reaction special function variable " + error->one(FLERR,"Fix bond/react: Reaction special function variable " "name does not exist"); int ifrag = -1; if (fragid != "all") { ifrag = onemol->findfragment(fragid.c_str()); - if (ifrag < 0) error->one(FLERR,"Bond/react: Molecule fragment " + if (ifrag < 0) error->one(FLERR,"Fix bond/react: Molecule fragment " "in reaction special function does not exist"); } @@ -2427,13 +2429,11 @@ void FixBondReact::find_landlocked_atoms(int myrxn) // bad molecule templates check // if atoms change types, but aren't landlocked, that's bad for (int i = 0; i < twomol->natoms; i++) { - if (create_atoms[i][myrxn] == 0) { - if (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1] && landlocked_atoms[i][myrxn] == 0) { - char str[128]; - snprintf(str,128,"Bond/react: Atom type affected by reaction %s too close to template edge",rxn_name[myrxn]); - error->all(FLERR,str); - } - } + if ((create_atoms[i][myrxn] == 0) && + (twomol->type[i] != onemol->type[equivalences[i][1][myrxn]-1]) && + (landlocked_atoms[i][myrxn] == 0)) + error->all(FLERR, "Fix bond/react: Atom type affected by reaction {} is too close " + "to template edge", rxn_name[myrxn]); } // additionally, if a bond changes type, but neither involved atom is landlocked, bad @@ -2448,25 +2448,19 @@ void FixBondReact::find_landlocked_atoms(int myrxn) int onemol_batom; for (int m = 0; m < onemol->num_bond[onemol_atomi-1]; m++) { onemol_batom = onemol->bond_atom[onemol_atomi-1][m]; - if (onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) { - if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m]) { - char str[128]; - snprintf(str,128,"Bond/react: Bond type affected by reaction %s too close to template edge",rxn_name[myrxn]); - error->all(FLERR,str); - } - } + if ((onemol_batom == equivalences[twomol_atomj-1][1][myrxn]) && + (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomi-1][m])) + error->all(FLERR, "Fix bond/react: Bond type affected by reaction {} is " + "too close to template edge",rxn_name[myrxn]); } if (newton_bond) { int onemol_atomj = equivalences[twomol_atomj-1][1][myrxn]; for (int m = 0; m < onemol->num_bond[onemol_atomj-1]; m++) { onemol_batom = onemol->bond_atom[onemol_atomj-1][m]; - if (onemol_batom == equivalences[i][1][myrxn]) { - if (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m]) { - char str[128]; - snprintf(str,128,"Bond/react: Bond type affected by reaction %s too close to template edge",rxn_name[myrxn]); - error->all(FLERR,str); - } - } + if ((onemol_batom == equivalences[i][1][myrxn]) && + (twomol->bond_type[i][j] != onemol->bond_type[onemol_atomj-1][m])) + error->all(FLERR, "Fix bond/react: Bond type affected by reaction {} is " + "too close to template edge",rxn_name[myrxn]); } } } @@ -2481,7 +2475,7 @@ void FixBondReact::find_landlocked_atoms(int myrxn) int ii = reverse_equiv[i][1][myrxn] - 1; for (int j = 0; j < twomol_nxspecial[ii][0]; j++) { if (delete_atoms[equivalences[twomol_xspecial[ii][j]-1][1][myrxn]-1][myrxn] == 0) { - error->all(FLERR,"Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted"); + error->all(FLERR,"Fix bond/react: A deleted atom cannot remain bonded to an atom that is not deleted"); } } } @@ -2490,20 +2484,18 @@ void FixBondReact::find_landlocked_atoms(int myrxn) // also, if atoms change number of bonds, but aren't landlocked, that could be bad if (me == 0) for (int i = 0; i < twomol->natoms; i++) { - if (create_atoms[i][myrxn] == 0) { - if (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0] && landlocked_atoms[i][myrxn] == 0) { - char str[128]; - snprintf(str,128,"Bond/react: Atom affected by reaction %s too close to template edge",rxn_name[myrxn]); - error->warning(FLERR,str); + if ((create_atoms[i][myrxn] == 0) && + (twomol_nxspecial[i][0] != onemol_nxspecial[equivalences[i][1][myrxn]-1][0]) && + (landlocked_atoms[i][myrxn] == 0)) + error->warning(FLERR, "Fix bond/react: Atom affected by reaction {} is too close " + "to template edge",rxn_name[myrxn]); break; - } - } } // finally, if a created atom is not landlocked, bad! for (int i = 0; i < twomol->natoms; i++) { if (create_atoms[i][myrxn] == 1 && landlocked_atoms[i][myrxn] == 0) { - error->one(FLERR,"Bond/react: Created atom too close to template edge"); + error->one(FLERR,"Fix bond/react: Created atom too close to template edge"); } } } @@ -3098,7 +3090,7 @@ void FixBondReact::update_everything() nspecial[ilocal][2]++; } if (nspecial[ilocal][2] > atom->maxspecial) - error->one(FLERR,"Bond/react special bond generation overflow"); + error->one(FLERR,"Fix bond/react special bond generation overflow"); for (int n = nspecial[ilocal][2]-1; n > insert_num; n--) { special[ilocal][n] = special[ilocal][n-1]; } @@ -3191,7 +3183,7 @@ void FixBondReact::update_everything() dynamic_cast(ihistory)->check_cache(atom->map(update_mega_glove[jj+1][i]), insert_num); num_bond[atom->map(update_mega_glove[jj+1][i])]++; if (num_bond[atom->map(update_mega_glove[jj+1][i])] > atom->bond_per_atom) - error->one(FLERR,"Bond/react topology/atom exceed system topology/atom"); + error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom"); delta_bonds++; } } @@ -3271,7 +3263,7 @@ void FixBondReact::update_everything() angle_atom3[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->angle_atom3[j][p]-1][1][rxnID]][i]; num_angle[atom->map(update_mega_glove[jj+1][i])]++; if (num_angle[atom->map(update_mega_glove[jj+1][i])] > atom->angle_per_atom) - error->one(FLERR,"Bond/react topology/atom exceed system topology/atom"); + error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom"); delta_angle++; } } @@ -3354,7 +3346,7 @@ void FixBondReact::update_everything() dihedral_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->dihedral_atom4[j][p]-1][1][rxnID]][i]; num_dihedral[atom->map(update_mega_glove[jj+1][i])]++; if (num_dihedral[atom->map(update_mega_glove[jj+1][i])] > atom->dihedral_per_atom) - error->one(FLERR,"Bond/react topology/atom exceed system topology/atom"); + error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom"); delta_dihed++; } } @@ -3437,7 +3429,7 @@ void FixBondReact::update_everything() improper_atom4[atom->map(update_mega_glove[jj+1][i])][insert_num] = update_mega_glove[equivalences[twomol->improper_atom4[j][p]-1][1][rxnID]][i]; num_improper[atom->map(update_mega_glove[jj+1][i])]++; if (num_improper[atom->map(update_mega_glove[jj+1][i])] > atom->improper_per_atom) - error->one(FLERR,"Bond/react topology/atom exceed system topology/atom"); + error->one(FLERR,"Fix bond/react topology/atom exceed system topology/atom"); delta_imprp++; } } @@ -3609,7 +3601,7 @@ int FixBondReact::insert_atoms(tagint **my_mega_glove, int iupdate) int ipre = equivalences[j][1][rxnID]-1; // equiv pre-reaction template index if (!create_atoms[j][rxnID] && !delete_atoms[ipre][rxnID]) { if (atom->map(my_mega_glove[ipre+1][iupdate]) < 0) { - printf("WARNING: eligible atoms skipped for created-atoms fit on %d\n",me); + error->warning(FLERR," eligible atoms skipped for created-atoms fit on rank {}\n",me); continue; } iatom = atom->map(my_mega_glove[ipre+1][iupdate]); @@ -3812,7 +3804,7 @@ void FixBondReact::read(int myrxn) // skip 1st line of file eof = fgets(line,MAXLINE,fp); - if (eof == nullptr) error->one(FLERR,"Bond/react: Unexpected end of superimpose file"); + if (eof == nullptr) error->one(FLERR,"Fix bond/react: Unexpected end of superimpose file"); // read header lines // skip blank lines or lines that start with "#" @@ -3833,7 +3825,7 @@ void FixBondReact::read(int myrxn) else if (strstr(line,"equivalences")) { sscanf(line,"%d",&nequivalent); if (nequivalent != onemol->natoms) - error->one(FLERR,"Bond/react: Number of equivalences in map file must " + error->one(FLERR,"Fix bond/react: Number of equivalences in map file must " "equal number of atoms in reaction templates"); } else if (strstr(line,"deleteIDs")) sscanf(line,"%d",&ndelete); @@ -3857,16 +3849,16 @@ void FixBondReact::read(int myrxn) while (strlen(keyword)) { if (strcmp(keyword,"InitiatorIDs") == 0 || strcmp(keyword,"BondingIDs") == 0) { if (strcmp(keyword,"BondingIDs") == 0) - if (me == 0) error->warning(FLERR,"Bond/react: The BondingIDs section title has been deprecated. Please use InitiatorIDs instead."); + if (me == 0) error->warning(FLERR,"Fix bond/react: The BondingIDs section title has been deprecated. Please use InitiatorIDs instead."); bondflag = 1; readline(line); sscanf(line,"%d",&ibonding[myrxn]); if (ibonding[myrxn] > onemol->natoms) - error->one(FLERR,"Bond/react: Invalid template atom ID in map file"); + error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); readline(line); sscanf(line,"%d",&jbonding[myrxn]); if (jbonding[myrxn] > onemol->natoms) - error->one(FLERR,"Bond/react: Invalid template atom ID in map file"); + error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); } else if (strcmp(keyword,"EdgeIDs") == 0) { EdgeIDs(line, myrxn); } else if (strcmp(keyword,"Equivalences") == 0) { @@ -3880,7 +3872,7 @@ void FixBondReact::read(int myrxn) ChiralCenters(line, myrxn); } else if (strcmp(keyword,"Constraints") == 0) { ReadConstraints(line, myrxn); - } else error->one(FLERR,"Bond/react: Unknown section in map file"); + } else error->one(FLERR,"Fix bond/react: Unknown section in map file"); parse_keyword(1,line,keyword); @@ -3888,7 +3880,7 @@ void FixBondReact::read(int myrxn) // error check if (bondflag == 0 || equivflag == 0) - error->all(FLERR,"Bond/react: Map file missing InitiatorIDs or Equivalences section\n"); + error->all(FLERR,"Fix bond/react: Map file missing InitiatorIDs or Equivalences section\n"); } void FixBondReact::EdgeIDs(char *line, int myrxn) @@ -3900,7 +3892,7 @@ void FixBondReact::EdgeIDs(char *line, int myrxn) readline(line); sscanf(line,"%d",&tmp); if (tmp > onemol->natoms) - error->one(FLERR,"Bond/react: Invalid template atom ID in map file"); + error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); edge[tmp-1][myrxn] = 1; } } @@ -3913,7 +3905,7 @@ void FixBondReact::Equivalences(char *line, int myrxn) readline(line); sscanf(line,"%d %d",&tmp1,&tmp2); if (tmp1 > onemol->natoms || tmp2 > twomol->natoms) - error->one(FLERR,"Bond/react: Invalid template atom ID in map file"); + error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); //equivalences is-> clmn 1: post-reacted, clmn 2: pre-reacted equivalences[tmp2-1][0][myrxn] = tmp2; equivalences[tmp2-1][1][myrxn] = tmp1; @@ -3930,7 +3922,7 @@ void FixBondReact::DeleteAtoms(char *line, int myrxn) readline(line); sscanf(line,"%d",&tmp); if (tmp > onemol->natoms) - error->one(FLERR,"Bond/react: Invalid template atom ID in map file"); + error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); delete_atoms[tmp-1][myrxn] = 1; } } @@ -3962,17 +3954,17 @@ void FixBondReact::ChiralCenters(char *line, int myrxn) readline(line); sscanf(line,"%d",&tmp); if (tmp > onemol->natoms) - error->one(FLERR,"Bond/react: Invalid template atom ID in map file"); + error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); chiral_atoms[tmp-1][0][myrxn] = 1; if (onemol->xflag == 0) - error->one(FLERR,"Bond/react: Molecule template 'Coords' section required for chiralIDs keyword"); + error->one(FLERR,"Fix bond/react: Molecule template 'Coords' section required for chiralIDs keyword"); if ((int) onemol_nxspecial[tmp-1][0] != 4) - error->one(FLERR,"Bond/react: Chiral atoms must have exactly four first neighbors"); + error->one(FLERR,"Fix bond/react: Chiral atoms must have exactly four first neighbors"); for (int j = 0; j < 4; j++) { for (int k = j+1; k < 4; k++) { if (onemol->type[onemol_xspecial[tmp-1][j]-1] == onemol->type[onemol_xspecial[tmp-1][k]-1]) - error->one(FLERR,"Bond/react: First neighbors of chiral atoms must be of mutually different types"); + error->one(FLERR,"Fix bond/react: First neighbors of chiral atoms must be of mutually different types"); } } // record order of atom types, and coords @@ -3998,7 +3990,7 @@ void FixBondReact::ReadConstraints(char *line, int myrxn) for (int i = 0; i < nconstraints[myrxn]; i++) { readline(line); // find left parentheses, add to constraintstr, and update line - for (int j = 0; j < strlen(line); j++) { + for (int j = 0; j < (int)strlen(line); j++) { if (line[j] == '(') strcat(constraintstr[myrxn],"("); if (isalpha(line[j])) { line = line + j; @@ -4017,7 +4009,7 @@ void FixBondReact::ReadConstraints(char *line, int myrxn) while (lptr[0] != ' ') lptr++; // skip second 'word' } // find right parentheses - for (int j = 0; j < strlen(lptr); j++) + for (int j = 0; j < (int)strlen(lptr); j++) if (lptr[j] == ')') strcat(constraintstr[myrxn],")"); // find logic symbols, and trim line via ptr if ((ptr = strstr(lptr,"&&"))) { @@ -4078,14 +4070,14 @@ void FixBondReact::ReadConstraints(char *line, int myrxn) constraints[i][myrxn].id[0] = -1; // optional molecule fragment if (isalpha(strargs[0][0])) { int ifragment = onemol->findfragment(strargs[0]); - if (ifragment < 0) error->one(FLERR,"Bond/react: Molecule fragment does not exist"); + if (ifragment < 0) error->one(FLERR,"Fix bond/react: Molecule fragment does not exist"); else constraints[i][myrxn].id[0] = ifragment; } } else if (strcmp(constraint_type,"custom") == 0) { constraints[i][myrxn].type = CUSTOM; std::vector args = utils::split_words(line); constraints[i][myrxn].str = args[1]; - } else error->one(FLERR,"Bond/react: Illegal constraint type in 'Constraints' section of map file"); + } else error->one(FLERR,"Fix bond/react: Illegal constraint type in 'Constraints' section of map file"); } strcat(constraintstr[myrxn],")"); // close boolean constraint logic string delete [] constraint_type; @@ -4102,12 +4094,12 @@ void FixBondReact::readID(char *strarg, int iconstr, int myrxn, int i) if (isalpha(strarg[0])) { constraints[iconstr][myrxn].idtype[i] = FRAG; // fragment vs. atom ID flag int ifragment = onemol->findfragment(strarg); - if (ifragment < 0) error->one(FLERR,"Bond/react: Molecule fragment does not exist"); + if (ifragment < 0) error->one(FLERR,"Fix bond/react: Molecule fragment does not exist"); constraints[iconstr][myrxn].id[i] = ifragment; } else { constraints[iconstr][myrxn].idtype[i] = ATOM; // fragment vs. atom ID flag int iatom = atoi(strarg); - if (iatom > onemol->natoms) error->one(FLERR,"Bond/react: Invalid template atom ID in map file"); + if (iatom > onemol->natoms) error->one(FLERR,"Fix bond/react: Invalid template atom ID in map file"); constraints[iconstr][myrxn].id[i] = iatom; } } @@ -4115,11 +4107,7 @@ void FixBondReact::readID(char *strarg, int iconstr, int myrxn, int i) void FixBondReact::open(char *file) { fp = fopen(file,"r"); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Bond/react: Cannot open map file %s",file); - error->one(FLERR,str); - } + if (fp == nullptr) error->one(FLERR, "Fix bond/react: Cannot open map file {}",file); } void FixBondReact::readline(char *line) @@ -4130,7 +4118,7 @@ void FixBondReact::readline(char *line) else n = strlen(line) + 1; } MPI_Bcast(&n,1,MPI_INT,0,world); - if (n == 0) error->all(FLERR,"Bond/react: Unexpected end of map file"); + if (n == 0) error->all(FLERR,"Fix bond/react: Unexpected end of map file"); MPI_Bcast(line,n,MPI_CHAR,0,world); } From 40cc4fa51083ce96d8af5ff53c308ec5982cc5be Mon Sep 17 00:00:00 2001 From: Taylor Barnes Date: Tue, 5 Jul 2022 19:09:23 +0000 Subject: [PATCH 04/72] Fix some errors in fix_mdi_qm.cpp --- src/MDI/fix_mdi_qm.cpp | 51 ++++++++++++++++++++++++++++++------------ 1 file changed, 37 insertions(+), 14 deletions(-) diff --git a/src/MDI/fix_mdi_qm.cpp b/src/MDI/fix_mdi_qm.cpp index db1c59ada9..bc2a3843ce 100644 --- a/src/MDI/fix_mdi_qm.cpp +++ b/src/MDI/fix_mdi_qm.cpp @@ -242,14 +242,28 @@ void FixMDIQM::init() reallocate(); - int ierr = MDI_Send_command(">NATOMS", mdicomm); - if (ierr) error->all(FLERR, "MDI: >NATOMS command"); - int n = static_cast (atom->natoms); - ierr = MDI_Send(&n, 1, MDI_INT, mdicomm); - if (ierr) error->all(FLERR, "MDI: >NATOMS data"); + int natoms_exists; + int ierr = MDI_Check_command_exists("@DEFAULT", ">NATOMS", mdicomm, &natoms_exists); + if (ierr) error->all(FLERR, "MDI: >NATOMS command check"); + if ( natoms_exists ) { + ierr = MDI_Send_command(">NATOMS", mdicomm); + if (ierr) error->all(FLERR, "MDI: >NATOMS command"); + int n = static_cast (atom->natoms); + ierr = MDI_Send(&n, 1, MDI_INT, mdicomm); + if (ierr) error->all(FLERR, "MDI: >NATOMS data"); + } - if (elements) send_elements(); - else send_types(); + int elements_exists; + int types_exists; + ierr = MDI_Check_command_exists("@DEFAULT", ">ELEMENTS", mdicomm, &elements_exists); + if (ierr) error->all(FLERR, "MDI: >ELEMENTS command check"); + ierr = MDI_Check_command_exists("@DEFAULT", ">TYPES", mdicomm, &types_exists); + if (ierr) error->all(FLERR, "MDI: >TYPES command check"); + if ( elements && elements_exists ) { + send_elements(); + } else if ( types_exists ) { + send_types(); + } send_box(); } @@ -502,13 +516,18 @@ void FixMDIQM::send_box() { double cell[9]; - int ierr = MDI_Send_command(">CELL_DISPL", mdicomm); - if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command"); - cell[0] = domain->boxlo[0] * lmp2mdi_length; - cell[1] = domain->boxlo[1] * lmp2mdi_length; - cell[2] = domain->boxlo[2] * lmp2mdi_length; - ierr = MDI_Send(cell, 3, MDI_DOUBLE, mdicomm); - if (ierr) error->all(FLERR, "MDI: >CELL_DISPL data"); + int celldispl_exists; + int ierr = MDI_Check_command_exists("@DEFAULT", ">NATOMS", mdicomm, &celldispl_exists); + if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command check"); + if ( celldispl_exists ) { + ierr = MDI_Send_command(">CELL_DISPL", mdicomm); + if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command"); + cell[0] = domain->boxlo[0] * lmp2mdi_length; + cell[1] = domain->boxlo[1] * lmp2mdi_length; + cell[2] = domain->boxlo[2] * lmp2mdi_length; + ierr = MDI_Send(cell, 3, MDI_DOUBLE, mdicomm); + if (ierr) error->all(FLERR, "MDI: >CELL_DISPL data"); + } ierr = MDI_Send_command(">CELL", mdicomm); if (ierr) error->all(FLERR, "MDI: >CELL command"); @@ -521,6 +540,10 @@ void FixMDIQM::send_box() cell[6] = domain->xz; cell[7] = domain->yz; cell[8] = domain->boxhi[2] - domain->boxlo[2]; + + // convert the cell units to bohr + for (int icell = 0; icell < 9; icell++) cell[icell] *= lmp2mdi_length; + ierr = MDI_Send(cell, 9, MDI_DOUBLE, mdicomm); if (ierr) error->all(FLERR, "MDI: >CELL data"); } From b7457fe834a3d1eee20d30fa1dca198493a91d6d Mon Sep 17 00:00:00 2001 From: Vaibhav Palkar Date: Wed, 6 Jul 2022 10:55:14 -0400 Subject: [PATCH 05/72] Initial commit for pair style srp-react files --- doc/src/pair_srp.rst | 30 +- doc/src/pair_style.rst | 1 + examples/PACKAGES/srp_react/README | 16 + examples/PACKAGES/srp_react/gel_equil.dat | 22959 ++++++++++++++++++++ examples/PACKAGES/srp_react/in.srp_react | 95 + src/.gitignore | 4 + src/MC/fix_bond_break.h | 1 + src/MC/fix_bond_create.h | 1 + src/MISC/fix_srp.h | 2 +- src/MISC/fix_srp_react.cpp | 186 + src/MISC/fix_srp_react.h | 50 + src/MISC/pair_srp.cpp | 2 +- src/MISC/pair_srp.h | 2 +- src/MISC/pair_srp_react.cpp | 239 + src/MISC/pair_srp_react.h | 46 + 15 files changed, 23630 insertions(+), 4 deletions(-) create mode 100644 examples/PACKAGES/srp_react/README create mode 100644 examples/PACKAGES/srp_react/gel_equil.dat create mode 100644 examples/PACKAGES/srp_react/in.srp_react create mode 100644 src/MISC/fix_srp_react.cpp create mode 100644 src/MISC/fix_srp_react.h create mode 100644 src/MISC/pair_srp_react.cpp create mode 100644 src/MISC/pair_srp_react.h diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index ea094aa720..adc0eceda9 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -1,18 +1,23 @@ .. index:: pair_style srp +.. index:: pair_style srp/react pair_style srp command ====================== +pair_style srp/react command +============================ Syntax """""" .. code-block:: LAMMPS pair_style srp cutoff btype dist keyword value ... + pair_style srp/react cutoff btype dist react-id keyword value ... * cutoff = global cutoff for SRP interactions (distance units) * btype = bond type to apply SRP interactions to (can be wildcard, see below) * distance = *min* or *mid* +* react-id = id of either fix bond/break or fix bond/create * zero or more keyword/value pairs may be appended * keyword = *exclude* @@ -36,13 +41,19 @@ Examples pair_coeff 1 2 none pair_coeff 2 2 srp 40.0 + fix create all bond/create 100 1 2 1.0 1 prob 0.2 19852 + pair_style hybrid dpd 1.0 1.0 12345 srp/react 0.8 * min create exclude yes + pair_coeff 1 1 dpd 60.0 50 1.0 + pair_coeff 1 2 none + pair_coeff 2 2 srp/react 40.0 + pair_style hybrid srp 0.8 2 mid pair_coeff 1 1 none pair_coeff 1 2 none pair_coeff 2 2 srp 100.0 0.8 Description -""""""""""" + Style *srp* computes a soft segmental repulsive potential (SRP) that acts between pairs of bonds. This potential is useful for preventing @@ -121,6 +132,18 @@ at the cutoff distance :math:`r_c`. ---------- +Pair style *srp/react* interfaces the pair style *srp* with the +bond breaking and formation mechanisms provided by fix *bond/break* +and fix *bond/create*, respectively. When using this pair style, whenever a +bond breaking (or formation) reaction occurs, the corresponding fictitious +particle is deleted (or inserted) during the same simulation time step as +the reaction. This is useful in the simulation of reactive systems involving +large polymeric molecules :ref:`(Palkar) ` where the segmental repulsive +potential is necessary to minimize topological violations, and also needs to be +turned on and off according to the progress of the reaction. + +---------- + Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" @@ -178,3 +201,8 @@ The default keyword value is exclude = yes. **(Sirk)** Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J Chem Phys, 136 (13) 134903, 2012. + +.. _Palkar: + +**(Palkar)** Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022 + diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 7e9414cee9..62416652c8 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -347,6 +347,7 @@ accelerated styles exist. * :doc:`spin/magelec ` - * :doc:`spin/neel ` - * :doc:`srp ` - +* :doc:`srp/react ` - * :doc:`sw ` - Stillinger-Weber 3-body potential * :doc:`sw/angle/table ` - Stillinger-Weber potential with tabulated angular term * :doc:`sw/mod ` - modified Stillinger-Weber 3-body potential diff --git a/examples/PACKAGES/srp_react/README b/examples/PACKAGES/srp_react/README new file mode 100644 index 0000000000..acd15581c2 --- /dev/null +++ b/examples/PACKAGES/srp_react/README @@ -0,0 +1,16 @@ +This directory contains an input script for performing +simulations with the srp/react pair style. The pair style +srp/react interfaces fix bond/break and fix bond/create commands +with the segmental repulsive potential. This is useful in simulating +reactions with soft potentials such as DPD where minimizing +topological violations is important. + +The input script in.srp_react is an example of a simulation of +a degrading nanogel particle. An initial equilibrated structure +of a nanogel particle (prior to degradation) is read from the +restart file. The degradation reaction is simulated via +the fix bond/break command. The simulation will generate the +file bonds_broken.txt containing the number of bonds +broken and fraction of bonds intact over the simulation time. +For more details see the LAMMPS online documentation and the +paper: Palkar, V., & Kuksenok, O. (2022). JPC B, 126, 336. diff --git a/examples/PACKAGES/srp_react/gel_equil.dat b/examples/PACKAGES/srp_react/gel_equil.dat new file mode 100644 index 0000000000..2810b3e88f --- /dev/null +++ b/examples/PACKAGES/srp_react/gel_equil.dat @@ -0,0 +1,22959 @@ +LAMMPS data file via write_data, version 23 Jun 2022, timestep = 100000 + +11017 atoms +6 atom types +892 bonds +2 bond types + +0 15 xlo xhi +0 15 ylo yhi +0 15 zlo zhi + +Masses + +1 1 +2 1 +3 1 +4 1 +5 1 +6 1 + +Bond Coeffs # harmonic + +1 500 0.7 +2 500 0.7 + +Atoms # molecular + +3219 0 5 1.5005152028734012 0.5011364106673206 0.2656058939414602 0 0 1 +7899 0 5 1.873972462657195 0.5245856049803095 0.022037513075714443 1 1 -2 +5762 0 5 2.2443993617410314 0.13004729397394033 0.46822806718201093 1 1 0 +8458 0 5 2.808587147924791 0.4715466695566604 0.524827158633283 2 1 1 +6738 0 5 3.458421236793845 0.5555112144892218 0.1210724034170614 1 0 1 +8269 0 5 4.20805662626085 0.19300434177544545 0.6810891498997496 1 0 1 +3777 0 5 4.960191961793781 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662 +865 2 662 663 +866 1 811 812 +867 2 812 813 +868 1 810 811 +869 1 525 526 +870 1 524 525 +871 1 808 809 +872 1 807 808 +873 1 800 804 +874 1 800 810 +875 1 800 816 +876 1 800 819 +877 1 816 817 +878 1 820 821 +879 1 819 820 +880 2 821 822 +881 1 515 516 +882 1 516 517 +883 1 670 671 +884 1 494 495 +885 1 492 517 +886 1 492 550 +887 1 492 650 +888 1 492 659 +889 1 658 659 +890 1 669 670 +891 1 657 658 +892 1 655 656 diff --git a/examples/PACKAGES/srp_react/in.srp_react b/examples/PACKAGES/srp_react/in.srp_react new file mode 100644 index 0000000000..e63c13f7a7 --- /dev/null +++ b/examples/PACKAGES/srp_react/in.srp_react @@ -0,0 +1,95 @@ +## srp_react example script +## Author: Vaibhav Palkar +## +## Simulates controlled degradation of a nanogel particle +## in a simulation box and prints statistics regarding +## the fraction of bonds broken over time. + +variable rseeddpd equal 26817 +variable rseedvel equal 5991 +variable breakstep equal 10 +variable probbreak equal 0.0009 +variable rseedbreak equal 6777 + +# simulation time +#*********************************************** +variable mainsteps equal 10000 + +# simulation setup +#*********************************************** +units lj +atom_style molecular +boundary p p p +bond_style harmonic +#lattice fcc 3.0 +comm_modify cutoff 4.0 vel yes + +# initial nanogel +#*********************************************** +read_data gel_equil.dat + +# define groups, create solvent atoms +#************************************************** +group Npoly type 1 2 3 4 +group water type 5 +group N_all type 1 2 3 4 5 + +# density check +#*********************************************** +variable N_atoms equal count(all) +variable tdens equal count(all)/vol +print "The system density is now ${tdens}" + +# bond break settings +# #*********************************************** +fix break N_all bond/break ${breakstep} 2 0 prob ${probbreak} ${rseedbreak} + +# interaction parameter setting +#*********************************************** +mass * 1.0 +bond_coeff * 500.0 0.70 +special_bonds lj 1 1 1 +newton on + +pair_style hybrid dpd 1.0 1.0 ${rseeddpd} srp/react 0.8 * mid break +#*********************************************** +pair_coeff *5 *5 dpd 78.000 4.5 1.0 +pair_coeff *4 5 dpd 79.500 4.5 1.0 +pair_coeff *5 6 none +pair_coeff 6 6 srp/react 80.00 0.800 + +# initial velocity +#*********************************************** +velocity all create 1.0 ${rseedvel} dist gaussian mom yes + +# integrator control +#*********************************************** +neighbor 0.3 bin +neigh_modify every 1 delay 5 check no +timestep 0.02 + +# Access variables of fix bond/break +#********************************************** +variable Nbreak equal f_break[2] # Number of bonds broken +variable TIME equal time + +# ensemble setting +#*********************************************** +fix 1 all nve + +# print bonds breaking stats +# *********************************************** +variable TotBreak equal 100 # total breakable bonds in current system +fix print_bonds_broken all print 100 "${TIME} ${Nbreak} $((v_TotBreak-v_Nbreak)/v_TotBreak)" file bonds_broken.txt screen no title "time bonds_broken fraction_bonds_intact" + +# thermo output +#*********************************************** +thermo 100 +thermo_style custom step temp pe ke etotal epair +thermo_modify flush yes norm no + +reset_timestep 0 +#dump 1 Npoly custom 5000 traj.lammpstrj id type x y z +#********************************************* +run ${mainsteps} +#*********************************************** diff --git a/src/.gitignore b/src/.gitignore index 4c1cf49b3b..e3f6f07841 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -1522,6 +1522,8 @@ /fix_smd_wall_surface.h /fix_srp.cpp /fix_srp.h +/fix_srp_react.cpp +/fix_srp_react.h /fix_tfmc.cpp /fix_tfmc.h /fix_ttm.cpp @@ -1562,6 +1564,8 @@ /pair_smd_ulsph.h /pair_srp.cpp /pair_srp.h +/pair_srp_react.cpp +/pair_srp_react.h /pair_thole.cpp /pair_thole.h /pair_buck_mdf.cpp diff --git a/src/MC/fix_bond_break.h b/src/MC/fix_bond_break.h index afc9df6cc6..6fdb6a3a20 100644 --- a/src/MC/fix_bond_break.h +++ b/src/MC/fix_bond_break.h @@ -25,6 +25,7 @@ FixStyle(bond/break,FixBondBreak); namespace LAMMPS_NS { class FixBondBreak : public Fix { + friend class FixSRPREACT; public: FixBondBreak(class LAMMPS *, int, char **); ~FixBondBreak() override; diff --git a/src/MC/fix_bond_create.h b/src/MC/fix_bond_create.h index 929e656722..469394af32 100644 --- a/src/MC/fix_bond_create.h +++ b/src/MC/fix_bond_create.h @@ -25,6 +25,7 @@ FixStyle(bond/create,FixBondCreate); namespace LAMMPS_NS { class FixBondCreate : public Fix { + friend class FixSRPREACT; public: FixBondCreate(class LAMMPS *, int, char **); ~FixBondCreate() override; diff --git a/src/MISC/fix_srp.h b/src/MISC/fix_srp.h index d0e2da1483..9cbb0a1213 100644 --- a/src/MISC/fix_srp.h +++ b/src/MISC/fix_srp.h @@ -54,7 +54,7 @@ class FixSRP : public Fix { double **array; - private: + protected: int btype; int bptype; }; diff --git a/src/MISC/fix_srp_react.cpp b/src/MISC/fix_srp_react.cpp new file mode 100644 index 0000000000..2e12cd82b7 --- /dev/null +++ b/src/MISC/fix_srp_react.cpp @@ -0,0 +1,186 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Vaibhav Palkar (Kuksenok Lab, Clemson University) + based on the pair srp code by Timothy Sirk (ARL) + +This pair style interfaces the pair style srp with the stochastic reaction +fixes bond/break and bond/create by updating pseudo beads corresponding to +bonds as bond breaking and formation takes place. This is useful in +simulation of reactions in polymers with soft potentials such as DPD. + +See the doc page for pair_style srp/react command for usage instructions. + +There is an example script for this package in examples/PACKAGES/srp_react/. +------------------------------------------------------------------------- */ + +#include "fix_srp_react.h" + +#include "atom.h" +#include "atom_vec.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neighbor.h" + +#include "fix_bond_break.h" +#include "fix_bond_create.h" + +#include +#include + +using namespace LAMMPS_NS; +using namespace FixConst; + +/* ---------------------------------------------------------------------- */ + +FixSRPREACT::FixSRPREACT(LAMMPS *lmp, int narg, char **arg) : FixSRP(lmp, narg, arg) +{ + // default idbreak and idcreate = NULL + idbreak = nullptr; + idcreate = nullptr; +} + +/* ---------------------------------------------------------------------- */ + +int FixSRPREACT::setmask() +{ + int mask = 0; + mask |= PRE_FORCE; + mask |= PRE_EXCHANGE; + mask |= POST_RUN; + mask |= POST_NEIGHBOR; + + return mask; +} + +/* ---------------------------------------------------------------------- */ + +void FixSRPREACT::init() +{ + if (force->pair_match("hybrid",1) == nullptr && force->pair_match("hybrid/overlay",1) == nullptr) + error->all(FLERR,"Cannot use pair srp without pair_style hybrid"); + + int has_rigid = 0; + for (int i = 0; i < modify->nfix; i++) + if (utils::strmatch(modify->fix[i]->style,"^rigid")) ++has_rigid; + + if (has_rigid > 0) + error->all(FLERR,"Pair srp is not compatible with rigid fixes."); + + if ((bptype < 1) || (bptype > atom->ntypes)) + error->all(FLERR,"Illegal bond particle type"); + + // this fix must come before any fix which migrates atoms in its pre_exchange() + // because this fix's pre_exchange() creates per-atom data structure + // that data must be current for atom migration to carry it along + + for (int i = 0; i < modify->nfix; i++) { + if (modify->fix[i] == this) break; + if (modify->fix[i]->pre_exchange_migrate) + error->all(FLERR,"Fix SRP comes after a fix which " + "migrates atoms in pre_exchange"); + } + + // setup neigh exclusions for diff atom types + // bond particles do not interact with other types + // type bptype only interacts with itself + + for (int z = 1; z < atom->ntypes; z++) { + if (z == bptype) + continue; + neighbor->modify_params(fmt::format("exclude type {} {}",z,bptype)); + } + + // find fix bond break + if( idbreak != nullptr ) + f_bb = (FixBondBreak *) modify->get_fix_by_id(idbreak); + + // find fix bond create + if( idcreate != nullptr ) + f_bc = (FixBondCreate *) modify->get_fix_by_id(idcreate); + + // free memory + delete [] idbreak; + delete [] idcreate; +} + +/* ---------------------------------------------------------------------- + rebuild bond particle array +------------------------------------------------------------------------- */ +void FixSRPREACT::post_neighbor() +{ + // store ncalls as it is reset in fix srp setup pre force + int ncalls = neighbor->ncalls; + + if( idbreak != nullptr) + if(f_bb->breakcount) + { + setup_pre_force(0); + + //reset break count before exiting + // not reseting breakcount would lead to redundant rebuilds + f_bb->breakcount=0; + + // count additional call during setup_pre_force + neighbor->ncalls = ncalls+1; + } + if( idcreate != nullptr) + if(f_bc->createcount) + { + setup_pre_force(0); + + //reset create count before exiting + // not reseting createcount would lead to redundant rebuilds + f_bc->createcount=0; + + // count additional call during setup_pre_force + neighbor->ncalls = ncalls+1; + } +} + +/* ---------------------------------------------------------------------- + interface with pair class + in addition to bond type and bond particle type, + pair srp react sets id of either fix bond break or bond create +------------------------------------------------------------------------- */ + +int FixSRPREACT::modify_param(int /*narg*/, char **arg) +{ + if (strcmp(arg[0],"btype") == 0) { + btype = utils::inumeric(FLERR,arg[1],false,lmp); + return 2; + } + if (strcmp(arg[0],"bptype") == 0) { + bptype = utils::inumeric(FLERR,arg[1],false,lmp); + return 2; + } + if (strcmp(arg[0],"bond/break") == 0) { + int n = strlen(arg[1]) + 1; + idbreak = new char[n]; + strcpy(idbreak,arg[1]); + return 2; + } + if (strcmp(arg[0],"bond/create") == 0) { + int n = strlen(arg[1]) + 1; + idcreate = new char[n]; + strcpy(idcreate,arg[1]); + return 2; + } + return 0; +} diff --git a/src/MISC/fix_srp_react.h b/src/MISC/fix_srp_react.h new file mode 100644 index 0000000000..1b48c64385 --- /dev/null +++ b/src/MISC/fix_srp_react.h @@ -0,0 +1,50 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS +// clang-format off +FixStyle(SRPREACT,FixSRPREACT); +// clang-format on +#else + +#ifndef LMP_FIX_SRP_REACT_H +#define LMP_FIX_SRP_REACT_H + +#include "fix_srp.h" + +namespace LAMMPS_NS { + +class FixSRPREACT : public FixSRP { + public: + FixSRPREACT(class LAMMPS *, int, char **); + int setmask() override; + void init() override; + void post_neighbor() override; + int modify_param(int, char **) override; + + private: + + class FixBondBreak* f_bb; + char *idbreak; + class FixBondCreate* f_bc; + char *idcreate; +}; + +} // namespace LAMMPS_NS + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ diff --git a/src/MISC/pair_srp.cpp b/src/MISC/pair_srp.cpp index 3667d0a2c2..21869c3ca0 100644 --- a/src/MISC/pair_srp.cpp +++ b/src/MISC/pair_srp.cpp @@ -126,7 +126,7 @@ PairSRP::~PairSRP() } // check nfix in case all fixes have already been deleted - if (modify->nfix) modify->delete_fix(f_srp->id); + if (modify->nfix && modify->get_fix_by_id(f_srp->id)!=nullptr) modify->delete_fix(f_srp->id); } /* ---------------------------------------------------------------------- diff --git a/src/MISC/pair_srp.h b/src/MISC/pair_srp.h index 03e7248d69..da04ba2ab1 100644 --- a/src/MISC/pair_srp.h +++ b/src/MISC/pair_srp.h @@ -40,7 +40,7 @@ class PairSRP : public Pair { void write_restart_settings(FILE *) override; void read_restart_settings(FILE *) override; - private: + protected: inline void onetwoexclude(int *&, int &, int *&, int *&, int **&); inline void remapBonds(int &); void allocate(); diff --git a/src/MISC/pair_srp_react.cpp b/src/MISC/pair_srp_react.cpp new file mode 100644 index 0000000000..46e058bad2 --- /dev/null +++ b/src/MISC/pair_srp_react.cpp @@ -0,0 +1,239 @@ +// clang-format off +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Vaibhav Palkar (Kuksenok Lab, Clemson University) + based on the pair srp code by Timothy Sirk (ARL) + +This pair style interfaces the pair style srp with the stochastic reaction +fixes bond/break and bond/create by updating pseudo beads corresponding to +bonds as bond breaking and formation takes place. This is useful in +simulation of reactions in polymers with soft potentials such as DPD. + +See the doc page for pair_style srp/react command for usage instructions. + +There is an example script for this package in examples/PACKAGES/srp_react/. +------------------------------------------------------------------------- */ + +#include "pair_srp_react.h" + +#include "atom.h" +#include "citeme.h" +#include "comm.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "fix_srp_react.h" +#include "force.h" +#include "memory.h" +#include "modify.h" +#include "neigh_list.h" +#include "neighbor.h" +#include "output.h" +#include "thermo.h" + +#include +#include + +using namespace LAMMPS_NS; + +static const char cite_srpreact[] = + "@Article{palkar2022\n" + " author = {Palkar, Vaibhav and Kuksenok, Olga},\n" + " title = {Controlling Degradation and Erosion of Polymer Networks: Insights from Mesoscale Modeling},\n" + " journal = {J. Phys. Chem. B},\n" + " year = {2022},\n" + " volume = {126},\n" + " pages = {336-346}\n" + "}\n\n"; + +static int srp_instance = 0; + +/* ---------------------------------------------------------------------- + constructor + ---------------------------------------------------------------------- */ + +PairSRPREACT::PairSRPREACT(LAMMPS *lmp) : PairSRP(lmp) +{ + + if (lmp->citeme) lmp->citeme->add(cite_srpreact); + + // pair srp/react has its own fix, hence delete fix srp instance + // created in the constructor of pair srp + for( int ifix = 0; ifixnfix; ifix++) + if( strcmp(modify->get_fix_by_index(ifix)->style, "SRP") == 0) + modify->delete_fix(ifix); + + // similar to fix SRP, create fix SRP REACT instance here with unique fix id + f_srp = (FixSRPREACT *) modify->add_fix(fmt::format("{:02d}_FIX_SRP_REACT all SRPREACT",srp_instance)); + ++srp_instance; +} + +/* ---------------------------------------------------------------------- + global settings + ------------------------------------------------------------------------- */ + +void PairSRPREACT::settings(int narg, char **arg) +{ + if (narg < 3 || narg > 8) + error->all(FLERR,"Illegal pair_style command"); + + if (atom->tag_enable == 0) + error->all(FLERR,"Pair_style srp requires atom IDs"); + + cut_global = utils::numeric(FLERR,arg[0],false,lmp); + // wildcard + if (strcmp(arg[1],"*") == 0) { + btype = 0; + } else { + btype = utils::inumeric(FLERR,arg[1],false,lmp); + if ((btype > atom->nbondtypes) || (btype <= 0)) + error->all(FLERR,"Illegal pair_style command"); + } + + // settings + midpoint = false; + min = false; + + if (strcmp(arg[2],"min") == 0) min = true; + else if (strcmp(arg[2],"mid") == 0) midpoint = true; + else + error->all(FLERR,"Illegal pair_style command"); + + // default for bond/break and bond/create settings + bond_create=false; + bond_break=false; + idbreak = nullptr; + idcreate= nullptr; + + // find whether id is of bond/break or bond/create + const char* reactid = arg[3]; + if(strcmp(modify->get_fix_by_id(reactid)->style,"bond/break") == 0) + { + bond_break = true; + int n = strlen(reactid) + 1; + idbreak = new char[n]; + strcpy(idbreak,reactid); + } + else if(strcmp(modify->get_fix_by_id(reactid)->style,"bond/create") == 0) + { + bond_create = true; + int n = strlen(reactid) + 1; + idcreate = new char[n]; + strcpy(idcreate,reactid); + } + else + error->all(FLERR,"Illegal pair_style command"); + + int iarg = 4; + // default exclude 1-2 + // scaling for 1-2, etc not supported + exclude = 1; + + // use last atom type by default for bond particles + bptype = atom->ntypes; + + while (iarg < narg) { + if (strcmp(arg[iarg],"exclude") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal pair srp command"); + exclude = utils::logical(FLERR, arg[iarg+1], false, lmp); + if (min && !exclude) error->all(FLERR,"Illegal exclude option in pair srp command"); + iarg += 2; + } else if (strcmp(arg[iarg],"bptype") == 0) { + if (iarg+2 > narg) error->all(FLERR,"Illegal pair srp command"); + bptype = utils::inumeric(FLERR,arg[iarg+1],false,lmp); + if ((bptype < 1) || (bptype > atom->ntypes)) + error->all(FLERR,"Illegal bond particle type for srp"); + iarg += 2; + } else error->all(FLERR,"Illegal pair srp command"); + } + + // reset cutoffs if explicitly set + if (allocated) { + int i,j; + for (i = 1; i <= bptype; i++) + for (j = i; j <= bptype; j++) + if (setflag[i][j]) cut[i][j] = cut_global; + } +} + +/* ---------------------------------------------------------------------- + init specific to this pair style + ------------------------------------------------------------------------- */ + +void PairSRPREACT::init_style() +{ + if (!force->newton_pair) + error->all(FLERR,"PairSRPREACT: Pair srp requires newton pair on"); + + // verify that fix SRP is still defined and has not been changed. + + if (strcmp(f_srp->style,"SRPREACT") != 0) + error->all(FLERR,"Fix SRP has been changed unexpectedly"); + + if (comm->me == 0) + utils::logmesg(lmp,"Using type {} for bond particles\n",bptype); + + // set bond and bond particle types in fix srp + // bonds of this type will be represented by bond particles + // if bond type is 0, then all bonds have bond particles + // btype = bond type + + char c0[20]; + char* arg0[2]; + sprintf(c0, "%d", btype); + arg0[0] = (char *) "btype"; + arg0[1] = c0; + f_srp->modify_params(2, arg0); + + // bptype = bond particle type + sprintf(c0, "%d", bptype); + arg0[0] = (char *) "bptype"; + arg0[1] = c0; + f_srp->modify_params(2, arg0); + + // if using fix bond/break, set id of fix bond/break in fix srp + // idbreak = id of fix bond break + if( bond_break ) + { + sprintf(c0, "%s", idbreak); + arg0[0] = (char *) "bond/break"; + arg0[1] = c0; + f_srp->modify_params(2, arg0); + delete [] idbreak; + } + + // if using fix bond/create, set id of fix bond/create in fix srp + // idcreate = id of fix bond break + if( bond_create ) + { + sprintf(c0, "%s", idcreate); + arg0[0] = (char *) "bond/create"; + arg0[1] = c0; + f_srp->modify_params(2, arg0); + delete [] idcreate; + } + + // bond particles do not contribute to energy or virial + // bond particles do not belong to group all + // but thermo normalization is by nall + // therefore should turn off normalization + char *arg1[2]; + arg1[0] = (char *) "norm"; + arg1[1] = (char *) "no"; + output->thermo->modify_params(2, arg1); + if (comm->me == 0) error->message(FLERR,"Thermo normalization turned off by pair srp"); + + neighbor->request(this,instance_me); +} diff --git a/src/MISC/pair_srp_react.h b/src/MISC/pair_srp_react.h new file mode 100644 index 0000000000..86e2c68111 --- /dev/null +++ b/src/MISC/pair_srp_react.h @@ -0,0 +1,46 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://www.lammps.org/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef PAIR_CLASS +// clang-format off +PairStyle(srp/react,PairSRPREACT); +// clang-format on +#else + +#ifndef LMP_PAIR_SRP_REACT_H +#define LMP_PAIR_SRP_REACT_H + +#include "pair_srp.h" + +namespace LAMMPS_NS { + +class PairSRPREACT : public PairSRP { + public: + PairSRPREACT(class LAMMPS *); + void settings(int, char **) override; + void init_style() override; + + private: + char *idbreak; + char *idcreate; + bool bond_create, bond_break; +}; + +} // namespace LAMMPS_NS + +#endif +#endif + +/* ERROR/WARNING messages: + +*/ From 569136e1604d9637a2e1668dadc05f50d3e3a1c1 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Wed, 6 Jul 2022 14:35:16 -0600 Subject: [PATCH 06/72] Redoing groups in compute contact/atom --- doc/src/compute_contact_atom.rst | 10 +++++- src/GRANULAR/compute_contact_atom.cpp | 52 ++++++++++++++++----------- src/GRANULAR/compute_contact_atom.h | 4 +++ 3 files changed, 44 insertions(+), 22 deletions(-) diff --git a/doc/src/compute_contact_atom.rst b/doc/src/compute_contact_atom.rst index 20dcbfae29..23b5f4639d 100644 --- a/doc/src/compute_contact_atom.rst +++ b/doc/src/compute_contact_atom.rst @@ -8,10 +8,11 @@ Syntax .. parsed-literal:: - compute ID group-ID contact/atom + compute ID group-ID contact/atom group2-ID * ID, group-ID are documented in :doc:`compute ` command * contact/atom = style name of this compute command +* group2-ID = optional argument to restrict which atoms to consider for contacts (see below) Examples """""""" @@ -19,6 +20,7 @@ Examples .. code-block:: LAMMPS compute 1 all contact/atom + compute 1 all contact/atom mygroup Description """"""""""" @@ -45,6 +47,9 @@ overview of LAMMPS output options. The per-atom vector values will be a number >= 0.0, as explained above. +The optional *group2-ID* argument allows to specify from which group atoms +contribute to the coordination number. Default setting is group 'all'. + Restrictions """""""""""" @@ -63,4 +68,7 @@ Related commands Default """"""" +*group2-ID* = all + + none diff --git a/src/GRANULAR/compute_contact_atom.cpp b/src/GRANULAR/compute_contact_atom.cpp index 5a07d14eb8..26018f7bfb 100644 --- a/src/GRANULAR/compute_contact_atom.cpp +++ b/src/GRANULAR/compute_contact_atom.cpp @@ -18,6 +18,7 @@ #include "comm.h" #include "error.h" #include "force.h" +#include "group.h" #include "memory.h" #include "modify.h" #include "neigh_list.h" @@ -34,7 +35,16 @@ ComputeContactAtom::ComputeContactAtom(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg), contact(nullptr) { - if (narg != 3) error->all(FLERR,"Illegal compute contact/atom command"); + if (narg != 3 && narg != 4) error->all(FLERR,"Illegal compute contact/atom command"); + + jgroup = group->find("all"); + jgroupbit = group->bitmask[jgroup]; + if (narg == 4) { + group2 = utils::strdup(arg[3]); + jgroup = group->find(group2); + if (jgroup == -1) error->all(FLERR, "Compute contact/atom group2 ID does not exist"); + jgroupbit = group->bitmask[jgroup]; + } peratom_flag = 1; size_peratom_cols = 0; @@ -120,28 +130,28 @@ void ComputeContactAtom::compute_peratom() for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - if (mask[i] & groupbit) { - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - radi = radius[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx*delx + dely*dely + delz*delz; - radsum = radi + radius[j]; - radsumsq = radsum*radsum; - if (rsq <= radsumsq) { - contact[i] += 1.0; - contact[j] += 1.0; - } + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + radsum = radi + radius[j]; + radsumsq = radsum * radsum; + if (rsq <= radsumsq) { + // Only tally for atoms in compute group (groupbit) if neighbor is in group2 (jgroupbit) + if ((mask[i] & groupbit) && (mask[j] & jgroupbit)) contact[i] += 1.0; + if ((mask[j] & groupbit) && (mask[i] & jgroupbit)) contact[j] += 1.0; } } } diff --git a/src/GRANULAR/compute_contact_atom.h b/src/GRANULAR/compute_contact_atom.h index f01815e666..04157b5455 100644 --- a/src/GRANULAR/compute_contact_atom.h +++ b/src/GRANULAR/compute_contact_atom.h @@ -37,6 +37,10 @@ class ComputeContactAtom : public Compute { private: int nmax; + + char *group2; + int jgroup, jgroupbit; + class NeighList *list; double *contact; }; From 4aa0132860f7bfdd259fde9611796ef5d0465318 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 7 Jul 2022 10:35:34 -0400 Subject: [PATCH 07/72] cosmetic --- doc/src/pair_srp.rst | 18 +++++++++--------- src/MISC/fix_srp_react.cpp | 12 ++++++------ src/MISC/fix_srp_react.h | 4 ---- src/MISC/pair_srp_react.cpp | 6 +++--- src/MISC/pair_srp_react.h | 4 ---- 5 files changed, 18 insertions(+), 26 deletions(-) diff --git a/doc/src/pair_srp.rst b/doc/src/pair_srp.rst index adc0eceda9..6c9a128447 100644 --- a/doc/src/pair_srp.rst +++ b/doc/src/pair_srp.rst @@ -132,14 +132,14 @@ at the cutoff distance :math:`r_c`. ---------- -Pair style *srp/react* interfaces the pair style *srp* with the -bond breaking and formation mechanisms provided by fix *bond/break* -and fix *bond/create*, respectively. When using this pair style, whenever a -bond breaking (or formation) reaction occurs, the corresponding fictitious -particle is deleted (or inserted) during the same simulation time step as -the reaction. This is useful in the simulation of reactive systems involving -large polymeric molecules :ref:`(Palkar) ` where the segmental repulsive -potential is necessary to minimize topological violations, and also needs to be +Pair style *srp/react* interfaces the pair style *srp* with the +bond breaking and formation mechanisms provided by fix *bond/break* +and fix *bond/create*, respectively. When using this pair style, whenever a +bond breaking (or formation) reaction occurs, the corresponding fictitious +particle is deleted (or inserted) during the same simulation time step as +the reaction. This is useful in the simulation of reactive systems involving +large polymeric molecules :ref:`(Palkar) ` where the segmental repulsive +potential is necessary to minimize topological violations, and also needs to be turned on and off according to the progress of the reaction. ---------- @@ -204,5 +204,5 @@ Chem Phys, 136 (13) 134903, 2012. .. _Palkar: -**(Palkar)** Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022 +**(Palkar)** Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022 diff --git a/src/MISC/fix_srp_react.cpp b/src/MISC/fix_srp_react.cpp index 2e12cd82b7..f4e790927d 100644 --- a/src/MISC/fix_srp_react.cpp +++ b/src/MISC/fix_srp_react.cpp @@ -13,13 +13,13 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Vaibhav Palkar (Kuksenok Lab, Clemson University) + Contributing author: Vaibhav Palkar (Kuksenok Lab, Clemson University) based on the pair srp code by Timothy Sirk (ARL) This pair style interfaces the pair style srp with the stochastic reaction fixes bond/break and bond/create by updating pseudo beads corresponding to bonds as bond breaking and formation takes place. This is useful in -simulation of reactions in polymers with soft potentials such as DPD. +simulation of reactions in polymers with soft potentials such as DPD. See the doc page for pair_style srp/react command for usage instructions. @@ -110,7 +110,7 @@ void FixSRPREACT::init() // find fix bond break if( idbreak != nullptr ) f_bb = (FixBondBreak *) modify->get_fix_by_id(idbreak); - + // find fix bond create if( idcreate != nullptr ) f_bc = (FixBondCreate *) modify->get_fix_by_id(idcreate); @@ -136,7 +136,7 @@ void FixSRPREACT::post_neighbor() //reset break count before exiting // not reseting breakcount would lead to redundant rebuilds f_bb->breakcount=0; - + // count additional call during setup_pre_force neighbor->ncalls = ncalls+1; } @@ -148,7 +148,7 @@ void FixSRPREACT::post_neighbor() //reset create count before exiting // not reseting createcount would lead to redundant rebuilds f_bc->createcount=0; - + // count additional call during setup_pre_force neighbor->ncalls = ncalls+1; } @@ -156,7 +156,7 @@ void FixSRPREACT::post_neighbor() /* ---------------------------------------------------------------------- interface with pair class - in addition to bond type and bond particle type, + in addition to bond type and bond particle type, pair srp react sets id of either fix bond break or bond create ------------------------------------------------------------------------- */ diff --git a/src/MISC/fix_srp_react.h b/src/MISC/fix_srp_react.h index 1b48c64385..8b583db6af 100644 --- a/src/MISC/fix_srp_react.h +++ b/src/MISC/fix_srp_react.h @@ -44,7 +44,3 @@ class FixSRPREACT : public FixSRP { #endif #endif - -/* ERROR/WARNING messages: - -*/ diff --git a/src/MISC/pair_srp_react.cpp b/src/MISC/pair_srp_react.cpp index 46e058bad2..4f0720d27b 100644 --- a/src/MISC/pair_srp_react.cpp +++ b/src/MISC/pair_srp_react.cpp @@ -13,13 +13,13 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Vaibhav Palkar (Kuksenok Lab, Clemson University) + Contributing author: Vaibhav Palkar (Kuksenok Lab, Clemson University) based on the pair srp code by Timothy Sirk (ARL) This pair style interfaces the pair style srp with the stochastic reaction fixes bond/break and bond/create by updating pseudo beads corresponding to bonds as bond breaking and formation takes place. This is useful in -simulation of reactions in polymers with soft potentials such as DPD. +simulation of reactions in polymers with soft potentials such as DPD. See the doc page for pair_style srp/react command for usage instructions. @@ -213,7 +213,7 @@ void PairSRPREACT::init_style() f_srp->modify_params(2, arg0); delete [] idbreak; } - + // if using fix bond/create, set id of fix bond/create in fix srp // idcreate = id of fix bond break if( bond_create ) diff --git a/src/MISC/pair_srp_react.h b/src/MISC/pair_srp_react.h index 86e2c68111..39663996b0 100644 --- a/src/MISC/pair_srp_react.h +++ b/src/MISC/pair_srp_react.h @@ -40,7 +40,3 @@ class PairSRPREACT : public PairSRP { #endif #endif - -/* ERROR/WARNING messages: - -*/ From 6b22886064be450a5a4905ef19cda28c9caca8ae Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 7 Jul 2022 10:39:11 -0400 Subject: [PATCH 08/72] small docs fixes --- doc/src/Commands_pair.rst | 1 + doc/utils/sphinx-config/false_positives.txt | 1 + 2 files changed, 2 insertions(+) diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 11334ea2d1..0710a8dd9e 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -268,6 +268,7 @@ OPT. * :doc:`spin/magelec ` * :doc:`spin/neel ` * :doc:`srp ` + * :doc:`srp/react ` * :doc:`sw (giko) ` * :doc:`sw/angle/table ` * :doc:`sw/mod (o) ` diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 77a1da6643..fbc0cc8bd1 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1688,6 +1688,7 @@ kTln ktypeN Kub Kubo +Kuksenok Kumagai Kumar Kurebayashi From 63c048ef5963045d425e0a9b5675c1ba628c18c6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 7 Jul 2022 12:35:55 -0400 Subject: [PATCH 09/72] simplify, modernize, and apply clang-format --- src/MISC/fix_srp.cpp | 31 +++++------ src/MISC/fix_srp.h | 1 + src/MISC/fix_srp_react.cpp | 111 ++++++++++++------------------------- src/MISC/fix_srp_react.h | 8 +-- 4 files changed, 53 insertions(+), 98 deletions(-) diff --git a/src/MISC/fix_srp.cpp b/src/MISC/fix_srp.cpp index 1fb15aafd3..f4f9abc629 100644 --- a/src/MISC/fix_srp.cpp +++ b/src/MISC/fix_srp.cpp @@ -68,6 +68,8 @@ FixSRP::FixSRP(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) btype = -1; bptype = -1; + pair_name = "srp"; + // zero for (int i = 0; i < atom->nmax; i++) for (int m = 0; m < 2; m++) @@ -101,15 +103,11 @@ int FixSRP::setmask() void FixSRP::init() { - if (force->pair_match("hybrid",1) == nullptr && force->pair_match("hybrid/overlay",1) == nullptr) - error->all(FLERR,"Cannot use pair srp without pair_style hybrid"); + if (!force->pair_match("^hybrid",0)) + error->all(FLERR,"Cannot use pair {} without pair_style hybrid", pair_name); - int has_rigid = 0; - for (int i = 0; i < modify->nfix; i++) - if (utils::strmatch(modify->fix[i]->style,"^rigid")) ++has_rigid; - - if (has_rigid > 0) - error->all(FLERR,"Pair srp is not compatible with rigid fixes."); + if (modify->get_fix_by_style("^rigid").size() > 0) + error->all(FLERR,"Pair {} is not compatible with rigid fixes.", pair_name); if ((bptype < 1) || (bptype > atom->ntypes)) error->all(FLERR,"Illegal bond particle type"); @@ -118,11 +116,10 @@ void FixSRP::init() // because this fix's pre_exchange() creates per-atom data structure // that data must be current for atom migration to carry it along - for (int i = 0; i < modify->nfix; i++) { - if (modify->fix[i] == this) break; - if (modify->fix[i]->pre_exchange_migrate) - error->all(FLERR,"Fix SRP comes after a fix which " - "migrates atoms in pre_exchange"); + for (auto ifix : modify->get_fix_list()) { + if (ifix == this) break; + if (ifix->pre_exchange_migrate) + error->all(FLERR,"Fix {} comes after a fix which migrates atoms in pre_exchange", style); } // setup neigh exclusions for diff atom types @@ -274,8 +271,8 @@ void FixSRP::setup_pre_force(int /*zz*/) // stop if cutghost is insufficient if (cutneighmax_srp > cutghostmin) - error->all(FLERR,"Communication cutoff too small for fix srp. " - "Need {:.8}, current {:.8}", cutneighmax_srp, cutghostmin); + error->all(FLERR,"Communication cutoff too small for fix {}. " + "Need {:.8}, current {:.8}", style, cutneighmax_srp, cutghostmin); // assign tags for new atoms, update map atom->tag_extend(); @@ -345,11 +342,11 @@ void FixSRP::pre_exchange() if (atom->type[ii] != bptype) continue; i = atom->map(static_cast(array[ii][0])); - if (i < 0) error->all(FLERR,"Fix SRP failed to map atom"); + if (i < 0) error->all(FLERR,"Fix {} failed to map atom", style); i = domain->closest_image(ii,i); j = atom->map(static_cast(array[ii][1])); - if (j < 0) error->all(FLERR,"Fix SRP failed to map atom"); + if (j < 0) error->all(FLERR,"Fix {} failed to map atom", style); j = domain->closest_image(ii,j); // position of bond particle ii diff --git a/src/MISC/fix_srp.h b/src/MISC/fix_srp.h index 9cbb0a1213..48f1f77a86 100644 --- a/src/MISC/fix_srp.h +++ b/src/MISC/fix_srp.h @@ -57,6 +57,7 @@ class FixSRP : public Fix { protected: int btype; int bptype; + std::string pair_name; }; } // namespace LAMMPS_NS diff --git a/src/MISC/fix_srp_react.cpp b/src/MISC/fix_srp_react.cpp index f4e790927d..7ead11314b 100644 --- a/src/MISC/fix_srp_react.cpp +++ b/src/MISC/fix_srp_react.cpp @@ -1,4 +1,3 @@ -// clang-format off /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator https://www.lammps.org/, Sandia National Laboratories @@ -28,32 +27,33 @@ There is an example script for this package in examples/PACKAGES/srp_react/. #include "fix_srp_react.h" -#include "atom.h" -#include "atom_vec.h" -#include "comm.h" -#include "domain.h" -#include "error.h" -#include "force.h" -#include "memory.h" #include "modify.h" #include "neighbor.h" #include "fix_bond_break.h" #include "fix_bond_create.h" -#include #include using namespace LAMMPS_NS; using namespace FixConst; +// clang-format on /* ---------------------------------------------------------------------- */ -FixSRPREACT::FixSRPREACT(LAMMPS *lmp, int narg, char **arg) : FixSRP(lmp, narg, arg) +FixSRPREACT::FixSRPREACT(LAMMPS *lmp, int narg, char **arg) : + FixSRP(lmp, narg, arg), f_bb(nullptr), idbreak(nullptr), f_bc(nullptr), idcreate(nullptr) { - // default idbreak and idcreate = NULL - idbreak = nullptr; - idcreate = nullptr; + pair_name = "srp/react"; +} + +/* ---------------------------------------------------------------------- */ + +FixSRPREACT::~FixSRPREACT() +{ + // free memory + delete[] idbreak; + delete[] idcreate; } /* ---------------------------------------------------------------------- */ @@ -73,51 +73,13 @@ int FixSRPREACT::setmask() void FixSRPREACT::init() { - if (force->pair_match("hybrid",1) == nullptr && force->pair_match("hybrid/overlay",1) == nullptr) - error->all(FLERR,"Cannot use pair srp without pair_style hybrid"); - - int has_rigid = 0; - for (int i = 0; i < modify->nfix; i++) - if (utils::strmatch(modify->fix[i]->style,"^rigid")) ++has_rigid; - - if (has_rigid > 0) - error->all(FLERR,"Pair srp is not compatible with rigid fixes."); - - if ((bptype < 1) || (bptype > atom->ntypes)) - error->all(FLERR,"Illegal bond particle type"); - - // this fix must come before any fix which migrates atoms in its pre_exchange() - // because this fix's pre_exchange() creates per-atom data structure - // that data must be current for atom migration to carry it along - - for (int i = 0; i < modify->nfix; i++) { - if (modify->fix[i] == this) break; - if (modify->fix[i]->pre_exchange_migrate) - error->all(FLERR,"Fix SRP comes after a fix which " - "migrates atoms in pre_exchange"); - } - - // setup neigh exclusions for diff atom types - // bond particles do not interact with other types - // type bptype only interacts with itself - - for (int z = 1; z < atom->ntypes; z++) { - if (z == bptype) - continue; - neighbor->modify_params(fmt::format("exclude type {} {}",z,bptype)); - } + FixSRP::init(); // find fix bond break - if( idbreak != nullptr ) - f_bb = (FixBondBreak *) modify->get_fix_by_id(idbreak); + if (idbreak) f_bb = (FixBondBreak *) modify->get_fix_by_id(idbreak); // find fix bond create - if( idcreate != nullptr ) - f_bc = (FixBondCreate *) modify->get_fix_by_id(idcreate); - - // free memory - delete [] idbreak; - delete [] idcreate; + if (idcreate) f_bc = (FixBondCreate *) modify->get_fix_by_id(idcreate); } /* ---------------------------------------------------------------------- @@ -128,30 +90,31 @@ void FixSRPREACT::post_neighbor() // store ncalls as it is reset in fix srp setup pre force int ncalls = neighbor->ncalls; - if( idbreak != nullptr) - if(f_bb->breakcount) - { + if (f_bb) { + if (f_bb->breakcount) { setup_pre_force(0); //reset break count before exiting // not reseting breakcount would lead to redundant rebuilds - f_bb->breakcount=0; + f_bb->breakcount = 0; // count additional call during setup_pre_force - neighbor->ncalls = ncalls+1; + neighbor->ncalls = ncalls + 1; } - if( idcreate != nullptr) - if(f_bc->createcount) - { + } + + if (f_bc) { + if (f_bc->createcount) { setup_pre_force(0); //reset create count before exiting // not reseting createcount would lead to redundant rebuilds - f_bc->createcount=0; + f_bc->createcount = 0; // count additional call during setup_pre_force - neighbor->ncalls = ncalls+1; + neighbor->ncalls = ncalls + 1; } + } } /* ---------------------------------------------------------------------- @@ -162,24 +125,20 @@ void FixSRPREACT::post_neighbor() int FixSRPREACT::modify_param(int /*narg*/, char **arg) { - if (strcmp(arg[0],"btype") == 0) { - btype = utils::inumeric(FLERR,arg[1],false,lmp); + if (strcmp(arg[0], "btype") == 0) { + btype = utils::inumeric(FLERR, arg[1], false, lmp); return 2; } - if (strcmp(arg[0],"bptype") == 0) { - bptype = utils::inumeric(FLERR,arg[1],false,lmp); + if (strcmp(arg[0], "bptype") == 0) { + bptype = utils::inumeric(FLERR, arg[1], false, lmp); return 2; } - if (strcmp(arg[0],"bond/break") == 0) { - int n = strlen(arg[1]) + 1; - idbreak = new char[n]; - strcpy(idbreak,arg[1]); + if (strcmp(arg[0], "bond/break") == 0) { + idbreak = utils::strdup(arg[1]); return 2; } - if (strcmp(arg[0],"bond/create") == 0) { - int n = strlen(arg[1]) + 1; - idcreate = new char[n]; - strcpy(idcreate,arg[1]); + if (strcmp(arg[0], "bond/create") == 0) { + idcreate = utils::strdup(arg[1]); return 2; } return 0; diff --git a/src/MISC/fix_srp_react.h b/src/MISC/fix_srp_react.h index 8b583db6af..e892631416 100644 --- a/src/MISC/fix_srp_react.h +++ b/src/MISC/fix_srp_react.h @@ -27,20 +27,18 @@ namespace LAMMPS_NS { class FixSRPREACT : public FixSRP { public: FixSRPREACT(class LAMMPS *, int, char **); + ~FixSRPREACT() override; int setmask() override; void init() override; void post_neighbor() override; int modify_param(int, char **) override; private: - - class FixBondBreak* f_bb; + class FixBondBreak *f_bb; char *idbreak; - class FixBondCreate* f_bc; + class FixBondCreate *f_bc; char *idcreate; }; - } // namespace LAMMPS_NS - #endif #endif From 5496781ecd58b0c59f60bc9d0326128107ae4253 Mon Sep 17 00:00:00 2001 From: jtclemm Date: Thu, 7 Jul 2022 12:44:36 -0600 Subject: [PATCH 10/72] Optimizing group filters --- src/GRANULAR/compute_contact_atom.cpp | 45 ++++++++++++++++----------- 1 file changed, 27 insertions(+), 18 deletions(-) diff --git a/src/GRANULAR/compute_contact_atom.cpp b/src/GRANULAR/compute_contact_atom.cpp index 26018f7bfb..a502630fd4 100644 --- a/src/GRANULAR/compute_contact_atom.cpp +++ b/src/GRANULAR/compute_contact_atom.cpp @@ -125,33 +125,42 @@ void ComputeContactAtom::compute_peratom() int *mask = atom->mask; int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; + bool update_i_flag, update_j_flag; for (i = 0; i < nall; i++) contact[i] = 0.0; for (ii = 0; ii < inum; ii++) { i = ilist[ii]; - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - radi = radius[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; + // Only proceed if i is either part of the compute group or will contribute to contacts + if ((mask[i] & groupbit) || (mask[i] & jgroupbit)) { + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx * delx + dely * dely + delz * delz; - radsum = radi + radius[j]; - radsumsq = radsum * radsum; - if (rsq <= radsumsq) { // Only tally for atoms in compute group (groupbit) if neighbor is in group2 (jgroupbit) - if ((mask[i] & groupbit) && (mask[j] & jgroupbit)) contact[i] += 1.0; - if ((mask[j] & groupbit) && (mask[i] & jgroupbit)) contact[j] += 1.0; + update_i_flag = (mask[i] & groupbit) && (mask[j] & jgroupbit); + update_j_flag = (mask[j] & groupbit) && (mask[i] & jgroupbit); + + if (update_i_flag || update_j_flag) { + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + radsum = radi + radius[j]; + radsumsq = radsum * radsum; + if (rsq <= radsumsq) { + if (update_i_flag) contact[i] += 1.0; + if (update_j_flag) contact[j] += 1.0; + } + } } } } From d2ffc9dae81f7586bd781b076a4e4001bae2a921 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 7 Jul 2022 15:57:14 -0400 Subject: [PATCH 11/72] programming style updates, fix memory leaks and uninitialized access --- src/MISC/pair_srp.cpp | 5 ++-- src/MISC/pair_srp_react.cpp | 55 ++++++++++++++++--------------------- src/MISC/pair_srp_react.h | 3 +- 3 files changed, 27 insertions(+), 36 deletions(-) diff --git a/src/MISC/pair_srp.cpp b/src/MISC/pair_srp.cpp index 21869c3ca0..bb731cdc32 100644 --- a/src/MISC/pair_srp.cpp +++ b/src/MISC/pair_srp.cpp @@ -33,7 +33,6 @@ Please contact Timothy Sirk for questions (tim.sirk@us.army.mil). #include "comm.h" #include "domain.h" #include "error.h" -#include "fix.h" #include "fix_srp.h" #include "force.h" #include "memory.h" @@ -84,7 +83,7 @@ PairSRP::PairSRP(LAMMPS *lmp) : Pair(lmp), fix_id(nullptr) // will be invoked before other fixes that migrate atoms // this is checked for in FixSRP - f_srp = dynamic_cast( modify->add_fix(fmt::format("{:02d}_FIX_SRP all SRP",srp_instance))); + f_srp = dynamic_cast(modify->add_fix(fmt::format("{:02d}_FIX_SRP all SRP", srp_instance))); ++srp_instance; } @@ -439,7 +438,7 @@ void PairSRP::coeff(int narg, char **arg) void PairSRP::init_style() { if (!force->newton_pair) - error->all(FLERR,"PairSRP: Pair srp requires newton pair on"); + error->all(FLERR,"Pair srp requires newton pair on"); // verify that fix SRP is still defined and has not been changed. diff --git a/src/MISC/pair_srp_react.cpp b/src/MISC/pair_srp_react.cpp index 4f0720d27b..b302a9a509 100644 --- a/src/MISC/pair_srp_react.cpp +++ b/src/MISC/pair_srp_react.cpp @@ -31,9 +31,7 @@ There is an example script for this package in examples/PACKAGES/srp_react/. #include "atom.h" #include "citeme.h" #include "comm.h" -#include "domain.h" #include "error.h" -#include "fix.h" #include "fix_srp_react.h" #include "force.h" #include "memory.h" @@ -64,22 +62,28 @@ static int srp_instance = 0; constructor ---------------------------------------------------------------------- */ -PairSRPREACT::PairSRPREACT(LAMMPS *lmp) : PairSRP(lmp) +PairSRPREACT::PairSRPREACT(LAMMPS *lmp) : + PairSRP(lmp), idbreak(nullptr), idcreate(nullptr), bond_break(false), bond_create(false) { if (lmp->citeme) lmp->citeme->add(cite_srpreact); // pair srp/react has its own fix, hence delete fix srp instance // created in the constructor of pair srp - for( int ifix = 0; ifixnfix; ifix++) - if( strcmp(modify->get_fix_by_index(ifix)->style, "SRP") == 0) - modify->delete_fix(ifix); + for (auto ifix : modify->get_fix_by_style("SRP")) + modify->delete_fix(ifix->id); // similar to fix SRP, create fix SRP REACT instance here with unique fix id f_srp = (FixSRPREACT *) modify->add_fix(fmt::format("{:02d}_FIX_SRP_REACT all SRPREACT",srp_instance)); ++srp_instance; } +PairSRPREACT::~PairSRPREACT() +{ + delete[] idbreak; + delete[] idcreate; +} + /* ---------------------------------------------------------------------- global settings ------------------------------------------------------------------------- */ @@ -90,7 +94,7 @@ void PairSRPREACT::settings(int narg, char **arg) error->all(FLERR,"Illegal pair_style command"); if (atom->tag_enable == 0) - error->all(FLERR,"Pair_style srp requires atom IDs"); + error->all(FLERR,"Pair_style srp/react requires atom IDs"); cut_global = utils::numeric(FLERR,arg[0],false,lmp); // wildcard @@ -118,23 +122,14 @@ void PairSRPREACT::settings(int narg, char **arg) idcreate= nullptr; // find whether id is of bond/break or bond/create - const char* reactid = arg[3]; - if(strcmp(modify->get_fix_by_id(reactid)->style,"bond/break") == 0) - { + const char *reactid = arg[3]; + if (utils::strmatch(modify->get_fix_by_id(reactid)->style,"^bond/break")) { bond_break = true; - int n = strlen(reactid) + 1; - idbreak = new char[n]; - strcpy(idbreak,reactid); - } - else if(strcmp(modify->get_fix_by_id(reactid)->style,"bond/create") == 0) - { + idbreak = utils::strdup(reactid); + } else if (utils::strmatch(modify->get_fix_by_id(reactid)->style,"^bond/create")) { bond_create = true; - int n = strlen(reactid) + 1; - idcreate = new char[n]; - strcpy(idcreate,reactid); - } - else - error->all(FLERR,"Illegal pair_style command"); + idcreate = utils::strdup(reactid); + } else error->all(FLERR,"Illegal pair_style command"); int iarg = 4; // default exclude 1-2 @@ -175,12 +170,12 @@ void PairSRPREACT::settings(int narg, char **arg) void PairSRPREACT::init_style() { if (!force->newton_pair) - error->all(FLERR,"PairSRPREACT: Pair srp requires newton pair on"); + error->all(FLERR,"Pair srp/react requires newton pair on"); // verify that fix SRP is still defined and has not been changed. if (strcmp(f_srp->style,"SRPREACT") != 0) - error->all(FLERR,"Fix SRP has been changed unexpectedly"); + error->all(FLERR,"Fix SRPREACT has been changed unexpectedly"); if (comm->me == 0) utils::logmesg(lmp,"Using type {} for bond particles\n",bptype); @@ -205,24 +200,22 @@ void PairSRPREACT::init_style() // if using fix bond/break, set id of fix bond/break in fix srp // idbreak = id of fix bond break - if( bond_break ) - { + if (bond_break) { sprintf(c0, "%s", idbreak); arg0[0] = (char *) "bond/break"; arg0[1] = c0; f_srp->modify_params(2, arg0); - delete [] idbreak; + delete[] idbreak; } // if using fix bond/create, set id of fix bond/create in fix srp // idcreate = id of fix bond break - if( bond_create ) - { + if (bond_create) { sprintf(c0, "%s", idcreate); arg0[0] = (char *) "bond/create"; arg0[1] = c0; f_srp->modify_params(2, arg0); - delete [] idcreate; + delete[] idcreate; } // bond particles do not contribute to energy or virial @@ -233,7 +226,7 @@ void PairSRPREACT::init_style() arg1[0] = (char *) "norm"; arg1[1] = (char *) "no"; output->thermo->modify_params(2, arg1); - if (comm->me == 0) error->message(FLERR,"Thermo normalization turned off by pair srp"); + if (comm->me == 0) error->message(FLERR,"Thermo normalization turned off by pair srp/react"); neighbor->request(this,instance_me); } diff --git a/src/MISC/pair_srp_react.h b/src/MISC/pair_srp_react.h index 39663996b0..95a8163900 100644 --- a/src/MISC/pair_srp_react.h +++ b/src/MISC/pair_srp_react.h @@ -27,6 +27,7 @@ namespace LAMMPS_NS { class PairSRPREACT : public PairSRP { public: PairSRPREACT(class LAMMPS *); + ~PairSRPREACT() override; void settings(int, char **) override; void init_style() override; @@ -35,8 +36,6 @@ class PairSRPREACT : public PairSRP { char *idcreate; bool bond_create, bond_break; }; - } // namespace LAMMPS_NS - #endif #endif From 796bc28f94a23496b6a980a6215433043e486abf Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Fri, 8 Jul 2022 16:54:01 +0900 Subject: [PATCH 12/72] changed rstfile names, style names, and description about FF for SPICA --- doc/src/Commands_bond.rst | 2 +- doc/src/Commands_pair.rst | 6 +- doc/src/Errors_messages.rst | 8 +- doc/src/Packages_details.rst | 21 +++-- doc/src/Packages_list.rst | 8 +- doc/src/{angle_sdk.rst => angle_spica.rst} | 37 ++++---- doc/src/angle_style.rst | 2 +- doc/src/{pair_sdk.rst => pair_spica.rst} | 99 ++++++++++++--------- doc/src/pair_style.rst | 6 +- doc/utils/check-styles.py | 11 +-- doc/utils/sphinx-config/false_positives.txt | 8 ++ 11 files changed, 118 insertions(+), 90 deletions(-) rename doc/src/{angle_sdk.rst => angle_spica.rst} (52%) rename doc/src/{pair_sdk.rst => pair_spica.rst} (58%) diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index 28c0882c56..013109430b 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -92,7 +92,7 @@ OPT. * :doc:`harmonic (iko) ` * :doc:`mm3 ` * :doc:`quartic (o) ` - * :doc:`sdk (o) ` + * :doc:`spica (o) ` * :doc:`table (o) ` .. _dihedral: diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 11334ea2d1..4e7b18ce7d 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -179,9 +179,9 @@ OPT. * :doc:`lj/long/tip4p/long (o) ` * :doc:`lj/mdf ` * :doc:`lj/relres (o) ` - * :doc:`lj/sdk (gko) ` - * :doc:`lj/sdk/coul/long (go) ` - * :doc:`lj/sdk/coul/msm (o) ` + * :doc:`lj/spica (gko) ` + * :doc:`lj/spica/coul/long (go) ` + * :doc:`lj/spica/coul/msm (o) ` * :doc:`lj/sf/dipole/sf (go) ` * :doc:`lj/smooth (go) ` * :doc:`lj/smooth/linear (o) ` diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index 4e216828d3..86afdafe70 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -1291,7 +1291,7 @@ Doc page with :doc:`WARNING messages ` *Cannot use chosen neighbor list style with lj/gromacs/kk* Self-explanatory. -*Cannot use chosen neighbor list style with lj/sdk/kk* +*Cannot use chosen neighbor list style with lj/spica/kk* That style is not supported by Kokkos. *Cannot use chosen neighbor list style with pair eam/kk* @@ -1659,10 +1659,10 @@ Doc page with :doc:`WARNING messages ` *Cannot use newton pair with lj/gromacs/gpu pair style* Self-explanatory. -*Cannot use newton pair with lj/sdk/coul/long/gpu pair style* +*Cannot use newton pair with lj/spica/coul/long/gpu pair style* Self-explanatory. -*Cannot use newton pair with lj/sdk/gpu pair style* +*Cannot use newton pair with lj/spica/gpu pair style* Self-explanatory. *Cannot use newton pair with lj96/cut/gpu pair style* @@ -6782,7 +6782,7 @@ keyword to allow for additional bonds to be formed This is because the computation of constraint forces within a water molecule adds forces to atoms owned by other processors. -*Pair style lj/sdk/coul/long/gpu requires atom attribute q* +*Pair style lj/spica/coul/long/gpu requires atom attribute q* The atom style defined does not have this attribute. *Pair style nb3b/harmonic requires atom IDs* diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 59922bd939..24a8cc11b9 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -35,7 +35,7 @@ page gives those details. * :ref:`BPM ` * :ref:`BROWNIAN ` * :ref:`CG-DNA ` - * :ref:`CG-SDK ` + * :ref:`CG-SPICA ` * :ref:`CLASS2 ` * :ref:`COLLOID ` * :ref:`COLVARS ` @@ -365,27 +365,26 @@ The CG-DNA package requires that also the `MOLECULE `_ and ---------- -.. _PKG-CG-SDK: +.. _PKG-CG-SPICA: -CG-SDK package +CG-SPICA package ------------------ **Contents:** Several pair styles and an angle style which implement the -coarse-grained SDK model of Shinoda, DeVane, and Klein which enables -simulation of ionic liquids, electrolytes, lipids and charged amino -acids. +coarse-grained SPICA (formerly called SDK) model which enables +simulation of biological or soft material systems. **Author:** Axel Kohlmeyer (Temple U). **Supporting info:** -* src/CG-SDK: filenames -> commands -* src/CG-SDK/README -* :doc:`pair_style lj/sdk/\* ` -* :doc:`angle_style sdk ` -* examples/PACKAGES/cgsdk +* src/CG-SPICA: filenames -> commands +* src/CG-SPICA/README +* :doc:`pair_style lj/spica/\* ` +* :doc:`angle_style spica ` +* examples/PACKAGES/cgspica * https://www.lammps.org/pictures.html#cg ---------- diff --git a/doc/src/Packages_list.rst b/doc/src/Packages_list.rst index 3cd19e6e03..eb511cd139 100644 --- a/doc/src/Packages_list.rst +++ b/doc/src/Packages_list.rst @@ -73,10 +73,10 @@ whether an extra library is needed to build and use the package: - src/CG-DNA/README - PACKAGES/cgdna - no - * - :ref:`CG-SDK ` - - SDK coarse-graining model - - :doc:`pair_style lj/sdk ` - - PACKAGES/cgsdk + * - :ref:`CG-SPICA ` + - SPICA (SDK) coarse-graining model + - :doc:`pair_style lj/spica ` + - PACKAGES/cgspica - no * - :ref:`CLASS2 ` - class 2 force fields diff --git a/doc/src/angle_sdk.rst b/doc/src/angle_spica.rst similarity index 52% rename from doc/src/angle_sdk.rst rename to doc/src/angle_spica.rst index 50f4a5b360..4162ce5608 100644 --- a/doc/src/angle_sdk.rst +++ b/doc/src/angle_spica.rst @@ -1,32 +1,32 @@ -.. index:: angle_style sdk -.. index:: angle_style sdk/omp +.. index:: angle_style spica +.. index:: angle_style spica/omp -angle_style sdk command -======================= +angle_style spica command +========================= -Accelerator Variants: *sdk/omp* +Accelerator Variants: *spica/omp* Syntax """""" .. code-block:: LAMMPS - angle_style sdk + angle_style spica - angle_style sdk/omp + angle_style spica/omp Examples """""""" .. code-block:: LAMMPS - angle_style sdk + angle_style spica angle_coeff 1 300.0 107.0 Description """"""""""" -The *sdk* angle style is a combination of the harmonic angle potential, +The *spica* angle style is a combination of the harmonic angle potential, .. math:: @@ -34,10 +34,10 @@ The *sdk* angle style is a combination of the harmonic angle potential, where :math:`\theta_0` is the equilibrium value of the angle and :math:`K` a prefactor, with the *repulsive* part of the non-bonded -*lj/sdk* pair style between the atoms 1 and 3. This angle potential is -intended for coarse grained MD simulations with the CMM parameterization -using the :doc:`pair_style lj/sdk `. Relative to the -pair_style *lj/sdk*, however, the energy is shifted by +*lj/spica* pair style between the atoms 1 and 3. This angle potential is +intended for coarse grained MD simulations with the SPICA (formerly called SDK) parameterization +using the :doc:`pair_style lj/spica `. Relative to the +pair_style *lj/spica*, however, the energy is shifted by :math:`\epsilon`, to avoid sudden jumps. Note that the usual 1/2 factor is included in :math:`K`. @@ -51,9 +51,12 @@ The following coefficients must be defined for each angle type via the radians internally; hence :math:`K` is effectively energy per radian\^2. -The required *lj/sdk* parameters are extracted automatically from the +The required *lj/spica* parameters are extracted automatically from the pair_style. +Style *sdk*, the original implementation of style *spica*, is available +for backward compatibility. + ---------- .. include:: accel_styles.rst @@ -64,14 +67,14 @@ Restrictions """""""""""" This angle style can only be used if LAMMPS was built with the -CG-SDK package. See the :doc:`Build package ` doc +CG-SPICA package. See the :doc:`Build package ` doc page for more info. Related commands """""""""""""""" -:doc:`angle_coeff `, :doc:`angle_style harmonic `, :doc:`pair_style lj/sdk `, -:doc:`pair_style lj/sdk/coul/long ` +:doc:`angle_coeff `, :doc:`angle_style harmonic `, :doc:`pair_style lj/spica `, +:doc:`pair_style lj/spica/coul/long ` Default """"""" diff --git a/doc/src/angle_style.rst b/doc/src/angle_style.rst index c7001cff18..a0917f1b66 100644 --- a/doc/src/angle_style.rst +++ b/doc/src/angle_style.rst @@ -91,7 +91,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist. * :doc:`harmonic ` - harmonic angle * :doc:`mm3 ` - anharmonic angle * :doc:`quartic ` - angle with cubic and quartic terms -* :doc:`sdk ` - harmonic angle with repulsive SDK pair style between 1-3 atoms +* :doc:`spica ` - harmonic angle with repulsive SPICA pair style between 1-3 atoms * :doc:`table ` - tabulated by angle ---------- diff --git a/doc/src/pair_sdk.rst b/doc/src/pair_spica.rst similarity index 58% rename from doc/src/pair_sdk.rst rename to doc/src/pair_spica.rst index f389079e15..9bd6ee069c 100644 --- a/doc/src/pair_sdk.rst +++ b/doc/src/pair_spica.rst @@ -1,27 +1,27 @@ -.. index:: pair_style lj/sdk -.. index:: pair_style lj/sdk/gpu -.. index:: pair_style lj/sdk/kk -.. index:: pair_style lj/sdk/omp -.. index:: pair_style lj/sdk/coul/long -.. index:: pair_style lj/sdk/coul/long/gpu -.. index:: pair_style lj/sdk/coul/long/omp -.. index:: pair_style lj/sdk/coul/msm -.. index:: pair_style lj/sdk/coul/msm/omp +.. index:: pair_style lj/spica +.. index:: pair_style lj/spica/gpu +.. index:: pair_style lj/spica/kk +.. index:: pair_style lj/spica/omp +.. index:: pair_style lj/spica/coul/long +.. index:: pair_style lj/spica/coul/long/gpu +.. index:: pair_style lj/spica/coul/long/omp +.. index:: pair_style lj/spica/coul/msm +.. index:: pair_style lj/spica/coul/msm/omp -pair_style lj/sdk command -========================= +pair_style lj/spica command +=========================== -Accelerator Variants: *lj/sdk/gpu*, *lj/sdk/kk*, *lj/sdk/omp* +Accelerator Variants: *lj/spica/gpu*, *lj/spica/kk*, *lj/spica/omp* -pair_style lj/sdk/coul/long command -=================================== +pair_style lj/spica/coul/long command +===================================== -Accelerator Variants: *lj/sdk/coul/long/gpu*, *lj/sdk/coul/long/omp* +Accelerator Variants: *lj/spica/coul/long/gpu*, *lj/spica/coul/long/omp* -pair_style lj/sdk/coul/msm command -================================== +pair_style lj/spica/coul/msm command +==================================== -Accelerator Variants: *lj/sdk/coul/msm/omp* +Accelerator Variants: *lj/spica/coul/msm/omp* Syntax """""" @@ -30,14 +30,14 @@ Syntax pair_style style args -* style = *lj/sdk* or *lj/sdk/coul/long* +* style = *lj/spica* or *lj/spica/coul/long* * args = list of arguments for a particular style .. parsed-literal:: - *lj/sdk* args = cutoff + *lj/spica* args = cutoff cutoff = global cutoff for Lennard Jones interactions (distance units) - *lj/sdk/coul/long* args = cutoff (cutoff2) + *lj/spica/coul/long* args = cutoff (cutoff2) cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units) cutoff2 = global cutoff for Coulombic (optional) (distance units) @@ -46,21 +46,21 @@ Examples .. code-block:: LAMMPS - pair_style lj/sdk 2.5 + pair_style lj/spica 2.5 pair_coeff 1 1 lj12_6 1 1.1 2.8 - pair_style lj/sdk/coul/long 10.0 - pair_style lj/sdk/coul/long 10.0 12.0 + pair_style lj/spica/coul/long 10.0 + pair_style lj/spica/coul/long 10.0 12.0 pair_coeff 1 1 lj9_6 100.0 3.5 12.0 - pair_style lj/sdk/coul/msm 10.0 - pair_style lj/sdk/coul/msm 10.0 12.0 + pair_style lj/spica/coul/msm 10.0 + pair_style lj/spica/coul/msm 10.0 12.0 pair_coeff 1 1 lj9_6 100.0 3.5 12.0 Description """"""""""" -The *lj/sdk* styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential, +The *lj/spica* styles compute a 9/6, 12/4, 12/5, or 12/6 Lennard-Jones potential, given by .. math:: @@ -71,14 +71,19 @@ given by E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^4 \right] \qquad r < r_c \\ + E = & \frac{12}{7}\left(\frac{12}{5}\right)^{\left(\frac{5}{7}\right)} \epsilon + \left[ \left(\frac{\sigma}{r}\right)^{12} - + \left(\frac{\sigma}{r}\right)^5 \right] + \qquad r < r_c \\ E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c -as required for the SDK Coarse-grained MD parameterization discussed in -:ref:`(Shinoda) ` and :ref:`(DeVane) `. Rc is the cutoff. +as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in +:ref:`(Shinoda) `, :ref:`(DeVane) `, :ref:`(Seo) `, and :ref:`(Miyazaki) `. +Rc is the cutoff. -Style *lj/sdk/coul/long* computes the adds Coulombic interactions +Style *lj/spica/coul/long* computes the adds Coulombic interactions with an additional damping factor applied so it can be used in conjunction with the :doc:`kspace_style ` command and its *ewald* or *pppm* or *pppm/cg* option. The Coulombic cutoff @@ -92,7 +97,7 @@ above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: -* cg_type (lj9_6, lj12_4, or lj12_6) +* cg_type (lj9_6, lj12_4, lj12_5, or lj12_6) * epsilon (energy units) * sigma (distance units) * cutoff1 (distance units) @@ -108,11 +113,15 @@ and Coulombic interactions for this type pair. If both coefficients are specified, they are used as the LJ and Coulombic cutoffs for this type pair. -For *lj/sdk/coul/long* and *lj/sdk/coul/msm* only the LJ cutoff can be +For *lj/spica/coul/long* and *lj/spica/coul/msm* only the LJ cutoff can be specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the pair_style command. +The original implementation of the above styles are +style *lj/sdk*, *lj/sdk/coul/long*, and *lj/sdk/coul/msm*, +and available for backward compatibility. + ---------- .. include:: accel_styles.rst @@ -123,24 +132,24 @@ Mixing, shift, table, tail correction, restart, rRESPA info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" For atom type pairs I,J and I != J, the epsilon and sigma coefficients -and cutoff distance for all of the lj/sdk pair styles *cannot* be mixed, +and cutoff distance for all of the lj/spica pair styles *cannot* be mixed, since different pairs may have different exponents. So all parameters for all pairs have to be specified explicitly through the "pair_coeff" command. Defining then in a data file is also not supported, due to limitations of that file format. -All of the lj/sdk pair styles support the +All of the lj/spica pair styles support the :doc:`pair_modify ` shift option for the energy of the Lennard-Jones portion of the pair interaction. -The *lj/sdk/coul/long* pair styles support the +The *lj/spica/coul/long* pair styles support the :doc:`pair_modify ` table option since they can tabulate the short-range portion of the long-range Coulombic interaction. -All of the lj/sdk pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do +All of the lj/spica pair styles write their information to :doc:`binary restart files `, so pair_style and pair_coeff commands do not need to be specified in an input script that reads a restart file. -The lj/sdk and lj/cut/coul/long pair styles do not support +The lj/spica and lj/cut/coul/long pair styles do not support the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa ` command. ---------- @@ -148,8 +157,8 @@ the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style re Restrictions """""""""""" -All of the lj/sdk pair styles are part of the CG-SDK package. The -*lj/sdk/coul/long* style also requires the KSPACE package to be built +All of the lj/spica pair styles are part of the CG-SPICA package. The +*lj/spica/coul/long* style also requires the KSPACE package to be built (which is enabled by default). They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -157,7 +166,7 @@ doc page for more info. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`angle_style sdk ` +:doc:`pair_coeff `, :doc:`angle_style spica ` Default """"""" @@ -168,8 +177,16 @@ none .. _Shinoda3: -**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007). +**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27-36 (2007). .. _DeVane: **(DeVane)** Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008). + +.. _Seo: + +**(Seo)** Seo, Shinoda, J Chem Theory Comput, 15, 762-774 (2019). + +.. _Miyazaki: + +**(Miyazaki)** Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782-793 (2020). diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 7e9414cee9..3b8bc979b4 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -258,9 +258,9 @@ accelerated styles exist. * :doc:`lj/long/tip4p/long ` - long-range LJ and long-range Coulomb for TIP4P water * :doc:`lj/mdf ` - LJ potential with a taper function * :doc:`lj/relres ` - LJ using multiscale Relative Resolution (RelRes) methodology :ref:`(Chaimovich) `. -* :doc:`lj/sdk ` - LJ for SDK coarse-graining -* :doc:`lj/sdk/coul/long ` - LJ for SDK coarse-graining with long-range Coulomb -* :doc:`lj/sdk/coul/msm ` - LJ for SDK coarse-graining with long-range Coulomb via MSM +* :doc:`lj/spica ` - LJ for SPICA coarse-graining +* :doc:`lj/spica/coul/long ` - LJ for SPICA coarse-graining with long-range Coulomb +* :doc:`lj/spica/coul/msm ` - LJ for SPICA coarse-graining with long-range Coulomb via MSM * :doc:`lj/sf/dipole/sf ` - LJ with dipole interaction with shifted forces * :doc:`lj/smooth ` - smoothed Lennard-Jones potential * :doc:`lj/smooth/linear ` - linear smoothed LJ potential diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py index 9633c1080f..47d3dd5e3b 100755 --- a/doc/utils/check-styles.py +++ b/doc/utils/check-styles.py @@ -254,8 +254,9 @@ for command_type, entries in index.items(): print("Total number of style index entries:", total_index) +skip_angle = ('sdk') skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species') -skip_pair = ('meam/c','lj/sf','reax/c') +skip_pair = ('meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm') skip_compute = ('pressure/cylinder') counter = 0 @@ -269,8 +270,8 @@ counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) `",pair counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) ` -",pair,'Pair',skip=skip_pair,suffix=False) counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `",bond,'Bond',suffix=True) counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) ` -",bond,'Bond',suffix=False) -counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `",angle,'Angle',suffix=True) -counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) ` -",angle,'Angle',suffix=False) +counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `",angle,'Angle',skip=skip_angle,suffix=True) +counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) ` -",angle,'Angle',skip=skip_angle,suffix=False) counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `",dihedral,'Dihedral',suffix=True) counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) ` -",dihedral,'Dihedral',suffix=False) counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `",improper,'Improper',suffix=True) @@ -284,12 +285,12 @@ counter = 0 counter += check_style_index("compute", compute, index["compute"], skip=['pressure/cylinder']) counter += check_style_index("fix", fix, index["fix"], skip=['python','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species']) -counter += check_style_index("angle_style", angle, index["angle_style"]) +counter += check_style_index("angle_style", angle, index["angle_style"], skip=['sdk']) counter += check_style_index("bond_style", bond, index["bond_style"]) counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"]) counter += check_style_index("improper_style", improper, index["improper_style"]) counter += check_style_index("kspace_style", kspace, index["kspace_style"]) -counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf','reax/c']) +counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm']) if counter: print(f"Found {counter} issue(s) with style index") diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 77a1da6643..dc51ce2ac5 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -421,6 +421,8 @@ CGDNA cgs cgsdk CGSDK +cgspica +CGSPICA Chaimovich Chalopin Champaign @@ -2076,6 +2078,7 @@ Mishin Mishra mistyped mistyrose +Miyazaki Mj mK mkdir @@ -2471,6 +2474,7 @@ ohenrich ok Okabe Okamoto +Okazaki O'Keefe OKeefe oldlace @@ -2729,6 +2733,7 @@ pscrozi pseudodynamics pseudopotential pSp +pSPICA Pstart Pstop pstyle @@ -3087,6 +3092,7 @@ semiaxes semimetals Semin Sensable +Seo Sep seqdep Serpico @@ -3197,6 +3203,8 @@ Spellmeyer Speybroeck sph SPH +spica +SPICA Spickermann splined spparks From 20182a194f16558cbb487700997ac3ee979773ce Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Fri, 8 Jul 2022 17:01:56 +0900 Subject: [PATCH 13/72] changed a package name CG-SDK to CG-SPICA in files for cmake. --- cmake/CMakeLists.txt | 2 +- cmake/presets/all_off.cmake | 2 +- cmake/presets/all_on.cmake | 2 +- cmake/presets/mingw-cross.cmake | 2 +- cmake/presets/most.cmake | 2 +- cmake/presets/windows.cmake | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index b0b8bfd363..bc594dab7b 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -202,7 +202,7 @@ set(STANDARD_PACKAGES BPM BROWNIAN CG-DNA - CG-SDK + CG-SPICA CLASS2 COLLOID COLVARS diff --git a/cmake/presets/all_off.cmake b/cmake/presets/all_off.cmake index 895f26845f..3b62c9538b 100644 --- a/cmake/presets/all_off.cmake +++ b/cmake/presets/all_off.cmake @@ -11,7 +11,7 @@ set(ALL_PACKAGES BPM BROWNIAN CG-DNA - CG-SDK + CG-SPICA CLASS2 COLLOID COLVARS diff --git a/cmake/presets/all_on.cmake b/cmake/presets/all_on.cmake index 90b0f02c4b..ac4f6e389d 100644 --- a/cmake/presets/all_on.cmake +++ b/cmake/presets/all_on.cmake @@ -13,7 +13,7 @@ set(ALL_PACKAGES BPM BROWNIAN CG-DNA - CG-SDK + CG-SPICA CLASS2 COLLOID COLVARS diff --git a/cmake/presets/mingw-cross.cmake b/cmake/presets/mingw-cross.cmake index 13cfee9018..fcc2072807 100644 --- a/cmake/presets/mingw-cross.cmake +++ b/cmake/presets/mingw-cross.cmake @@ -7,7 +7,7 @@ set(WIN_PACKAGES BPM BROWNIAN CG-DNA - CG-SDK + CG-SPICA CLASS2 COLLOID COLVARS diff --git a/cmake/presets/most.cmake b/cmake/presets/most.cmake index 5e408f17cf..77ab8d4a9f 100644 --- a/cmake/presets/most.cmake +++ b/cmake/presets/most.cmake @@ -9,7 +9,7 @@ set(ALL_PACKAGES BPM BROWNIAN CG-DNA - CG-SDK + CG-SPICA CLASS2 COLLOID COLVARS diff --git a/cmake/presets/windows.cmake b/cmake/presets/windows.cmake index ce5387cef9..323323b991 100644 --- a/cmake/presets/windows.cmake +++ b/cmake/presets/windows.cmake @@ -5,7 +5,7 @@ set(WIN_PACKAGES BPM BROWNIAN CG-DNA - CG-SDK + CG-SPICA CLASS2 COLLOID COLVARS From c71e1cd4709ba2aab21989c9ec1b96eb8df67030 Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Fri, 8 Jul 2022 17:16:15 +0900 Subject: [PATCH 14/72] changed lammps inputs in examples for SPICA --- examples/PACKAGES/{cgsdk => cgspica}/README | 11 ++++++----- .../{cgsdk => cgspica}/peg-verlet/data.pegc12e8.gz | Bin .../{cgsdk => cgspica}/peg-verlet/in.pegc12e8 | 2 +- .../{cgsdk => cgspica}/peg-verlet/in.pegc12e8-angle | 4 ++-- .../peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 | 0 .../peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 | 0 .../peg-verlet/log.27Nov18.pegc12e8.g++.1 | 0 .../peg-verlet/log.27Nov18.pegc12e8.g++.4 | 0 .../{cgsdk => cgspica}/sds-monolayer/data.sds.gz | Bin .../{cgsdk => cgspica}/sds-monolayer/in.sds-hybrid | 4 ++-- .../{cgsdk => cgspica}/sds-monolayer/in.sds-regular | 4 ++-- .../sds-monolayer/log.27Nov18.sds-hybrid.g++.1 | 0 .../sds-monolayer/log.27Nov18.sds-hybrid.g++.4 | 0 .../sds-monolayer/log.27Nov18.sds-regular.g++.1 | 0 .../sds-monolayer/log.27Nov18.sds-regular.g++.4 | 0 15 files changed, 13 insertions(+), 12 deletions(-) rename examples/PACKAGES/{cgsdk => cgspica}/README (60%) rename examples/PACKAGES/{cgsdk => cgspica}/peg-verlet/data.pegc12e8.gz (100%) rename examples/PACKAGES/{cgsdk => cgspica}/peg-verlet/in.pegc12e8 (93%) rename examples/PACKAGES/{cgsdk => cgspica}/peg-verlet/in.pegc12e8-angle (87%) rename examples/PACKAGES/{cgsdk => cgspica}/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 (100%) rename examples/PACKAGES/{cgsdk => cgspica}/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 (100%) rename examples/PACKAGES/{cgsdk => cgspica}/peg-verlet/log.27Nov18.pegc12e8.g++.1 (100%) rename examples/PACKAGES/{cgsdk => cgspica}/peg-verlet/log.27Nov18.pegc12e8.g++.4 (100%) rename examples/PACKAGES/{cgsdk => cgspica}/sds-monolayer/data.sds.gz (100%) rename examples/PACKAGES/{cgsdk => cgspica}/sds-monolayer/in.sds-hybrid (91%) rename examples/PACKAGES/{cgsdk => cgspica}/sds-monolayer/in.sds-regular (91%) rename examples/PACKAGES/{cgsdk => cgspica}/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 (100%) rename examples/PACKAGES/{cgsdk => cgspica}/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 (100%) rename examples/PACKAGES/{cgsdk => cgspica}/sds-monolayer/log.27Nov18.sds-regular.g++.1 (100%) rename examples/PACKAGES/{cgsdk => cgspica}/sds-monolayer/log.27Nov18.sds-regular.g++.4 (100%) diff --git a/examples/PACKAGES/cgsdk/README b/examples/PACKAGES/cgspica/README similarity index 60% rename from examples/PACKAGES/cgsdk/README rename to examples/PACKAGES/cgspica/README index 09b9b0a8ea..448bdda2a7 100644 --- a/examples/PACKAGES/cgsdk/README +++ b/examples/PACKAGES/cgspica/README @@ -1,7 +1,8 @@ -LAMMPS CG-SDK example problems +LAMMPS CG-SPICA example problems -Each of these sub-directories contains a sample problem for the SDK -coarse grained MD potentials that you can run with LAMMPS. +Each of these sub-directories contains a sample problem for +the SPICA (formerly called SDK) coarse grained MD potentials +that you can run with LAMMPS. These are the two sample systems @@ -9,11 +10,11 @@ peg-verlet: coarse grained PEG surfactant/water mixture lamella verlet version this example uses the plain LJ term only, no charges. two variants are provided regular harmonic angles and - the SDK variant that includes 1-3 LJ repulsion. + the SPICA variant that includes 1-3 LJ repulsion. sds-monolayer: coarse grained SDS surfactant monolayers at water/vapor interface. - this example uses the SDK LJ term with coulomb and shows + this example uses the SPICA LJ term with coulomb and shows how to use the combined coulomb style vs. hybrid/overlay with possible optimizations due to the small number of charged particles in this system diff --git a/examples/PACKAGES/cgsdk/peg-verlet/data.pegc12e8.gz b/examples/PACKAGES/cgspica/peg-verlet/data.pegc12e8.gz similarity index 100% rename from examples/PACKAGES/cgsdk/peg-verlet/data.pegc12e8.gz rename to examples/PACKAGES/cgspica/peg-verlet/data.pegc12e8.gz diff --git a/examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8 b/examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8 similarity index 93% rename from examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8 rename to examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8 index b8e71b849f..037c1334a7 100644 --- a/examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8 +++ b/examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8 @@ -9,7 +9,7 @@ atom_style angle processors * * 1 # read topology and force field -pair_style lj/sdk 15.0 +pair_style lj/sdk 15.0 # compatible with "lj/spica" bond_style harmonic angle_style harmonic special_bonds lj/coul 0.0 0.0 1.0 diff --git a/examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8-angle b/examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8-angle similarity index 87% rename from examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8-angle rename to examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8-angle index 32773f4950..35b5fcdeb7 100644 --- a/examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8-angle +++ b/examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8-angle @@ -9,9 +9,9 @@ atom_style angle processors * * 1 # read topology and force field -pair_style lj/sdk 15.0 +pair_style lj/sdk 15.0 # compatible with "lj/spica" bond_style harmonic -angle_style sdk +angle_style sdk # compatible with "spica" special_bonds lj/coul 0.0 0.0 1.0 read_data data.pegc12e8.gz diff --git a/examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 b/examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 similarity index 100% rename from examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 rename to examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 diff --git a/examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 b/examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 similarity index 100% rename from examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 rename to examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 diff --git a/examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 b/examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8.g++.1 similarity index 100% rename from examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 rename to examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8.g++.1 diff --git a/examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 b/examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8.g++.4 similarity index 100% rename from examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 rename to examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8.g++.4 diff --git a/examples/PACKAGES/cgsdk/sds-monolayer/data.sds.gz b/examples/PACKAGES/cgspica/sds-monolayer/data.sds.gz similarity index 100% rename from examples/PACKAGES/cgsdk/sds-monolayer/data.sds.gz rename to examples/PACKAGES/cgspica/sds-monolayer/data.sds.gz diff --git a/examples/PACKAGES/cgsdk/sds-monolayer/in.sds-hybrid b/examples/PACKAGES/cgspica/sds-monolayer/in.sds-hybrid similarity index 91% rename from examples/PACKAGES/cgsdk/sds-monolayer/in.sds-hybrid rename to examples/PACKAGES/cgspica/sds-monolayer/in.sds-hybrid index eb3eca9c96..9fc1416635 100644 --- a/examples/PACKAGES/cgsdk/sds-monolayer/in.sds-hybrid +++ b/examples/PACKAGES/cgspica/sds-monolayer/in.sds-hybrid @@ -5,9 +5,9 @@ dimension 3 atom_style full processors * * 1 -pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5 +pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5 # "lj/sdk" is compatible with "lj/spica" bond_style harmonic -angle_style sdk +angle_style sdk # compatible with "spica" special_bonds lj/coul 0.0 0.0 1.0 read_data data.sds.gz diff --git a/examples/PACKAGES/cgsdk/sds-monolayer/in.sds-regular b/examples/PACKAGES/cgspica/sds-monolayer/in.sds-regular similarity index 91% rename from examples/PACKAGES/cgsdk/sds-monolayer/in.sds-regular rename to examples/PACKAGES/cgspica/sds-monolayer/in.sds-regular index 217c15697e..e64882aaa0 100644 --- a/examples/PACKAGES/cgsdk/sds-monolayer/in.sds-regular +++ b/examples/PACKAGES/cgspica/sds-monolayer/in.sds-regular @@ -5,9 +5,9 @@ dimension 3 atom_style full processors * * 1 -pair_style lj/sdk/coul/long 15.0 +pair_style lj/sdk/coul/long 15.0 # compatible with "lj/spica/coul/long" bond_style harmonic -angle_style sdk +angle_style sdk # compatible with "spica" special_bonds lj/coul 0.0 0.0 1.0 read_data data.sds.gz diff --git a/examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 b/examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 similarity index 100% rename from examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 rename to examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 diff --git a/examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 b/examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 similarity index 100% rename from examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 rename to examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 diff --git a/examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 b/examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-regular.g++.1 similarity index 100% rename from examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 rename to examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-regular.g++.1 diff --git a/examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 b/examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-regular.g++.4 similarity index 100% rename from examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 rename to examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-regular.g++.4 From fc741e0df6586f4d7cac8fcb72e92d53a3917093 Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Fri, 8 Jul 2022 17:28:50 +0900 Subject: [PATCH 15/72] changed names of files, and added a lj12-5 function type. --- lib/gpu/{lal_lj_sdk.cpp => lal_lj_spica.cpp} | 36 +++++++++---------- lib/gpu/{lal_lj_sdk.cu => lal_lj_spica.cu} | 14 +++++--- lib/gpu/{lal_lj_sdk.h => lal_lj_spica.h} | 6 ++-- ...al_lj_sdk_ext.cpp => lal_lj_spica_ext.cpp} | 18 +++++----- ..._lj_sdk_long.cpp => lal_lj_spica_long.cpp} | 14 ++++---- ...al_lj_sdk_long.cu => lal_lj_spica_long.cu} | 14 +++++--- ...{lal_lj_sdk_long.h => lal_lj_spica_long.h} | 4 +-- ...long_ext.cpp => lal_lj_spica_long_ext.cpp} | 18 +++++----- 8 files changed, 68 insertions(+), 56 deletions(-) rename lib/gpu/{lal_lj_sdk.cpp => lal_lj_spica.cpp} (81%) rename lib/gpu/{lal_lj_sdk.cu => lal_lj_spica.cu} (93%) rename lib/gpu/{lal_lj_sdk.h => lal_lj_spica.h} (95%) rename lib/gpu/{lal_lj_sdk_ext.cpp => lal_lj_spica_ext.cpp} (89%) rename lib/gpu/{lal_lj_sdk_long.cpp => lal_lj_spica_long.cpp} (94%) rename lib/gpu/{lal_lj_sdk_long.cu => lal_lj_spica_long.cu} (94%) rename lib/gpu/{lal_lj_sdk_long.h => lal_lj_spica_long.h} (96%) rename lib/gpu/{lal_lj_sdk_long_ext.cpp => lal_lj_spica_long_ext.cpp} (90%) diff --git a/lib/gpu/lal_lj_sdk.cpp b/lib/gpu/lal_lj_spica.cpp similarity index 81% rename from lib/gpu/lal_lj_sdk.cpp rename to lib/gpu/lal_lj_spica.cpp index 0da094c953..8ba13853a6 100644 --- a/lib/gpu/lal_lj_sdk.cpp +++ b/lib/gpu/lal_lj_spica.cpp @@ -1,9 +1,9 @@ /*************************************************************************** - lj_sdk.cpp + lj_spica.cpp ------------------- W. Michael Brown (ORNL) - Class for acceleration of the lj/sdk/cut pair style + Class for acceleration of the lj/spica/cut pair style __________________________________________________________________________ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) @@ -14,14 +14,14 @@ ***************************************************************************/ #if defined(USE_OPENCL) -#include "lj_sdk_cl.h" +#include "lj_spica_cl.h" #elif defined(USE_CUDART) -const char *lj_sdk=0; +const char *lj_spica=0; #else -#include "lj_sdk_cubin.h" +#include "lj_spica_cubin.h" #endif -#include "lal_lj_sdk.h" +#include "lal_lj_spica.h" #include namespace LAMMPS_AL { #define CGCMMT CGCMM @@ -53,33 +53,33 @@ int CGCMMT::init(const int ntypes, double **host_cutsq, const double gpu_split, FILE *_screen) { int success; success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, - _screen,lj_sdk,"k_lj_sdk"); + _screen,lj_spica,"k_lj_spica"); if (success!=0) return success; // If atom type constants fit in shared memory use fast kernel - int sdk_types=ntypes; + int spica_types=ntypes; shared_types=false; int max_shared_types=this->device->max_shared_types(); - if (sdk_types<=max_shared_types && this->_block_size>=max_shared_types) { - sdk_types=max_shared_types; + if (spica_types<=max_shared_types && this->_block_size>=max_shared_types) { + spica_types=max_shared_types; shared_types=true; } - _sdk_types=sdk_types; + _spica_types=spica_types; // Allocate a host write buffer for data initialization - UCL_H_Vec host_write(sdk_types*sdk_types*32,*(this->ucl_device), + UCL_H_Vec host_write(spica_types*spica_types*32,*(this->ucl_device), UCL_WRITE_ONLY); - for (int i=0; iucl_device),UCL_READ_ONLY); - this->atom->type_pack4(ntypes,sdk_types,lj1,host_write,host_cutsq, + lj1.alloc(spica_types*spica_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,spica_types,lj1,host_write,host_cutsq, host_cg_type,host_lj1,host_lj2); - lj3.alloc(sdk_types*sdk_types,*(this->ucl_device),UCL_READ_ONLY); - this->atom->type_pack4(ntypes,sdk_types,lj3,host_write,host_lj3,host_lj4, + lj3.alloc(spica_types*spica_types,*(this->ucl_device),UCL_READ_ONLY); + this->atom->type_pack4(ntypes,spica_types,lj3,host_write,host_lj3,host_lj4, host_offset); UCL_H_Vec dview; @@ -132,7 +132,7 @@ int CGCMMT::loop(const int eflag, const int vflag) { } else { this->k_pair.set_size(GX,BX); this->k_pair.run(&this->atom->x, &lj1, &lj3, - &_sdk_types, &sp_lj, &this->nbor->dev_nbor, + &_spica_types, &sp_lj, &this->nbor->dev_nbor, &this->_nbor_data->begin(), &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum, &nbor_pitch, &this->_threads_per_atom); diff --git a/lib/gpu/lal_lj_sdk.cu b/lib/gpu/lal_lj_spica.cu similarity index 93% rename from lib/gpu/lal_lj_sdk.cu rename to lib/gpu/lal_lj_spica.cu index 1bd9a93d5e..bae8bd57fa 100644 --- a/lib/gpu/lal_lj_sdk.cu +++ b/lib/gpu/lal_lj_spica.cu @@ -1,9 +1,9 @@ // ************************************************************************** -// lj_sdk.cu +// lj_spica.cu // ------------------- // W. Michael Brown (ORNL) // -// Device code for acceleration of the lj/sdk pair style +// Device code for acceleration of the lj/spica pair style // // __________________________________________________________________________ // This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) @@ -24,7 +24,7 @@ _texture_2d( pos_tex,int4); #define pos_tex x_ #endif -__kernel void k_lj_sdk(const __global numtyp4 *restrict x_, +__kernel void k_lj_spica(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1, const __global numtyp4 *restrict lj3, const int lj_types, @@ -91,6 +91,9 @@ __kernel void k_lj_sdk(const __global numtyp4 *restrict x_, } else if (lj1[mtype].y == 1) { inv2=r2inv*ucl_sqrt(r2inv); inv1=inv2*inv2; + } else if (lj1[mtype].y == 4) { + inv1=r2inv*r2inv*ucl_sqrt(r2inv); + inv2=inv1*r2inv; } else { inv1=r2inv*r2inv*r2inv; inv2=inv1; @@ -119,7 +122,7 @@ __kernel void k_lj_sdk(const __global numtyp4 *restrict x_, ans,engv); } -__kernel void k_lj_sdk_fast(const __global numtyp4 *restrict x_, +__kernel void k_lj_spica_fast(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1_in, const __global numtyp4 *restrict lj3_in, const __global numtyp *restrict sp_lj_in, @@ -192,6 +195,9 @@ __kernel void k_lj_sdk_fast(const __global numtyp4 *restrict x_, } else if (lj1[mtype].y == (numtyp)1) { inv2=r2inv*ucl_sqrt(r2inv); inv1=inv2*inv2; + } else if (lj1[mtype].y == (numtyp)4) { + inv1=r2inv*r2inv*ucl_sqrt(r2inv); + inv2=inv1*r2inv; } else { inv1=r2inv*r2inv*r2inv; inv2=inv1; diff --git a/lib/gpu/lal_lj_sdk.h b/lib/gpu/lal_lj_spica.h similarity index 95% rename from lib/gpu/lal_lj_sdk.h rename to lib/gpu/lal_lj_spica.h index 043bafdda8..ed6e5ab096 100644 --- a/lib/gpu/lal_lj_sdk.h +++ b/lib/gpu/lal_lj_spica.h @@ -1,9 +1,9 @@ /*************************************************************************** - lj_sdk.h + lj_spica.h ------------------- W. Michael Brown (ORNL) - Class for acceleration of the lj/sdk pair style + Class for acceleration of the lj/spica pair style __________________________________________________________________________ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) @@ -67,7 +67,7 @@ class CGCMM : public BaseAtomic { bool shared_types; /// Number of atom types - int _sdk_types; + int _spica_types; private: bool _allocated; diff --git a/lib/gpu/lal_lj_sdk_ext.cpp b/lib/gpu/lal_lj_spica_ext.cpp similarity index 89% rename from lib/gpu/lal_lj_sdk_ext.cpp rename to lib/gpu/lal_lj_spica_ext.cpp index 4497233861..1467c1806a 100644 --- a/lib/gpu/lal_lj_sdk_ext.cpp +++ b/lib/gpu/lal_lj_spica_ext.cpp @@ -1,9 +1,9 @@ /*************************************************************************** - lj_sdk.h + lj_spica.h ------------------- W. Michael Brown (ORNL) - Functions for LAMMPS access to lj/sdk pair acceleration routines + Functions for LAMMPS access to lj/spica pair acceleration routines __________________________________________________________________________ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) @@ -17,7 +17,7 @@ #include #include -#include "lal_lj_sdk.h" +#include "lal_lj_spica.h" using namespace std; using namespace LAMMPS_AL; @@ -27,7 +27,7 @@ static CGCMM CMMMF; // --------------------------------------------------------------------------- // Allocate memory on host and device and copy constants to device // --------------------------------------------------------------------------- -int sdk_gpu_init(const int ntypes, double **cutsq, int **cg_types, +int spica_gpu_init(const int ntypes, double **cutsq, int **cg_types, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **offset, double *special_lj, const int inum, const int nall, const int max_nbors, @@ -42,7 +42,7 @@ int sdk_gpu_init(const int ntypes, double **cutsq, int **cg_types, int gpu_rank=CMMMF.device->gpu_rank(); int procs_per_gpu=CMMMF.device->procs_per_gpu(); - CMMMF.device->init_message(screen,"lj/sdk",first_gpu,last_gpu); + CMMMF.device->init_message(screen,"lj/spica",first_gpu,last_gpu); bool message=false; if (CMMMF.device->replica_me()==0 && screen) @@ -89,11 +89,11 @@ int sdk_gpu_init(const int ntypes, double **cutsq, int **cg_types, return init_ok; } -void sdk_gpu_clear() { +void spica_gpu_clear() { CMMMF.clear(); } -int** sdk_gpu_compute_n(const int ago, const int inum_full, +int** spica_gpu_compute_n(const int ago, const int inum_full, const int nall, double **host_x, int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial, tagint **special, const bool eflag, const bool vflag, @@ -105,7 +105,7 @@ int** sdk_gpu_compute_n(const int ago, const int inum_full, vatom, host_start, ilist, jnum, cpu_time, success); } -void sdk_gpu_compute(const int ago, const int inum_full, const int nall, +void spica_gpu_compute(const int ago, const int inum_full, const int nall, double **host_x, int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag, const bool vflag, const bool eatom, const bool vatom, int &host_start, @@ -114,7 +114,7 @@ void sdk_gpu_compute(const int ago, const int inum_full, const int nall, firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success); } -double sdk_gpu_bytes() { +double spica_gpu_bytes() { return CMMMF.host_memory_usage(); } diff --git a/lib/gpu/lal_lj_sdk_long.cpp b/lib/gpu/lal_lj_spica_long.cpp similarity index 94% rename from lib/gpu/lal_lj_sdk_long.cpp rename to lib/gpu/lal_lj_spica_long.cpp index d78e8d84da..3a2c6c693a 100644 --- a/lib/gpu/lal_lj_sdk_long.cpp +++ b/lib/gpu/lal_lj_spica_long.cpp @@ -1,9 +1,9 @@ /*************************************************************************** - lj_sdk_long.cpp + lj_spica_long.cpp ------------------- W. Michael Brown (ORNL) - Class for acceleration of the lj/sdk/coul/long pair style + Class for acceleration of the lj/spica/coul/long pair style __________________________________________________________________________ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) @@ -14,14 +14,14 @@ ***************************************************************************/ #if defined(USE_OPENCL) -#include "lj_sdk_long_cl.h" +#include "lj_spica_long_cl.h" #elif defined(USE_CUDART) -const char *lj_sdk_long=0; +const char *lj_spica_long=0; #else -#include "lj_sdk_long_cubin.h" +#include "lj_spica_long_cubin.h" #endif -#include "lal_lj_sdk_long.h" +#include "lal_lj_spica_long.h" #include namespace LAMMPS_AL { #define CGCMMLongT CGCMMLong @@ -58,7 +58,7 @@ int CGCMMLongT::init(const int ntypes, double **host_cutsq, const double g_ewald) { int success; success=this->init_atomic(nlocal,nall,max_nbors,maxspecial,cell_size,gpu_split, - _screen,lj_sdk_long,"k_lj_sdk_long"); + _screen,lj_spica_long,"k_lj_spica_long"); if (success!=0) return success; diff --git a/lib/gpu/lal_lj_sdk_long.cu b/lib/gpu/lal_lj_spica_long.cu similarity index 94% rename from lib/gpu/lal_lj_sdk_long.cu rename to lib/gpu/lal_lj_spica_long.cu index 3972ed2076..12da967f2e 100644 --- a/lib/gpu/lal_lj_sdk_long.cu +++ b/lib/gpu/lal_lj_spica_long.cu @@ -1,9 +1,9 @@ // ************************************************************************** -// lj_sdk_long.cu +// lj_spica_long.cu // ------------------- // W. Michael Brown (ORNL) // -// Device code for acceleration of the lj/sdk/coul/long pair style +// Device code for acceleration of the lj/spica/coul/long pair style // // __________________________________________________________________________ // This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) @@ -29,7 +29,7 @@ _texture( q_tex,int2); #define q_tex q_ #endif -__kernel void k_lj_sdk_long(const __global numtyp4 *restrict x_, +__kernel void k_lj_spica_long(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1, const __global numtyp4 *restrict lj3, const int lj_types, @@ -107,6 +107,9 @@ __kernel void k_lj_sdk_long(const __global numtyp4 *restrict x_, } else if (lj3[mtype].x == (numtyp)1) { inv2=r2inv*ucl_rsqrt(rsq); inv1=inv2*inv2; + } else if (lj3[mtype].x == (numtyp)4) { + inv1=r2inv*r2inv*ucl_rsqrt(rsq); + inv2=inv1*r2inv; } else { inv1=r2inv*r2inv*r2inv; inv2=inv1; @@ -157,7 +160,7 @@ __kernel void k_lj_sdk_long(const __global numtyp4 *restrict x_, vflag,ans,engv); } -__kernel void k_lj_sdk_long_fast(const __global numtyp4 *restrict x_, +__kernel void k_lj_spica_long_fast(const __global numtyp4 *restrict x_, const __global numtyp4 *restrict lj1_in, const __global numtyp4 *restrict lj3_in, const __global numtyp *restrict sp_lj_in, @@ -236,6 +239,9 @@ __kernel void k_lj_sdk_long_fast(const __global numtyp4 *restrict x_, } else if (lj3[mtype].x == (numtyp)1) { inv2=r2inv*ucl_rsqrt(rsq); inv1=inv2*inv2; + } else if (lj3[mtype].x == (numtyp)4) { + inv1=r2inv*r2inv*ucl_rsqrt(rsq); + inv2=inv1*r2inv; } else { inv1=r2inv*r2inv*r2inv; inv2=inv1; diff --git a/lib/gpu/lal_lj_sdk_long.h b/lib/gpu/lal_lj_spica_long.h similarity index 96% rename from lib/gpu/lal_lj_sdk_long.h rename to lib/gpu/lal_lj_spica_long.h index 102b007b59..2b598168c1 100644 --- a/lib/gpu/lal_lj_sdk_long.h +++ b/lib/gpu/lal_lj_spica_long.h @@ -1,9 +1,9 @@ /*************************************************************************** - lj_sdk_long.h + lj_spica_long.h ------------------- W. Michael Brown (ORNL) - Class for acceleration of the lj/sdk/coul/long pair style + Class for acceleration of the lj/spica/coul/long pair style __________________________________________________________________________ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) diff --git a/lib/gpu/lal_lj_sdk_long_ext.cpp b/lib/gpu/lal_lj_spica_long_ext.cpp similarity index 90% rename from lib/gpu/lal_lj_sdk_long_ext.cpp rename to lib/gpu/lal_lj_spica_long_ext.cpp index 3170ac8b52..293801391f 100644 --- a/lib/gpu/lal_lj_sdk_long_ext.cpp +++ b/lib/gpu/lal_lj_spica_long_ext.cpp @@ -1,9 +1,9 @@ /*************************************************************************** - lj_sdk_long.h + lj_spica_long.h ------------------- W. Michael Brown (ORNL) - Functions for LAMMPS access to lj/sdk/coul/long acceleration functions + Functions for LAMMPS access to lj/spica/coul/long acceleration functions __________________________________________________________________________ This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) @@ -17,7 +17,7 @@ #include #include -#include "lal_lj_sdk_long.h" +#include "lal_lj_spica_long.h" using namespace std; using namespace LAMMPS_AL; @@ -27,7 +27,7 @@ static CGCMMLong CMMLMF; // --------------------------------------------------------------------------- // Allocate memory on host and device and copy constants to device // --------------------------------------------------------------------------- -int sdkl_gpu_init(const int ntypes, double **cutsq, int **cg_type, +int spical_gpu_init(const int ntypes, double **cutsq, int **cg_type, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **offset, double *special_lj, const int inum, const int nall, const int max_nbors, @@ -44,7 +44,7 @@ int sdkl_gpu_init(const int ntypes, double **cutsq, int **cg_type, int gpu_rank=CMMLMF.device->gpu_rank(); int procs_per_gpu=CMMLMF.device->procs_per_gpu(); - CMMLMF.device->init_message(screen,"lj/sdk/coul/long",first_gpu,last_gpu); + CMMLMF.device->init_message(screen,"lj/spica/coul/long",first_gpu,last_gpu); bool message=false; if (CMMLMF.device->replica_me()==0 && screen) @@ -93,11 +93,11 @@ int sdkl_gpu_init(const int ntypes, double **cutsq, int **cg_type, return init_ok; } -void sdkl_gpu_clear() { +void spical_gpu_clear() { CMMLMF.clear(); } -int** sdkl_gpu_compute_n(const int ago, const int inum_full, +int** spical_gpu_compute_n(const int ago, const int inum_full, const int nall, double **host_x, int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial, tagint **special, const bool eflag, const bool vflag, @@ -111,7 +111,7 @@ int** sdkl_gpu_compute_n(const int ago, const int inum_full, host_q,boxlo,prd); } -void sdkl_gpu_compute(const int ago, const int inum_full, const int nall, +void spical_gpu_compute(const int ago, const int inum_full, const int nall, double **host_x, int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag, const bool vflag, const bool eatom, const bool vatom, int &host_start, @@ -122,7 +122,7 @@ void sdkl_gpu_compute(const int ago, const int inum_full, const int nall, host_q,nlocal,boxlo,prd); } -double sdkl_gpu_bytes() { +double spical_gpu_bytes() { return CMMLMF.host_memory_usage(); } From 763aa632d995fc0e94fdd0a72f1cfa0e95d42b41 Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Fri, 8 Jul 2022 17:36:34 +0900 Subject: [PATCH 16/72] changed 'sdk' to 'spica' --- src/Depend.sh | 4 ++-- src/Makefile | 4 ++-- src/pair.h | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/src/Depend.sh b/src/Depend.sh index 98f3e5de4f..5ac56f60a7 100755 --- a/src/Depend.sh +++ b/src/Depend.sh @@ -106,7 +106,7 @@ if (test $1 = "INTERLAYER") then fi if (test $1 = "KSPACE") then - depend CG-SDK + depend CG-SPICA depend CORESHELL depend DIELECTRIC depend GPU @@ -167,7 +167,7 @@ if (test $1 = "ML-SNAP") then depend ML-IAP fi -if (test $1 = "CG-SDK") then +if (test $1 = "CG-SPICA") then depend GPU depend KOKKOS depend OPENMP diff --git a/src/Makefile b/src/Makefile index 649a1ad002..60f2ab65c3 100644 --- a/src/Makefile +++ b/src/Makefile @@ -57,7 +57,7 @@ PACKAGE = \ bpm \ brownian \ cg-dna \ - cg-sdk \ + cg-spica \ class2 \ colloid \ colvars \ @@ -152,7 +152,7 @@ PACKMOST = \ bpm \ brownian \ cg-dna \ - cg-sdk \ + cg-spica \ class2 \ colloid \ coreshell \ diff --git a/src/pair.h b/src/pair.h index 5bad9e14a3..4b8c6efd88 100644 --- a/src/pair.h +++ b/src/pair.h @@ -19,8 +19,8 @@ namespace LAMMPS_NS { class Pair : protected Pointers { - friend class AngleSDK; - friend class AngleSDKOMP; + friend class AngleSPICA; + friend class AngleSPICAOMP; friend class BondQuartic; friend class BondQuarticOMP; friend class DihedralCharmm; From 311596fb4f3a986c2b5600da640651271b9e32eb Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Fri, 8 Jul 2022 17:55:15 +0900 Subject: [PATCH 17/72] changed CG-SDK to CG-SPICA and added a lj12-5 function type. --- src/CG-SDK/README | 39 ----------- src/{CG-SDK => CG-SPICA}/Install.sh | 18 ++--- src/CG-SPICA/README | 58 ++++++++++++++++ .../angle_spica.cpp} | 53 +++++++++------ .../angle_sdk.h => CG-SPICA/angle_spica.h} | 15 ++-- .../lj_spica_common.h} | 21 +++--- .../pair_lj_spica.cpp} | 62 ++++++++++------- .../pair_lj_spica.h} | 15 ++-- .../pair_lj_spica_coul_long.cpp} | 68 +++++++++++-------- .../pair_lj_spica_coul_long.h} | 15 ++-- .../pair_lj_spica_coul_msm.cpp} | 33 ++++++--- .../pair_lj_spica_coul_msm.h} | 13 ++-- 12 files changed, 244 insertions(+), 166 deletions(-) delete mode 100644 src/CG-SDK/README rename src/{CG-SDK => CG-SPICA}/Install.sh (66%) create mode 100644 src/CG-SPICA/README rename src/{CG-SDK/angle_sdk.cpp => CG-SPICA/angle_spica.cpp} (90%) rename src/{CG-SDK/angle_sdk.h => CG-SPICA/angle_spica.h} (85%) rename src/{CG-SDK/lj_sdk_common.h => CG-SPICA/lj_spica_common.h} (77%) rename src/{CG-SDK/pair_lj_sdk.cpp => CG-SPICA/pair_lj_spica.cpp} (90%) rename src/{CG-SDK/pair_lj_sdk.h => CG-SPICA/pair_lj_spica.h} (88%) rename src/{CG-SDK/pair_lj_sdk_coul_long.cpp => CG-SPICA/pair_lj_spica_coul_long.cpp} (90%) rename src/{CG-SDK/pair_lj_sdk_coul_long.h => CG-SPICA/pair_lj_spica_coul_long.h} (85%) rename src/{CG-SDK/pair_lj_sdk_coul_msm.cpp => CG-SPICA/pair_lj_spica_coul_msm.cpp} (90%) rename src/{CG-SDK/pair_lj_sdk_coul_msm.h => CG-SPICA/pair_lj_spica_coul_msm.h} (80%) diff --git a/src/CG-SDK/README b/src/CG-SDK/README deleted file mode 100644 index c6bd90531e..0000000000 --- a/src/CG-SDK/README +++ /dev/null @@ -1,39 +0,0 @@ -This package implements 4 commands which can be used in a LAMMPS input -script: - -pair_style lj/sdk -pair_style lj/sdk/coul/long -pair_style lj/sdk/coul/msm -angle_style sdk - -These styles allow coarse grained MD simulations with the -parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007) -(SDK), with extensions to simulate ionic liquids, electrolytes, -lipids and charged amino acids. - -See the doc pages for these commands for details. - -There are example scripts for using this package in -examples/PACKAGES/cgsdk - -This is the second generation implementation reducing the the clutter -of the previous version. For many systems with long range -electrostatics, it will be faster to use pair_style hybrid/overlay -with lj/sdk and coul/long instead of the combined lj/sdk/coul/long -style, since the number of charged atom types is usually small. -To exploit this property, the use of the kspace_style pppm/cg is -recommended over regular pppm. - -The person who created this package is Axel Kohlmeyer at Temple U -(akohlmey at gmail.com). Contact him directly if you have questions. - ---------------------------------- - -Thanks for contributions, support and testing goes to - -Wataru Shinoda (Nagoya University) -Russell DeVane (Procter & Gamble) -Michael L. Klein (Temple University, Philadelphia) -Balasubramanian Sundaram (JNCASR, Bangalore) - -version: 1.0 / 2017-04-26 diff --git a/src/CG-SDK/Install.sh b/src/CG-SPICA/Install.sh similarity index 66% rename from src/CG-SDK/Install.sh rename to src/CG-SPICA/Install.sh index 8e2432343d..f8477c6e0c 100755 --- a/src/CG-SDK/Install.sh +++ b/src/CG-SPICA/Install.sh @@ -28,12 +28,12 @@ action () { # list of files with optional dependcies -action angle_sdk.cpp -action angle_sdk.h -action lj_sdk_common.h -action pair_lj_sdk.cpp -action pair_lj_sdk.h -action pair_lj_sdk_coul_long.cpp pppm.cpp -action pair_lj_sdk_coul_long.h pppm.cpp -action pair_lj_sdk_coul_msm.cpp msm.cpp -action pair_lj_sdk_coul_msm.h msm.cpp +action angle_spica.cpp +action angle_spica.h +action lj_spica_common.h +action pair_lj_spica.cpp +action pair_lj_spica.h +action pair_lj_spica_coul_long.cpp pppm.cpp +action pair_lj_spica_coul_long.h pppm.cpp +action pair_lj_spica_coul_msm.cpp msm.cpp +action pair_lj_spica_coul_msm.h msm.cpp diff --git a/src/CG-SPICA/README b/src/CG-SPICA/README new file mode 100644 index 0000000000..621ee18a39 --- /dev/null +++ b/src/CG-SPICA/README @@ -0,0 +1,58 @@ +This package implements 4 commands which can be used in a LAMMPS input +script: + +pair_style lj/spica +pair_style lj/spica/coul/long +pair_style lj/spica/coul/msm +angle_style spica + +These styles allow coarse grained MD simulations with the +parametrization of the SPICA (formerly called SDK) and the pSPICA +force fields, to simulate biological or soft material systems. +For details about the force fields using this implementation, +see the following papers: + SDK - Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007). + SPICA - Seo, Shinoda, J Chem Theory Comput, 15, 762 (2019). + pSPICA - Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782 (2020). +Summary information on these force fields can be found at this web site: +https://www.spica-ff.org + +See the doc pages for these commands for details. + +There are example scripts for using this package in +examples/PACKAGES/cgspica + +This is the third generation implementation (version 2.0) changing style +names and adding a new function type. The following pair and angle styles +are available for backward compatibility: + pair_style lj/sdk + pair_style lj/sdk/coul/long + pair_style lj/sdk/coul/msm + angle_style sdk + +The second generation implementation (version 1.0) is to reduce the clutter +of the previous version. For many systems with long range +electrostatics, it will be faster to use pair_style hybrid/overlay +with lj/spica and coul/long instead of the combined lj/spica/coul/long +style, since the number of charged atom types is usually small. +To exploit this property, the use of the kspace_style pppm/cg is +recommended over regular pppm. + +The person who created this package is Axel Kohlmeyer at Temple U +(akohlmey at gmail.com). Contact him directly if you have questions. + +The person who added a new function type (LJ12_5) to this package is +Yusuke Miyazaki at Okayama U (ymiyazaki93 at gmail.com). Contact him +if you have questions about his code. + +--------------------------------- + +Thanks for contributions, support and testing goes to + +Wataru Shinoda (Okayama University) +Russell DeVane (Procter & Gamble) +Michael L. Klein (Temple University, Philadelphia) +Balasubramanian Sundaram (JNCASR, Bangalore) + +version: 1.0 / 2017-04-26 +version: 2.0 / 2022-07-08 diff --git a/src/CG-SDK/angle_sdk.cpp b/src/CG-SPICA/angle_spica.cpp similarity index 90% rename from src/CG-SDK/angle_sdk.cpp rename to src/CG-SPICA/angle_spica.cpp index 5e649d7846..d25779d60c 100644 --- a/src/CG-SDK/angle_sdk.cpp +++ b/src/CG-SPICA/angle_spica.cpp @@ -16,10 +16,10 @@ Contributing author: Axel Kohlmeyer (Temple U) Variant of the harmonic angle potential for use with the - lj/sdk potential for coarse grained MD simulations. + lj/spica potential for coarse grained MD simulations. ------------------------------------------------------------------------- */ -#include "angle_sdk.h" +#include "angle_spica.h" #include #include "atom.h" @@ -33,21 +33,21 @@ #include "error.h" -#include "lj_sdk_common.h" +#include "lj_spica_common.h" using namespace LAMMPS_NS; using namespace MathConst; -using namespace LJSDKParms; +using namespace LJSPICAParms; #define SMALL 0.001 /* ---------------------------------------------------------------------- */ -AngleSDK::AngleSDK(LAMMPS *lmp) : Angle(lmp) { repflag = 0;} +AngleSPICA::AngleSPICA(LAMMPS *lmp) : Angle(lmp) { repflag = 0;} /* ---------------------------------------------------------------------- */ -AngleSDK::~AngleSDK() +AngleSPICA::~AngleSPICA() { if (allocated) { memory->destroy(setflag); @@ -61,7 +61,7 @@ AngleSDK::~AngleSDK() /* ---------------------------------------------------------------------- */ -void AngleSDK::compute(int eflag, int vflag) +void AngleSPICA::compute(int eflag, int vflag) { int i1,i2,i3,n,type; double delx1,dely1,delz1,delx2,dely2,delz2,delx3,dely3,delz3; @@ -158,6 +158,13 @@ void AngleSDK::compute(int eflag, int vflag) f13 = r6inv*(lj1[type1][type3]*r6inv - lj2[type1][type3]); if (eflag) e13 = r6inv*(lj3[type1][type3]*r6inv - lj4[type1][type3]); + + } else if (ljt == LJ12_5) { + const double r5inv = r2inv*r2inv*sqrt(r2inv); + const double r7inv = r5inv*r2inv; + + f13 = r5inv*(lj1[type1][type3]*r7inv - lj2[type1][type3]); + if (eflag) e13 = r5inv*(lj3[type1][type3]*r7inv - lj4[type1][type3]); } // make sure energy is 0.0 at the cutoff. @@ -217,7 +224,7 @@ void AngleSDK::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ -void AngleSDK::allocate() +void AngleSPICA::allocate() { allocated = 1; int n = atom->nangletypes; @@ -234,7 +241,7 @@ void AngleSDK::allocate() set coeffs for one or more types ------------------------------------------------------------------------- */ -void AngleSDK::coeff(int narg, char **arg) +void AngleSPICA::coeff(int narg, char **arg) { if ((narg < 3) || (narg > 6)) error->all(FLERR,"Incorrect args for angle coefficients"); @@ -278,21 +285,21 @@ void AngleSDK::coeff(int narg, char **arg) error check and initialize all values needed for force computation ------------------------------------------------------------------------- */ -void AngleSDK::init_style() +void AngleSPICA::init_style() { - // make sure we use an SDK pair_style and that we need the 1-3 repulsion + // make sure we use an SPICA pair_style and that we need the 1-3 repulsion repflag = 0; for (int i = 1; i <= atom->nangletypes; i++) if (repscale[i] > 0.0) repflag = 1; - // set up pointers to access SDK LJ parameters for 1-3 interactions + // set up pointers to access SPICA LJ parameters for 1-3 interactions if (repflag) { int itmp; if (force->pair == nullptr) - error->all(FLERR,"Angle style SDK requires use of a compatible with Pair style"); + error->all(FLERR,"Angle style SPICA requires use of a compatible with Pair style"); lj1 = (double **) force->pair->extract("lj1",itmp); lj2 = (double **) force->pair->extract("lj2",itmp); @@ -303,13 +310,13 @@ void AngleSDK::init_style() emin = (double **) force->pair->extract("emin",itmp); if (!lj1 || !lj2 || !lj3 || !lj4 || !lj_type || !rminsq || !emin) - error->all(FLERR,"Angle style SDK is incompatible with Pair style"); + error->all(FLERR,"Angle style SPICA is incompatible with Pair style"); } } /* ---------------------------------------------------------------------- */ -double AngleSDK::equilibrium_angle(int i) +double AngleSPICA::equilibrium_angle(int i) { return theta0[i]; } @@ -318,7 +325,7 @@ double AngleSDK::equilibrium_angle(int i) proc 0 writes out coeffs to restart file ------------------------------------------------------------------------- */ -void AngleSDK::write_restart(FILE *fp) +void AngleSPICA::write_restart(FILE *fp) { fwrite(&k[1],sizeof(double),atom->nangletypes,fp); fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp); @@ -329,7 +336,7 @@ void AngleSDK::write_restart(FILE *fp) proc 0 reads coeffs from restart file, bcasts them ------------------------------------------------------------------------- */ -void AngleSDK::read_restart(FILE *fp) +void AngleSPICA::read_restart(FILE *fp) { allocate(); @@ -349,7 +356,7 @@ void AngleSDK::read_restart(FILE *fp) proc 0 writes to data file ------------------------------------------------------------------------- */ -void AngleSDK::write_data(FILE *fp) +void AngleSPICA::write_data(FILE *fp) { for (int i = 1; i <= atom->nangletypes; i++) fprintf(fp,"%d %g %g\n",i,k[i],theta0[i]/MY_PI*180.0); @@ -357,7 +364,7 @@ void AngleSDK::write_data(FILE *fp) /* ---------------------------------------------------------------------- */ -void AngleSDK::ev_tally13(int i, int j, int nlocal, int newton_bond, +void AngleSPICA::ev_tally13(int i, int j, int nlocal, int newton_bond, double evdwl, double fpair, double delx, double dely, double delz) { @@ -439,7 +446,7 @@ void AngleSDK::ev_tally13(int i, int j, int nlocal, int newton_bond, /* ---------------------------------------------------------------------- */ -double AngleSDK::single(int type, int i1, int i2, int i3) +double AngleSPICA::single(int type, int i1, int i2, int i3) { double **x = atom->x; @@ -493,6 +500,12 @@ double AngleSDK::single(int type, int i1, int i2, int i3) const double r6inv = r2inv*r2inv*r2inv; e13 = r6inv*(lj3[type1][type3]*r6inv - lj4[type1][type3]); + + } else if (ljt == LJ12_5) { + const double r5inv = r2inv*r2inv*sqrt(r2inv); + const double r7inv = r5inv*r2inv; + + e13 = r5inv*(lj3[type1][type3]*r7inv - lj4[type1][type3]); } // make sure energy is 0.0 at the cutoff. diff --git a/src/CG-SDK/angle_sdk.h b/src/CG-SPICA/angle_spica.h similarity index 85% rename from src/CG-SDK/angle_sdk.h rename to src/CG-SPICA/angle_spica.h index 0db35444bf..e270ee5de5 100644 --- a/src/CG-SDK/angle_sdk.h +++ b/src/CG-SPICA/angle_spica.h @@ -13,21 +13,22 @@ #ifdef ANGLE_CLASS // clang-format off -AngleStyle(sdk,AngleSDK); +AngleStyle(spica,AngleSPICA); +AngleStyle(sdk,AngleSPICA); // clang-format on #else -#ifndef LMP_ANGLE_SDK_H -#define LMP_ANGLE_SDK_H +#ifndef LMP_ANGLE_SPICA_H +#define LMP_ANGLE_SPICA_H #include "angle.h" namespace LAMMPS_NS { -class AngleSDK : public Angle { +class AngleSPICA : public Angle { public: - AngleSDK(class LAMMPS *); - ~AngleSDK() override; + AngleSPICA(class LAMMPS *); + ~AngleSPICA() override; void compute(int, int) override; void coeff(int, char **) override; void init_style() override; @@ -42,7 +43,7 @@ class AngleSDK : public Angle { // scaling factor for repulsive 1-3 interaction double *repscale; - // parameters from SDK pair style + // parameters from SPICA pair style int **lj_type; double **lj1, **lj2, **lj3, **lj4; double **rminsq, **emin; diff --git a/src/CG-SDK/lj_sdk_common.h b/src/CG-SPICA/lj_spica_common.h similarity index 77% rename from src/CG-SDK/lj_sdk_common.h rename to src/CG-SPICA/lj_spica_common.h index 1157b89521..656b5dedb6 100644 --- a/src/CG-SDK/lj_sdk_common.h +++ b/src/CG-SPICA/lj_spica_common.h @@ -14,20 +14,21 @@ /* ---------------------------------------------------------------------- Common data for the Shinoda, DeVane, Klein (SDK) coarse grain model Contributing author: Axel Kohlmeyer (Temple U) + Contributing author (added LJ12_5) : Yusuke Miyazaki (Okayama U) ------------------------------------------------------------------------- */ -#ifndef LMP_LJ_SDK_COMMON_H -#define LMP_LJ_SDK_COMMON_H +#ifndef LMP_LJ_SPICA_COMMON_H +#define LMP_LJ_SPICA_COMMON_H #include namespace LAMMPS_NS { -namespace LJSDKParms { +namespace LJSPICAParms { // LJ type flags. list of supported LJ exponent combinations - enum { LJ_NOT_SET = 0, LJ9_6, LJ12_4, LJ12_6, NUM_LJ_TYPES }; + enum { LJ_NOT_SET = 0, LJ9_6, LJ12_4, LJ12_6, LJ12_5, NUM_LJ_TYPES }; -#if defined(LMP_NEED_SDK_FIND_LJ_TYPE) +#if defined(LMP_NEED_SPICA_FIND_LJ_TYPE) static int find_lj_type(const char *label, const char *const *const list) { for (int i = 0; i < NUM_LJ_TYPES; ++i) @@ -38,11 +39,11 @@ namespace LJSDKParms { #endif // clang-format off - static const char *const lj_type_list[] = {"none", "lj9_6", "lj12_4", "lj12_6"}; - static constexpr double lj_prefact[] = {0.0, 6.75, 2.59807621135332, 4.0}; - static constexpr double lj_pow1[] = {0.0, 9.00, 12.0, 12.0}; - static constexpr double lj_pow2[] = {0.0, 6.00, 4.0, 6.0}; + static const char *const lj_type_list[] = {"none", "lj9_6", "lj12_4", "lj12_6", "lj12_5"}; + static constexpr double lj_prefact[] = {0.0, 6.75, 2.59807621135332, 4.0, 3.20377984125109}; + static constexpr double lj_pow1[] = {0.0, 9.00, 12.0, 12.0, 12.0}; + static constexpr double lj_pow2[] = {0.0, 6.00, 4.0, 6.0, 5.0}; // clang-format on -} // namespace LJSDKParms +} // namespace LJSPICAParms } // namespace LAMMPS_NS #endif diff --git a/src/CG-SDK/pair_lj_sdk.cpp b/src/CG-SPICA/pair_lj_spica.cpp similarity index 90% rename from src/CG-SDK/pair_lj_sdk.cpp rename to src/CG-SPICA/pair_lj_spica.cpp index 597c1d59c4..6a14d12146 100644 --- a/src/CG-SDK/pair_lj_sdk.cpp +++ b/src/CG-SPICA/pair_lj_spica.cpp @@ -17,7 +17,7 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include "pair_lj_sdk.h" +#include "pair_lj_spica.h" #include #include @@ -29,15 +29,15 @@ #include "error.h" -#define LMP_NEED_SDK_FIND_LJ_TYPE 1 -#include "lj_sdk_common.h" +#define LMP_NEED_SPICA_FIND_LJ_TYPE 1 +#include "lj_spica_common.h" using namespace LAMMPS_NS; -using namespace LJSDKParms; +using namespace LJSPICAParms; /* ---------------------------------------------------------------------- */ -PairLJSDK::PairLJSDK(LAMMPS *lmp) : Pair(lmp) +PairLJSPICA::PairLJSPICA(LAMMPS *lmp) : Pair(lmp) { respa_enable = 0; single_enable = 1; @@ -46,7 +46,7 @@ PairLJSDK::PairLJSDK(LAMMPS *lmp) : Pair(lmp) /* ---------------------------------------------------------------------- */ -PairLJSDK::~PairLJSDK() +PairLJSPICA::~PairLJSPICA() { if (copymode) return; @@ -73,7 +73,7 @@ PairLJSDK::~PairLJSDK() /* ---------------------------------------------------------------------- */ -void PairLJSDK::compute(int eflag, int vflag) +void PairLJSPICA::compute(int eflag, int vflag) { ev_init(eflag,vflag); @@ -96,7 +96,7 @@ void PairLJSDK::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ template -void PairLJSDK::eval() +void PairLJSPICA::eval() { int i,j,ii,jj,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; @@ -170,6 +170,16 @@ void PairLJSDK::eval() if (EFLAG) evdwl = r6inv*(lj3[itype][jtype]*r6inv - lj4[itype][jtype]) - offset[itype][jtype]; + + } else if (ljt == LJ12_5) { + const double r5inv = r2inv*r2inv*sqrt(r2inv); + const double r7inv = r5inv*r2inv; + forcelj = r5inv*(lj1[itype][jtype]*r7inv + - lj2[itype][jtype]); + if (EFLAG) + evdwl = r5inv*(lj3[itype][jtype]*r7inv + - lj4[itype][jtype]) - offset[itype][jtype]; + } else continue; fpair = factor_lj*forcelj*r2inv; @@ -198,7 +208,7 @@ void PairLJSDK::eval() allocate all arrays ------------------------------------------------------------------------- */ -void PairLJSDK::allocate() +void PairLJSPICA::allocate() { allocated = 1; int n = atom->ntypes; @@ -233,7 +243,7 @@ void PairLJSDK::allocate() global settings ------------------------------------------------------------------------- */ -void PairLJSDK::settings(int narg, char **arg) +void PairLJSPICA::settings(int narg, char **arg) { if (narg != 1) error->all(FLERR,"Illegal pair_style command"); @@ -253,7 +263,7 @@ void PairLJSDK::settings(int narg, char **arg) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void PairLJSDK::coeff(int narg, char **arg) +void PairLJSPICA::coeff(int narg, char **arg) { if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients"); if (!allocated) allocate(); @@ -291,10 +301,10 @@ void PairLJSDK::coeff(int narg, char **arg) init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairLJSDK::init_one(int i, int j) +double PairLJSPICA::init_one(int i, int j) { if (setflag[i][j] == 0) - error->all(FLERR,"No mixing support for lj/sdk. " + error->all(FLERR,"No mixing support for lj/spica. " "Coefficients for all pairs need to be set explicitly."); const int ljt = lj_type[i][j]; @@ -321,7 +331,7 @@ double PairLJSDK::init_one(int i, int j) offset[j][i] = offset[i][j]; lj_type[j][i] = lj_type[i][j]; - // compute derived parameters for SDK angle potential + // compute derived parameters for SPICA angle potential const double eps = epsilon[i][j]; const double sig = sigma[i][j]; @@ -338,7 +348,7 @@ double PairLJSDK::init_one(int i, int j) // count total # of atoms of type I and J via Allreduce if (tail_flag) - error->all(FLERR,"Tail flag not supported by lj/sdk pair style"); + error->all(FLERR,"Tail flag not supported by lj/spica pair style"); return cut[i][j]; } @@ -347,7 +357,7 @@ double PairLJSDK::init_one(int i, int j) proc 0 writes to restart file ------------------------------------------------------------------------- */ -void PairLJSDK::write_restart(FILE *fp) +void PairLJSPICA::write_restart(FILE *fp) { write_restart_settings(fp); @@ -368,7 +378,7 @@ void PairLJSDK::write_restart(FILE *fp) proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ -void PairLJSDK::read_restart(FILE *fp) +void PairLJSPICA::read_restart(FILE *fp) { read_restart_settings(fp); allocate(); @@ -398,7 +408,7 @@ void PairLJSDK::read_restart(FILE *fp) proc 0 writes to restart file ------------------------------------------------------------------------- */ -void PairLJSDK::write_restart_settings(FILE *fp) +void PairLJSPICA::write_restart_settings(FILE *fp) { fwrite(&cut_global,sizeof(double),1,fp); fwrite(&offset_flag,sizeof(int),1,fp); @@ -410,7 +420,7 @@ void PairLJSDK::write_restart_settings(FILE *fp) proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ -void PairLJSDK::read_restart_settings(FILE *fp) +void PairLJSPICA::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { @@ -426,12 +436,12 @@ void PairLJSDK::read_restart_settings(FILE *fp) } /* ---------------------------------------------------------------------- - lj/sdk does not support per atom type output with mixing + lj/spica does not support per atom type output with mixing ------------------------------------------------------------------------- */ -void PairLJSDK::write_data(FILE *) +void PairLJSPICA::write_data(FILE *) { - error->one(FLERR, "Pair style lj/sdk requires using " + error->one(FLERR, "Pair style lj/spica requires using " "write_data with the 'pair ij' option"); } @@ -439,7 +449,7 @@ void PairLJSDK::write_data(FILE *) proc 0 writes all pairs to data file ------------------------------------------------------------------------- */ -void PairLJSDK::write_data_all(FILE *fp) +void PairLJSPICA::write_data_all(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) for (int j = i; j <= atom->ntypes; j++) @@ -449,7 +459,7 @@ void PairLJSDK::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJSDK::single(int, int, int itype, int jtype, double rsq, +double PairLJSPICA::single(int, int, int itype, int jtype, double rsq, double, double factor_lj, double &fforce) { @@ -475,7 +485,7 @@ double PairLJSDK::single(int, int, int itype, int jtype, double rsq, /* ---------------------------------------------------------------------- */ -void *PairLJSDK::extract(const char *str, int &dim) +void *PairLJSPICA::extract(const char *str, int &dim) { dim = 2; if (strcmp(str,"epsilon") == 0) return (void *) epsilon; @@ -492,7 +502,7 @@ void *PairLJSDK::extract(const char *str, int &dim) /* ---------------------------------------------------------------------- */ -double PairLJSDK::memory_usage() +double PairLJSPICA::memory_usage() { double bytes = Pair::memory_usage(); int n = atom->ntypes; diff --git a/src/CG-SDK/pair_lj_sdk.h b/src/CG-SPICA/pair_lj_spica.h similarity index 88% rename from src/CG-SDK/pair_lj_sdk.h rename to src/CG-SPICA/pair_lj_spica.h index 28cef78d44..6c016ccd7c 100644 --- a/src/CG-SDK/pair_lj_sdk.h +++ b/src/CG-SPICA/pair_lj_spica.h @@ -17,21 +17,22 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(lj/sdk,PairLJSDK); +PairStyle(lj/spica,PairLJSPICA); +PairStyle(lj/sdk,PairLJSPICA); // clang-format on #else -#ifndef LMP_PAIR_LJ_SDK_H -#define LMP_PAIR_LJ_SDK_H +#ifndef LMP_PAIR_LJ_SPICA_H +#define LMP_PAIR_LJ_SPICA_H #include "pair.h" namespace LAMMPS_NS { -class PairLJSDK : public Pair { +class PairLJSPICA : public Pair { public: - PairLJSDK(LAMMPS *); - ~PairLJSDK() override; + PairLJSPICA(LAMMPS *); + ~PairLJSPICA() override; void compute(int, int) override; void settings(int, char **) override; void coeff(int, char **) override; @@ -54,7 +55,7 @@ class PairLJSDK : public Pair { double **lj1, **lj2, **lj3, **lj4, **offset; // cutoff and offset for minimum of LJ potential - // to be used in SDK angle potential, which + // to be used in SPICA angle potential, which // uses only the repulsive part of the potential double **rminsq, **emin; diff --git a/src/CG-SDK/pair_lj_sdk_coul_long.cpp b/src/CG-SPICA/pair_lj_spica_coul_long.cpp similarity index 90% rename from src/CG-SDK/pair_lj_sdk_coul_long.cpp rename to src/CG-SPICA/pair_lj_spica_coul_long.cpp index e1d79789b8..416561c3a1 100644 --- a/src/CG-SDK/pair_lj_sdk_coul_long.cpp +++ b/src/CG-SPICA/pair_lj_spica_coul_long.cpp @@ -16,7 +16,7 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include "pair_lj_sdk_coul_long.h" +#include "pair_lj_spica_coul_long.h" #include "atom.h" #include "comm.h" @@ -30,11 +30,11 @@ #include #include -#define LMP_NEED_SDK_FIND_LJ_TYPE 1 -#include "lj_sdk_common.h" +#define LMP_NEED_SPICA_FIND_LJ_TYPE 1 +#include "lj_spica_common.h" using namespace LAMMPS_NS; -using namespace LJSDKParms; +using namespace LJSPICAParms; #define EWALD_F 1.12837917 #define EWALD_P 0.3275911 @@ -46,7 +46,7 @@ using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ -PairLJSDKCoulLong::PairLJSDKCoulLong(LAMMPS *lmp) : Pair(lmp) +PairLJSPICACoulLong::PairLJSPICACoulLong(LAMMPS *lmp) : Pair(lmp) { ewaldflag = pppmflag = 1; respa_enable = 0; @@ -56,7 +56,7 @@ PairLJSDKCoulLong::PairLJSDKCoulLong(LAMMPS *lmp) : Pair(lmp) /* ---------------------------------------------------------------------- */ -PairLJSDKCoulLong::~PairLJSDKCoulLong() +PairLJSPICACoulLong::~PairLJSPICACoulLong() { if (allocated) { memory->destroy(setflag); @@ -83,7 +83,7 @@ PairLJSDKCoulLong::~PairLJSDKCoulLong() /* ---------------------------------------------------------------------- */ -void PairLJSDKCoulLong::compute(int eflag, int vflag) +void PairLJSPICACoulLong::compute(int eflag, int vflag) { ev_init(eflag, vflag); @@ -111,7 +111,7 @@ void PairLJSDKCoulLong::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ -template void PairLJSDKCoulLong::eval() +template void PairLJSPICACoulLong::eval() { int i, ii, j, jj, jtype, itable; double qtmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul, fpair; @@ -223,6 +223,14 @@ template void PairLJSDKCoulLong::eval() if (EFLAG) evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype]; + + } else if (ljt == LJ12_5) { + const double r5inv = r2inv * r2inv * sqrt(r2inv); + const double r7inv = r5inv * r2inv; + forcelj = r5inv * (lj1[itype][jtype] * r7inv - lj2[itype][jtype]); + if (EFLAG) + evdwl = + r5inv * (lj3[itype][jtype] * r7inv - lj4[itype][jtype]) - offset[itype][jtype]; } forcelj *= factor_lj; if (EFLAG) evdwl *= factor_lj; @@ -252,7 +260,7 @@ template void PairLJSDKCoulLong::eval() allocate all arrays ------------------------------------------------------------------------- */ -void PairLJSDKCoulLong::allocate() +void PairLJSPICACoulLong::allocate() { allocated = 1; int np1 = atom->ntypes + 1; @@ -288,7 +296,7 @@ void PairLJSDKCoulLong::allocate() global settings ------------------------------------------------------------------------- */ -void PairLJSDKCoulLong::settings(int narg, char **arg) +void PairLJSPICACoulLong::settings(int narg, char **arg) { if (narg < 1 || narg > 2) error->all(FLERR, "Illegal pair_style command"); @@ -312,7 +320,7 @@ void PairLJSDKCoulLong::settings(int narg, char **arg) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void PairLJSDKCoulLong::coeff(int narg, char **arg) +void PairLJSPICACoulLong::coeff(int narg, char **arg) { if (narg < 5 || narg > 6) error->all(FLERR, "Incorrect args for pair coefficients"); if (!allocated) allocate(); @@ -349,7 +357,7 @@ void PairLJSDKCoulLong::coeff(int narg, char **arg) init specific to this pair style ------------------------------------------------------------------------- */ -void PairLJSDKCoulLong::init_style() +void PairLJSPICACoulLong::init_style() { if (!atom->q_flag) error->all(FLERR, "Pair style lj/cut/coul/long requires atom attribute q"); @@ -371,11 +379,11 @@ void PairLJSDKCoulLong::init_style() init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairLJSDKCoulLong::init_one(int i, int j) +double PairLJSPICACoulLong::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR, - "No mixing support for lj/sdk/coul/long. " + "No mixing support for lj/spica/coul/long. " "Coefficients for all pairs need to be set explicitly."); const int ljt = lj_type[i][j]; @@ -406,7 +414,7 @@ double PairLJSDKCoulLong::init_one(int i, int j) offset[j][i] = offset[i][j]; lj_type[j][i] = lj_type[i][j]; - // compute LJ derived parameters for SDK angle potential (LJ only!) + // compute LJ derived parameters for SPICA angle potential (LJ only!) const double eps = epsilon[i][j]; const double sig = sigma[i][j]; @@ -422,7 +430,7 @@ double PairLJSDKCoulLong::init_one(int i, int j) // compute I,J contribution to long-range tail correction // count total # of atoms of type I and J via Allreduce - if (tail_flag) error->all(FLERR, "Tail flag not supported by lj/sdk/coul/long pair style"); + if (tail_flag) error->all(FLERR, "Tail flag not supported by lj/spica/coul/long pair style"); return cut; } @@ -431,7 +439,7 @@ double PairLJSDKCoulLong::init_one(int i, int j) proc 0 writes to restart file ------------------------------------------------------------------------- */ -void PairLJSDKCoulLong::write_restart(FILE *fp) +void PairLJSPICACoulLong::write_restart(FILE *fp) { write_restart_settings(fp); @@ -452,7 +460,7 @@ void PairLJSDKCoulLong::write_restart(FILE *fp) proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ -void PairLJSDKCoulLong::read_restart(FILE *fp) +void PairLJSPICACoulLong::read_restart(FILE *fp) { read_restart_settings(fp); allocate(); @@ -482,7 +490,7 @@ void PairLJSDKCoulLong::read_restart(FILE *fp) proc 0 writes to restart file ------------------------------------------------------------------------- */ -void PairLJSDKCoulLong::write_restart_settings(FILE *fp) +void PairLJSPICACoulLong::write_restart_settings(FILE *fp) { fwrite(&cut_lj_global, sizeof(double), 1, fp); fwrite(&cut_coul, sizeof(double), 1, fp); @@ -497,7 +505,7 @@ void PairLJSDKCoulLong::write_restart_settings(FILE *fp) proc 0 reads from restart file, bcasts ------------------------------------------------------------------------- */ -void PairLJSDKCoulLong::read_restart_settings(FILE *fp) +void PairLJSPICACoulLong::read_restart_settings(FILE *fp) { if (comm->me == 0) { utils::sfread(FLERR, &cut_lj_global, sizeof(double), 1, fp, nullptr, error); @@ -518,13 +526,13 @@ void PairLJSDKCoulLong::read_restart_settings(FILE *fp) } /* ---------------------------------------------------------------------- - lj/sdk does not support per atom type output with mixing + lj/spica does not support per atom type output with mixing ------------------------------------------------------------------------- */ -void PairLJSDKCoulLong::write_data(FILE *) +void PairLJSPICACoulLong::write_data(FILE *) { error->one(FLERR, - "Pair style lj/sdk/coul/* requires using " + "Pair style lj/spica/coul/* requires using " "write_data with the 'pair ij' option"); } @@ -532,7 +540,7 @@ void PairLJSDKCoulLong::write_data(FILE *) proc 0 writes all pairs to data file ------------------------------------------------------------------------- */ -void PairLJSDKCoulLong::write_data_all(FILE *fp) +void PairLJSPICACoulLong::write_data_all(FILE *fp) { for (int i = 1; i <= atom->ntypes; i++) for (int j = i; j <= atom->ntypes; j++) @@ -542,7 +550,7 @@ void PairLJSDKCoulLong::write_data_all(FILE *fp) /* ---------------------------------------------------------------------- */ -double PairLJSDKCoulLong::single(int i, int j, int itype, int jtype, double rsq, double factor_coul, +double PairLJSPICACoulLong::single(int i, int j, int itype, int jtype, double rsq, double factor_coul, double factor_lj, double &fforce) { double r2inv, r, grij, expm2, t, erfc, prefactor; @@ -605,6 +613,12 @@ double PairLJSDKCoulLong::single(int i, int j, int itype, int jtype, double rsq, const double r6inv = r2inv * r2inv * r2inv; forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]); philj = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype]; + + } else if (ljt == LJ12_5) { + const double r5inv = r2inv * r2inv * sqrt(r2inv); + const double r7inv = r5inv * r2inv; + forcelj = r5inv * (lj1[itype][jtype] * r7inv - lj2[itype][jtype]); + philj = r5inv * (lj3[itype][jtype] * r7inv - lj4[itype][jtype]) - offset[itype][jtype]; } forcelj *= factor_lj; philj *= factor_lj; @@ -617,7 +631,7 @@ double PairLJSDKCoulLong::single(int i, int j, int itype, int jtype, double rsq, /* ---------------------------------------------------------------------- */ -void *PairLJSDKCoulLong::extract(const char *str, int &dim) +void *PairLJSPICACoulLong::extract(const char *str, int &dim) { dim = 2; if (strcmp(str, "epsilon") == 0) return (void *) epsilon; @@ -637,7 +651,7 @@ void *PairLJSDKCoulLong::extract(const char *str, int &dim) /* ---------------------------------------------------------------------- */ -double PairLJSDKCoulLong::memory_usage() +double PairLJSPICACoulLong::memory_usage() { double bytes = Pair::memory_usage(); int n = atom->ntypes; diff --git a/src/CG-SDK/pair_lj_sdk_coul_long.h b/src/CG-SPICA/pair_lj_spica_coul_long.h similarity index 85% rename from src/CG-SDK/pair_lj_sdk_coul_long.h rename to src/CG-SPICA/pair_lj_spica_coul_long.h index 6a81a921b5..dce60e5e77 100644 --- a/src/CG-SDK/pair_lj_sdk_coul_long.h +++ b/src/CG-SPICA/pair_lj_spica_coul_long.h @@ -17,21 +17,22 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(lj/sdk/coul/long,PairLJSDKCoulLong); +PairStyle(lj/spica/coul/long,PairLJSPICACoulLong); +PairStyle(lj/sdk/coul/long,PairLJSPICACoulLong); // clang-format on #else -#ifndef LMP_PAIR_LJ_SDK_COUL_LONG_H -#define LMP_PAIR_LJ_SDK_COUL_LONG_H +#ifndef LMP_PAIR_LJ_SPICA_COUL_LONG_H +#define LMP_PAIR_LJ_SPICA_COUL_LONG_H #include "pair.h" namespace LAMMPS_NS { -class PairLJSDKCoulLong : public Pair { +class PairLJSPICACoulLong : public Pair { public: - PairLJSDKCoulLong(class LAMMPS *); - ~PairLJSDKCoulLong() override; + PairLJSPICACoulLong(class LAMMPS *); + ~PairLJSPICACoulLong() override; void compute(int, int) override; void settings(int, char **) override; void coeff(int, char **) override; @@ -55,7 +56,7 @@ class PairLJSDKCoulLong : public Pair { int **lj_type; // cutoff and offset for minimum of LJ potential - // to be used in SDK angle potential, which + // to be used in SPICA angle potential, which // uses only the repulsive part of the potential double **rminsq, **emin; diff --git a/src/CG-SDK/pair_lj_sdk_coul_msm.cpp b/src/CG-SPICA/pair_lj_spica_coul_msm.cpp similarity index 90% rename from src/CG-SDK/pair_lj_sdk_coul_msm.cpp rename to src/CG-SPICA/pair_lj_spica_coul_msm.cpp index fb7a1fdddc..536c01595c 100644 --- a/src/CG-SDK/pair_lj_sdk_coul_msm.cpp +++ b/src/CG-SPICA/pair_lj_spica_coul_msm.cpp @@ -17,7 +17,7 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include "pair_lj_sdk_coul_msm.h" +#include "pair_lj_spica_coul_msm.h" #include "atom.h" #include "error.h" @@ -28,14 +28,14 @@ #include #include -#include "lj_sdk_common.h" +#include "lj_spica_common.h" using namespace LAMMPS_NS; -using namespace LJSDKParms; +using namespace LJSPICAParms; /* ---------------------------------------------------------------------- */ -PairLJSDKCoulMSM::PairLJSDKCoulMSM(LAMMPS *lmp) : PairLJSDKCoulLong(lmp) +PairLJSPICACoulMSM::PairLJSPICACoulMSM(LAMMPS *lmp) : PairLJSPICACoulLong(lmp) { ewaldflag = pppmflag = 0; msmflag = 1; @@ -45,7 +45,7 @@ PairLJSDKCoulMSM::PairLJSDKCoulMSM(LAMMPS *lmp) : PairLJSDKCoulLong(lmp) /* ---------------------------------------------------------------------- */ -void PairLJSDKCoulMSM::compute(int eflag, int vflag) +void PairLJSPICACoulMSM::compute(int eflag, int vflag) { if (force->kspace->scalar_pressure_flag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' with Pair style"); @@ -71,7 +71,7 @@ void PairLJSDKCoulMSM::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ template -void PairLJSDKCoulMSM::eval_msm() +void PairLJSPICACoulMSM::eval_msm() { int i,ii,j,jj,jtype,itable; double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair; @@ -187,6 +187,15 @@ void PairLJSDKCoulMSM::eval_msm() if (EFLAG) evdwl = r6inv*(lj3[itype][jtype]*r6inv - lj4[itype][jtype]) - offset[itype][jtype]; + + } else if (ljt == LJ12_5) { + const double r5inv = r2inv*r2inv*sqrt(r2inv); + const double r7inv = r5inv*r2inv; + forcelj = r5inv*(lj1[itype][jtype]*r7inv + - lj2[itype][jtype]); + if (EFLAG) + evdwl = r5inv*(lj3[itype][jtype]*r7inv + - lj4[itype][jtype]) - offset[itype][jtype]; } forcelj *= factor_lj; if (EFLAG) evdwl *= factor_lj; @@ -215,7 +224,7 @@ void PairLJSDKCoulMSM::eval_msm() /* ---------------------------------------------------------------------- */ -double PairLJSDKCoulMSM::single(int i, int j, int itype, int jtype, +double PairLJSPICACoulMSM::single(int i, int j, int itype, int jtype, double rsq, double factor_coul, double factor_lj, double &fforce) @@ -283,6 +292,14 @@ double PairLJSDKCoulMSM::single(int i, int j, int itype, int jtype, - lj2[itype][jtype]); philj = r6inv*(lj3[itype][jtype]*r6inv - lj4[itype][jtype]) - offset[itype][jtype]; + + } else if (ljt == LJ12_5) { + const double r5inv = r2inv*r2inv*sqrt(r2inv); + const double r7inv = r5inv*r2inv; + forcelj = r5inv*(lj1[itype][jtype]*r7inv + - lj2[itype][jtype]); + philj = r5inv*(lj3[itype][jtype]*r7inv + - lj4[itype][jtype]) - offset[itype][jtype]; } forcelj *= factor_lj; philj *= factor_lj; @@ -295,7 +312,7 @@ double PairLJSDKCoulMSM::single(int i, int j, int itype, int jtype, /* ---------------------------------------------------------------------- */ -void *PairLJSDKCoulMSM::extract(const char *str, int &dim) +void *PairLJSPICACoulMSM::extract(const char *str, int &dim) { dim = 2; if (strcmp(str,"epsilon") == 0) return (void *) epsilon; diff --git a/src/CG-SDK/pair_lj_sdk_coul_msm.h b/src/CG-SPICA/pair_lj_spica_coul_msm.h similarity index 80% rename from src/CG-SDK/pair_lj_sdk_coul_msm.h rename to src/CG-SPICA/pair_lj_spica_coul_msm.h index 1b43f39ec9..be43b5ba52 100644 --- a/src/CG-SDK/pair_lj_sdk_coul_msm.h +++ b/src/CG-SPICA/pair_lj_spica_coul_msm.h @@ -17,20 +17,21 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(lj/sdk/coul/msm,PairLJSDKCoulMSM); +PairStyle(lj/spica/coul/msm,PairLJSPICACoulMSM); +PairStyle(lj/sdk/coul/msm,PairLJSPICACoulMSM); // clang-format on #else -#ifndef LMP_PAIR_LJ_SDK_COUL_MSM_H -#define LMP_PAIR_LJ_SDK_COUL_MSM_H +#ifndef LMP_PAIR_LJ_SPICA_COUL_MSM_H +#define LMP_PAIR_LJ_SPICA_COUL_MSM_H -#include "pair_lj_sdk_coul_long.h" +#include "pair_lj_spica_coul_long.h" namespace LAMMPS_NS { -class PairLJSDKCoulMSM : public PairLJSDKCoulLong { +class PairLJSPICACoulMSM : public PairLJSPICACoulLong { public: - PairLJSDKCoulMSM(class LAMMPS *); + PairLJSPICACoulMSM(class LAMMPS *); void compute(int, int) override; double single(int, int, int, int, double, double, double, double &) override; void *extract(const char *, int &) override; From 116098022f331fca72bccec50f7a0123a7dd3e46 Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Fri, 8 Jul 2022 18:04:04 +0900 Subject: [PATCH 18/72] changed file names and added a lj12-5 function type in GPU pkg. --- src/GPU/Install.sh | 8 +-- ...pu.cpp => pair_lj_spica_coul_long_gpu.cpp} | 50 +++++++++++-------- ...ng_gpu.h => pair_lj_spica_coul_long_gpu.h} | 15 +++--- ...r_lj_sdk_gpu.cpp => pair_lj_spica_gpu.cpp} | 45 ++++++++++------- ...{pair_lj_sdk_gpu.h => pair_lj_spica_gpu.h} | 15 +++--- 5 files changed, 75 insertions(+), 58 deletions(-) rename src/GPU/{pair_lj_sdk_coul_long_gpu.cpp => pair_lj_spica_coul_long_gpu.cpp} (86%) rename src/GPU/{pair_lj_sdk_coul_long_gpu.h => pair_lj_spica_coul_long_gpu.h} (73%) rename src/GPU/{pair_lj_sdk_gpu.cpp => pair_lj_spica_gpu.cpp} (83%) rename src/GPU/{pair_lj_sdk_gpu.h => pair_lj_spica_gpu.h} (79%) diff --git a/src/GPU/Install.sh b/src/GPU/Install.sh index f13e87d317..1768ec024f 100755 --- a/src/GPU/Install.sh +++ b/src/GPU/Install.sh @@ -121,10 +121,10 @@ action pair_lj_expand_coul_long_gpu.cpp pair_lj_expand_coul_long.cpp action pair_lj_expand_coul_long_gpu.h pair_lj_expand_coul_long.cpp action pair_lj_gromacs_gpu.cpp pair_lj_gromacs.cpp action pair_lj_gromacs_gpu.h pair_lj_gromacs.h -action pair_lj_sdk_coul_long_gpu.cpp pair_lj_sdk_coul_long.cpp -action pair_lj_sdk_coul_long_gpu.h pair_lj_sdk_coul_long.cpp -action pair_lj_sdk_gpu.cpp pair_lj_sdk.cpp -action pair_lj_sdk_gpu.h pair_lj_sdk.cpp +action pair_lj_spica_coul_long_gpu.cpp pair_lj_spica_coul_long.cpp +action pair_lj_spica_coul_long_gpu.h pair_lj_spica_coul_long.cpp +action pair_lj_spica_gpu.cpp pair_lj_spica.cpp +action pair_lj_spica_gpu.h pair_lj_spica.cpp action pair_mie_cut_gpu.cpp pair_mie_cut.cpp action pair_mie_cut_gpu.h pair_mie_cut.h action pair_morse_gpu.cpp diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_spica_coul_long_gpu.cpp similarity index 86% rename from src/GPU/pair_lj_sdk_coul_long_gpu.cpp rename to src/GPU/pair_lj_spica_coul_long_gpu.cpp index 8638f3d21d..9c72fe5ed3 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp +++ b/src/GPU/pair_lj_spica_coul_long_gpu.cpp @@ -15,7 +15,7 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include "pair_lj_sdk_coul_long_gpu.h" +#include "pair_lj_spica_coul_long_gpu.h" #include "atom.h" #include "domain.h" @@ -41,34 +41,34 @@ using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition -int sdkl_gpu_init(const int ntypes, double **cutsq, int **lj_type, double **host_lj1, +int spical_gpu_init(const int ntypes, double **cutsq, int **lj_type, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **offset, double *special_lj, const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen, double **host_cut_ljsq, double host_cut_coulsq, double *host_special_coul, const double qqrd2e, const double g_ewald); -void sdkl_gpu_clear(); -int **sdkl_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x, +void spical_gpu_clear(); +int **spical_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x, int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial, tagint **special, const bool eflag, const bool vflag, const bool eatom, const bool vatom, int &host_start, int **ilist, int **jnum, const double cpu_time, bool &success, double *host_q, double *boxlo, double *prd); -void sdkl_gpu_compute(const int ago, const int inum, const int nall, double **host_x, +void spical_gpu_compute(const int ago, const int inum, const int nall, double **host_x, int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag, const bool vflag, const bool eatom, const bool vatom, int &host_start, const double cpu_time, bool &success, double *host_q, const int nlocal, double *boxlo, double *prd); -double sdkl_gpu_bytes(); +double spical_gpu_bytes(); -#include "lj_sdk_common.h" +#include "lj_spica_common.h" -using namespace LJSDKParms; +using namespace LJSPICAParms; /* ---------------------------------------------------------------------- */ -PairLJSDKCoulLongGPU::PairLJSDKCoulLongGPU(LAMMPS *lmp) : - PairLJSDKCoulLong(lmp), gpu_mode(GPU_FORCE) +PairLJSPICACoulLongGPU::PairLJSPICACoulLongGPU(LAMMPS *lmp) : + PairLJSPICACoulLong(lmp), gpu_mode(GPU_FORCE) { respa_enable = 0; reinitflag = 0; @@ -81,14 +81,14 @@ PairLJSDKCoulLongGPU::PairLJSDKCoulLongGPU(LAMMPS *lmp) : free all arrays ------------------------------------------------------------------------- */ -PairLJSDKCoulLongGPU::~PairLJSDKCoulLongGPU() +PairLJSPICACoulLongGPU::~PairLJSPICACoulLongGPU() { - sdkl_gpu_clear(); + spical_gpu_clear(); } /* ---------------------------------------------------------------------- */ -void PairLJSDKCoulLongGPU::compute(int eflag, int vflag) +void PairLJSPICACoulLongGPU::compute(int eflag, int vflag) { ev_init(eflag, vflag); @@ -110,7 +110,7 @@ void PairLJSDKCoulLongGPU::compute(int eflag, int vflag) domain->bbox(domain->sublo_lamda, domain->subhi_lamda, sublo, subhi); } inum = atom->nlocal; - firstneigh = sdkl_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, + firstneigh = spical_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, atom->nspecial, atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh, cpu_time, success, atom->q, domain->boxlo, domain->prd); @@ -119,7 +119,7 @@ void PairLJSDKCoulLongGPU::compute(int eflag, int vflag) ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; - sdkl_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh, + spical_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh, eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success, atom->q, atom->nlocal, domain->boxlo, domain->prd); } @@ -142,9 +142,9 @@ void PairLJSDKCoulLongGPU::compute(int eflag, int vflag) init specific to this pair style ------------------------------------------------------------------------- */ -void PairLJSDKCoulLongGPU::init_style() +void PairLJSPICACoulLongGPU::init_style() { - if (!atom->q_flag) error->all(FLERR, "Pair style lj/sdk/coul/long/gpu requires atom attribute q"); + if (!atom->q_flag) error->all(FLERR, "Pair style lj/spica/coul/long/gpu requires atom attribute q"); // Repeat cutsq calculation because done after call to init_style double maxcut = -1.0; @@ -177,7 +177,7 @@ void PairLJSDKCoulLongGPU::init_style() if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial; int mnf = 5e-2 * neighbor->oneatom; int success = - sdkl_gpu_init(atom->ntypes + 1, cutsq, lj_type, lj1, lj2, lj3, lj4, offset, force->special_lj, + spical_gpu_init(atom->ntypes + 1, cutsq, lj_type, lj1, lj2, lj3, lj4, offset, force->special_lj, atom->nlocal, atom->nlocal + atom->nghost, mnf, maxspecial, cell_size, gpu_mode, screen, cut_ljsq, cut_coulsq, force->special_coul, force->qqrd2e, g_ewald); GPU_EXTRA::check_flag(success, error, world); @@ -187,15 +187,15 @@ void PairLJSDKCoulLongGPU::init_style() /* ---------------------------------------------------------------------- */ -double PairLJSDKCoulLongGPU::memory_usage() +double PairLJSPICACoulLongGPU::memory_usage() { double bytes = Pair::memory_usage(); - return bytes + sdkl_gpu_bytes(); + return bytes + spical_gpu_bytes(); } /* ---------------------------------------------------------------------- */ template -void PairLJSDKCoulLongGPU::cpu_compute(int start, int inum, int *ilist, int *numneigh, +void PairLJSPICACoulLongGPU::cpu_compute(int start, int inum, int *ilist, int *numneigh, int **firstneigh) { int i, j, ii, jj; @@ -307,6 +307,14 @@ void PairLJSDKCoulLongGPU::cpu_compute(int start, int inum, int *ilist, int *num if (EFLAG) evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype]; + + } else if (ljt == LJ12_5) { + const double r5inv = r2inv * r2inv * sqrt(r2inv); + const double r7inv = r5inv * r2inv; + forcelj = r5inv * (lj1[itype][jtype] * r7inv - lj2[itype][jtype]); + if (EFLAG) + evdwl = + r5inv * (lj3[itype][jtype] * r7inv - lj4[itype][jtype]) - offset[itype][jtype]; } if (EFLAG) evdwl *= factor_lj; diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.h b/src/GPU/pair_lj_spica_coul_long_gpu.h similarity index 73% rename from src/GPU/pair_lj_sdk_coul_long_gpu.h rename to src/GPU/pair_lj_spica_coul_long_gpu.h index 02cac49d0b..3fd267fe5a 100644 --- a/src/GPU/pair_lj_sdk_coul_long_gpu.h +++ b/src/GPU/pair_lj_spica_coul_long_gpu.h @@ -13,21 +13,22 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(lj/sdk/coul/long/gpu,PairLJSDKCoulLongGPU); +PairStyle(lj/spica/coul/long/gpu,PairLJSPICACoulLongGPU); +PairStyle(lj/sdk/coul/long/gpu,PairLJSPICACoulLongGPU); // clang-format on #else -#ifndef LMP_PAIR_LJ_SDK_COUL_LONG_GPU_H -#define LMP_PAIR_LJ_SDK_COUL_LONG_GPU_H +#ifndef LMP_PAIR_LJ_SPICA_COUL_LONG_GPU_H +#define LMP_PAIR_LJ_SPICA_COUL_LONG_GPU_H -#include "pair_lj_sdk_coul_long.h" +#include "pair_lj_spica_coul_long.h" namespace LAMMPS_NS { -class PairLJSDKCoulLongGPU : public PairLJSDKCoulLong { +class PairLJSPICACoulLongGPU : public PairLJSPICACoulLong { public: - PairLJSDKCoulLongGPU(LAMMPS *lmp); - ~PairLJSDKCoulLongGPU() override; + PairLJSPICACoulLongGPU(LAMMPS *lmp); + ~PairLJSPICACoulLongGPU() override; template void cpu_compute(int, int, int *, int *, int **); void compute(int, int) override; void init_style() override; diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_spica_gpu.cpp similarity index 83% rename from src/GPU/pair_lj_sdk_gpu.cpp rename to src/GPU/pair_lj_spica_gpu.cpp index 21e079e06f..394480428c 100644 --- a/src/GPU/pair_lj_sdk_gpu.cpp +++ b/src/GPU/pair_lj_spica_gpu.cpp @@ -15,7 +15,7 @@ Contributing author: Mike Brown (SNL) ------------------------------------------------------------------------- */ -#include "pair_lj_sdk_gpu.h" +#include "pair_lj_spica_gpu.h" #include "atom.h" #include "domain.h" @@ -32,29 +32,29 @@ using namespace LAMMPS_NS; // External functions from cuda library for atom decomposition -int sdk_gpu_init(const int ntypes, double **cutsq, int **cg_types, double **host_lj1, +int spica_gpu_init(const int ntypes, double **cutsq, int **cg_types, double **host_lj1, double **host_lj2, double **host_lj3, double **host_lj4, double **offset, double *special_lj, const int nlocal, const int nall, const int max_nbors, const int maxspecial, const double cell_size, int &gpu_mode, FILE *screen); -void sdk_gpu_clear(); -int **sdk_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x, +void spica_gpu_clear(); +int **spica_gpu_compute_n(const int ago, const int inum, const int nall, double **host_x, int *host_type, double *sublo, double *subhi, tagint *tag, int **nspecial, tagint **special, const bool eflag, const bool vflag, const bool eatom, const bool vatom, int &host_start, int **ilist, int **jnum, const double cpu_time, bool &success); -void sdk_gpu_compute(const int ago, const int inum, const int nall, double **host_x, int *host_type, +void spica_gpu_compute(const int ago, const int inum, const int nall, double **host_x, int *host_type, int *ilist, int *numj, int **firstneigh, const bool eflag, const bool vflag, const bool eatom, const bool vatom, int &host_start, const double cpu_time, bool &success); -double sdk_gpu_bytes(); +double spica_gpu_bytes(); -#include "lj_sdk_common.h" +#include "lj_spica_common.h" -using namespace LJSDKParms; +using namespace LJSPICAParms; /* ---------------------------------------------------------------------- */ -PairLJSDKGPU::PairLJSDKGPU(LAMMPS *lmp) : PairLJSDK(lmp), gpu_mode(GPU_FORCE) +PairLJSPICAGPU::PairLJSPICAGPU(LAMMPS *lmp) : PairLJSPICA(lmp), gpu_mode(GPU_FORCE) { respa_enable = 0; reinitflag = 0; @@ -67,14 +67,14 @@ PairLJSDKGPU::PairLJSDKGPU(LAMMPS *lmp) : PairLJSDK(lmp), gpu_mode(GPU_FORCE) free all arrays ------------------------------------------------------------------------- */ -PairLJSDKGPU::~PairLJSDKGPU() +PairLJSPICAGPU::~PairLJSPICAGPU() { - sdk_gpu_clear(); + spica_gpu_clear(); } /* ---------------------------------------------------------------------- */ -void PairLJSDKGPU::compute(int eflag, int vflag) +void PairLJSPICAGPU::compute(int eflag, int vflag) { ev_init(eflag, vflag); @@ -97,7 +97,7 @@ void PairLJSDKGPU::compute(int eflag, int vflag) } inum = atom->nlocal; firstneigh = - sdk_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, + spica_gpu_compute_n(neighbor->ago, inum, nall, atom->x, atom->type, sublo, subhi, atom->tag, atom->nspecial, atom->special, eflag, vflag, eflag_atom, vflag_atom, host_start, &ilist, &numneigh, cpu_time, success); } else { @@ -105,7 +105,7 @@ void PairLJSDKGPU::compute(int eflag, int vflag) ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; - sdk_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh, + spica_gpu_compute(neighbor->ago, inum, nall, atom->x, atom->type, ilist, numneigh, firstneigh, eflag, vflag, eflag_atom, vflag_atom, host_start, cpu_time, success); } if (!success) error->one(FLERR, "Insufficient memory on accelerator"); @@ -127,7 +127,7 @@ void PairLJSDKGPU::compute(int eflag, int vflag) init specific to this pair style ------------------------------------------------------------------------- */ -void PairLJSDKGPU::init_style() +void PairLJSPICAGPU::init_style() { // Repeat cutsq calculation because done after call to init_style @@ -149,7 +149,7 @@ void PairLJSDKGPU::init_style() int maxspecial = 0; if (atom->molecular != Atom::ATOMIC) maxspecial = atom->maxspecial; int mnf = 5e-2 * neighbor->oneatom; - int success = sdk_gpu_init(atom->ntypes + 1, cutsq, lj_type, lj1, lj2, lj3, lj4, offset, + int success = spica_gpu_init(atom->ntypes + 1, cutsq, lj_type, lj1, lj2, lj3, lj4, offset, force->special_lj, atom->nlocal, atom->nlocal + atom->nghost, mnf, maxspecial, cell_size, gpu_mode, screen); GPU_EXTRA::check_flag(success, error, world); @@ -159,15 +159,15 @@ void PairLJSDKGPU::init_style() /* ---------------------------------------------------------------------- */ -double PairLJSDKGPU::memory_usage() +double PairLJSPICAGPU::memory_usage() { double bytes = Pair::memory_usage(); - return bytes + sdk_gpu_bytes(); + return bytes + spica_gpu_bytes(); } /* ---------------------------------------------------------------------- */ template -void PairLJSDKGPU::cpu_compute(int start, int inum, int *ilist, int *numneigh, int **firstneigh) +void PairLJSPICAGPU::cpu_compute(int start, int inum, int *ilist, int *numneigh, int **firstneigh) { int i, j, ii, jj, jtype; double xtmp, ytmp, ztmp, delx, dely, delz, evdwl, fpair; @@ -228,6 +228,13 @@ void PairLJSDKGPU::cpu_compute(int start, int inum, int *ilist, int *numneigh, i forcelj = r6inv * (lj1[itype][jtype] * r6inv - lj2[itype][jtype]); if (EFLAG) evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype]; + + } else if (ljt == LJ12_5) { + const double r5inv = r2inv * r2inv * sqrt(r2inv); + const double r7inv = r5inv * r2inv; + forcelj = r5inv * (lj1[itype][jtype] * r7inv - lj2[itype][jtype]); + if (EFLAG) + evdwl = r5inv * (lj3[itype][jtype] * r7inv - lj4[itype][jtype]) - offset[itype][jtype]; } else continue; diff --git a/src/GPU/pair_lj_sdk_gpu.h b/src/GPU/pair_lj_spica_gpu.h similarity index 79% rename from src/GPU/pair_lj_sdk_gpu.h rename to src/GPU/pair_lj_spica_gpu.h index 529349ed0d..e8953d90da 100644 --- a/src/GPU/pair_lj_sdk_gpu.h +++ b/src/GPU/pair_lj_spica_gpu.h @@ -13,21 +13,22 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(lj/sdk/gpu,PairLJSDKGPU); +PairStyle(lj/spica/gpu,PairLJSPICAGPU); +PairStyle(lj/sdk/gpu,PairLJSPICAGPU); // clang-format on #else -#ifndef LMP_PAIR_LJ_SDK_GPU_H -#define LMP_PAIR_LJ_SDK_GPU_H +#ifndef LMP_PAIR_LJ_SPICA_GPU_H +#define LMP_PAIR_LJ_SPICA_GPU_H -#include "pair_lj_sdk.h" +#include "pair_lj_spica.h" namespace LAMMPS_NS { -class PairLJSDKGPU : public PairLJSDK { +class PairLJSPICAGPU : public PairLJSPICA { public: - PairLJSDKGPU(LAMMPS *lmp); - ~PairLJSDKGPU() override; + PairLJSPICAGPU(LAMMPS *lmp); + ~PairLJSPICAGPU() override; template void cpu_compute(int, int, int *, int *, int **); void compute(int, int) override; void init_style() override; From 60b189672ee7bd2a767165cfd706b94f7bc2617a Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Fri, 8 Jul 2022 18:09:37 +0900 Subject: [PATCH 19/72] changed file names and added a lj12-5 function type in KOKKOS pkg. --- src/KOKKOS/Install.sh | 4 +- ...dk_kokkos.cpp => pair_lj_spica_kokkos.cpp} | 57 +++++++++++-------- ...lj_sdk_kokkos.h => pair_lj_spica_kokkos.h} | 43 +++++++------- 3 files changed, 59 insertions(+), 45 deletions(-) rename src/KOKKOS/{pair_lj_sdk_kokkos.cpp => pair_lj_spica_kokkos.cpp} (84%) rename src/KOKKOS/{pair_lj_sdk_kokkos.h => pair_lj_spica_kokkos.h} (65%) diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index 314205ea3e..8b83555b8c 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -292,8 +292,8 @@ action pair_lj_gromacs_coul_gromacs_kokkos.cpp pair_lj_gromacs_coul_gromacs.cpp action pair_lj_gromacs_coul_gromacs_kokkos.h pair_lj_gromacs_coul_gromacs.h action pair_lj_gromacs_kokkos.cpp pair_lj_gromacs.cpp action pair_lj_gromacs_kokkos.h pair_lj_gromacs.h -action pair_lj_sdk_kokkos.cpp pair_lj_sdk.cpp -action pair_lj_sdk_kokkos.h pair_lj_sdk.h +action pair_lj_spica_kokkos.cpp pair_lj_spica.cpp +action pair_lj_spica_kokkos.h pair_lj_spica.h action pair_meam_kokkos.cpp pair_meam.cpp action pair_meam_kokkos.h pair_meam.h action pair_morse_kokkos.cpp diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.cpp b/src/KOKKOS/pair_lj_spica_kokkos.cpp similarity index 84% rename from src/KOKKOS/pair_lj_sdk_kokkos.cpp rename to src/KOKKOS/pair_lj_spica_kokkos.cpp index aed03f157d..4e77edb200 100644 --- a/src/KOKKOS/pair_lj_sdk_kokkos.cpp +++ b/src/KOKKOS/pair_lj_spica_kokkos.cpp @@ -12,7 +12,7 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "pair_lj_sdk_kokkos.h" +#include "pair_lj_spica_kokkos.h" #include "atom_kokkos.h" #include "atom_masks.h" @@ -26,13 +26,13 @@ #include "respa.h" #include "update.h" -#include "lj_sdk_common.h" +#include "lj_spica_common.h" #include #include using namespace LAMMPS_NS; -using namespace LJSDKParms; +using namespace LJSPICAParms; #define KOKKOS_CUDA_MAX_THREADS 256 #define KOKKOS_CUDA_MIN_BLOCKS 8 @@ -40,7 +40,7 @@ using namespace LJSDKParms; /* ---------------------------------------------------------------------- */ template -PairLJSDKKokkos::PairLJSDKKokkos(LAMMPS *lmp) : PairLJSDK(lmp) +PairLJSPICAKokkos::PairLJSPICAKokkos(LAMMPS *lmp) : PairLJSPICA(lmp) { respa_enable = 0; @@ -54,7 +54,7 @@ PairLJSDKKokkos::PairLJSDKKokkos(LAMMPS *lmp) : PairLJSDK(lmp) /* ---------------------------------------------------------------------- */ template -PairLJSDKKokkos::~PairLJSDKKokkos() +PairLJSPICAKokkos::~PairLJSPICAKokkos() { if (copymode) return; @@ -68,7 +68,7 @@ PairLJSDKKokkos::~PairLJSDKKokkos() /* ---------------------------------------------------------------------- */ template -void PairLJSDKKokkos::compute(int eflag_in, int vflag_in) +void PairLJSPICAKokkos::compute(int eflag_in, int vflag_in) { eflag = eflag_in; vflag = vflag_in; @@ -112,7 +112,7 @@ void PairLJSDKKokkos::compute(int eflag_in, int vflag_in) // loop over neighbors of my atoms - EV_FLOAT ev = pair_compute,void >(this,(NeighListKokkos*)list); + EV_FLOAT ev = pair_compute,void >(this,(NeighListKokkos*)list); if (eflag) eng_vdwl += ev.evdwl; if (vflag_global) { @@ -141,7 +141,7 @@ void PairLJSDKKokkos::compute(int eflag_in, int vflag_in) template template KOKKOS_INLINE_FUNCTION -F_FLOAT PairLJSDKKokkos:: +F_FLOAT PairLJSPICAKokkos:: compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { (void) i; (void) j; @@ -167,19 +167,25 @@ compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, c const double r6inv = r2inv*r2inv*r2inv; return r6inv*(lj_1*r6inv - lj_2) * r2inv; + } else if (ljt == LJ12_5) { + + const F_FLOAT r5inv = r2inv*r2inv*sqrt(r2inv); + const F_FLOAT r7inv = r5inv*r2inv; + return r5inv*(lj_1*r7inv - lj_2) * r2inv; + } - if (ljt!=LJ12_4 && ljt!=LJ9_6 && ljt!=LJ12_6) return 0.0;*/ + if (ljt!=LJ12_4 && ljt!=LJ9_6 && ljt!=LJ12_6 && ljt!=LJ12_5) return 0.0;*/ const F_FLOAT r4inv=r2inv*r2inv; const F_FLOAT r6inv=r2inv*r4inv; - const F_FLOAT a = ljt==LJ12_4?r4inv:r6inv; - const F_FLOAT b = ljt==LJ12_4?r4inv:(ljt==LJ9_6?1.0/sqrt(r2inv):r2inv); + const F_FLOAT a = ljt==LJ12_4?r4inv:(ljt==LJ12_5?r4inv*sqrt(r2inv):r6inv); + const F_FLOAT b = ljt==LJ12_4?r4inv:(ljt==LJ9_6?1.0/sqrt(r2inv):(ljt==LJ12_5?r2inv*sqrt(r2inv):r2inv)); return a* ( lj_1*r6inv*b - lj_2 * r2inv); } template template KOKKOS_INLINE_FUNCTION -F_FLOAT PairLJSDKKokkos:: +F_FLOAT PairLJSPICAKokkos:: compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const { (void) i; (void) j; @@ -203,6 +209,11 @@ compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, c } else if (ljt == LJ12_6) { const double r6inv = r2inv*r2inv*r2inv; return r6inv*(lj_3*r6inv - lj_4) - offset; + + } else if (ljt == LJ12_5) { + const F_FLOAT r5inv = r2inv*r2inv*sqrt(r2inv); + const F_FLOAT r7inv = r5inv*r2inv; + return r5inv*(lj_3*r7inv - lj_4) - offset; } else return 0.0; } @@ -212,15 +223,15 @@ compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, c ------------------------------------------------------------------------- */ template -void PairLJSDKKokkos::allocate() +void PairLJSPICAKokkos::allocate() { - PairLJSDK::allocate(); + PairLJSPICA::allocate(); int n = atom->ntypes; memory->destroy(cutsq); memoryKK->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq"); d_cutsq = k_cutsq.template view(); - k_params = Kokkos::DualView("PairLJSDK::params",n+1,n+1); + k_params = Kokkos::DualView("PairLJSPICA::params",n+1,n+1); params = k_params.template view(); } @@ -229,11 +240,11 @@ void PairLJSDKKokkos::allocate() ------------------------------------------------------------------------- */ template -void PairLJSDKKokkos::settings(int narg, char **arg) +void PairLJSPICAKokkos::settings(int narg, char **arg) { if (narg > 2) error->all(FLERR,"Illegal pair_style command"); - PairLJSDK::settings(1,arg); + PairLJSPICA::settings(1,arg); } /* ---------------------------------------------------------------------- @@ -241,9 +252,9 @@ void PairLJSDKKokkos::settings(int narg, char **arg) ------------------------------------------------------------------------- */ template -void PairLJSDKKokkos::init_style() +void PairLJSPICAKokkos::init_style() { - PairLJSDK::init_style(); + PairLJSPICA::init_style(); // error if rRESPA with inner levels @@ -270,9 +281,9 @@ void PairLJSDKKokkos::init_style() ------------------------------------------------------------------------- */ template -double PairLJSDKKokkos::init_one(int i, int j) +double PairLJSPICAKokkos::init_one(int i, int j) { - double cutone = PairLJSDK::init_one(i,j); + double cutone = PairLJSPICA::init_one(i,j); k_params.h_view(i,j).lj1 = lj1[i][j]; k_params.h_view(i,j).lj2 = lj2[i][j]; @@ -297,9 +308,9 @@ double PairLJSDKKokkos::init_one(int i, int j) namespace LAMMPS_NS { -template class PairLJSDKKokkos; +template class PairLJSPICAKokkos; #ifdef LMP_KOKKOS_GPU -template class PairLJSDKKokkos; +template class PairLJSPICAKokkos; #endif } diff --git a/src/KOKKOS/pair_lj_sdk_kokkos.h b/src/KOKKOS/pair_lj_spica_kokkos.h similarity index 65% rename from src/KOKKOS/pair_lj_sdk_kokkos.h rename to src/KOKKOS/pair_lj_spica_kokkos.h index edc42c7f6a..ba6c996df4 100644 --- a/src/KOKKOS/pair_lj_sdk_kokkos.h +++ b/src/KOKKOS/pair_lj_spica_kokkos.h @@ -13,31 +13,34 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(lj/sdk/kk,PairLJSDKKokkos); -PairStyle(lj/sdk/kk/device,PairLJSDKKokkos); -PairStyle(lj/sdk/kk/host,PairLJSDKKokkos); +PairStyle(lj/spica/kk,PairLJSPICAKokkos); +PairStyle(lj/spica/kk/device,PairLJSPICAKokkos); +PairStyle(lj/spica/kk/host,PairLJSPICAKokkos); +PairStyle(lj/sdk/kk,PairLJSPICAKokkos); +PairStyle(lj/sdk/kk/device,PairLJSPICAKokkos); +PairStyle(lj/sdk/kk/host,PairLJSPICAKokkos); // clang-format on #else // clang-format off -#ifndef LMP_PAIR_LJ_SDK_KOKKOS_H -#define LMP_PAIR_LJ_SDK_KOKKOS_H +#ifndef LMP_PAIR_LJ_SPICA_KOKKOS_H +#define LMP_PAIR_LJ_SPICA_KOKKOS_H #include "pair_kokkos.h" -#include "pair_lj_sdk.h" +#include "pair_lj_spica.h" #include "neigh_list_kokkos.h" namespace LAMMPS_NS { template -class PairLJSDKKokkos : public PairLJSDK { +class PairLJSPICAKokkos : public PairLJSPICA { public: enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF}; enum {COUL_FLAG=0}; typedef DeviceType device_type; typedef ArrayTypes AT; - PairLJSDKKokkos(class LAMMPS *); - ~PairLJSDKKokkos() override; + PairLJSPICAKokkos(class LAMMPS *); + ~PairLJSPICAKokkos() override; void compute(int, int) override; @@ -95,17 +98,17 @@ class PairLJSDKKokkos : public PairLJSDK { int nlocal,nall,eflag,vflag; void allocate() override; - friend struct PairComputeFunctor; - friend struct PairComputeFunctor; - friend struct PairComputeFunctor; - friend struct PairComputeFunctor; - friend struct PairComputeFunctor; - friend struct PairComputeFunctor; - friend EV_FLOAT pair_compute_neighlist(PairLJSDKKokkos*,NeighListKokkos*); - friend EV_FLOAT pair_compute_neighlist(PairLJSDKKokkos*,NeighListKokkos*); - friend EV_FLOAT pair_compute_neighlist(PairLJSDKKokkos*,NeighListKokkos*); - friend EV_FLOAT pair_compute(PairLJSDKKokkos*,NeighListKokkos*); - friend void pair_virial_fdotr_compute(PairLJSDKKokkos*); + friend struct PairComputeFunctor; + friend struct PairComputeFunctor; + friend struct PairComputeFunctor; + friend struct PairComputeFunctor; + friend struct PairComputeFunctor; + friend struct PairComputeFunctor; + friend EV_FLOAT pair_compute_neighlist(PairLJSPICAKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute_neighlist(PairLJSPICAKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute_neighlist(PairLJSPICAKokkos*,NeighListKokkos*); + friend EV_FLOAT pair_compute(PairLJSPICAKokkos*,NeighListKokkos*); + friend void pair_virial_fdotr_compute(PairLJSPICAKokkos*); }; } From 07633622e66269741af662a9179d24fdfe36694e Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Fri, 8 Jul 2022 18:18:39 +0900 Subject: [PATCH 20/72] changed file names and added a lj12-5 function type in OPENMP pkg. --- ...{angle_sdk_omp.cpp => angle_spica_omp.cpp} | 21 ++++++++++----- .../{angle_sdk_omp.h => angle_spica_omp.h} | 13 ++++----- ...mp.cpp => pair_lj_spica_coul_long_omp.cpp} | 27 ++++++++++++------- ...ng_omp.h => pair_lj_spica_coul_long_omp.h} | 13 ++++----- ...omp.cpp => pair_lj_spica_coul_msm_omp.cpp} | 27 ++++++++++++------- ...msm_omp.h => pair_lj_spica_coul_msm_omp.h} | 13 ++++----- ...r_lj_sdk_omp.cpp => pair_lj_spica_omp.cpp} | 27 ++++++++++++------- ...{pair_lj_sdk_omp.h => pair_lj_spica_omp.h} | 13 ++++----- src/OPENMP/thr_omp.cpp | 2 +- 9 files changed, 97 insertions(+), 59 deletions(-) rename src/OPENMP/{angle_sdk_omp.cpp => angle_spica_omp.cpp} (91%) rename src/OPENMP/{angle_sdk_omp.h => angle_spica_omp.h} (82%) rename src/OPENMP/{pair_lj_sdk_coul_long_omp.cpp => pair_lj_spica_coul_long_omp.cpp} (89%) rename src/OPENMP/{pair_lj_sdk_coul_long_omp.h => pair_lj_spica_coul_long_omp.h} (77%) rename src/OPENMP/{pair_lj_sdk_coul_msm_omp.cpp => pair_lj_spica_coul_msm_omp.cpp} (89%) rename src/OPENMP/{pair_lj_sdk_coul_msm_omp.h => pair_lj_spica_coul_msm_omp.h} (77%) rename src/OPENMP/{pair_lj_sdk_omp.cpp => pair_lj_spica_omp.cpp} (87%) rename src/OPENMP/{pair_lj_sdk_omp.h => pair_lj_spica_omp.h} (81%) diff --git a/src/OPENMP/angle_sdk_omp.cpp b/src/OPENMP/angle_spica_omp.cpp similarity index 91% rename from src/OPENMP/angle_sdk_omp.cpp rename to src/OPENMP/angle_spica_omp.cpp index e82121959b..f6198eab50 100644 --- a/src/OPENMP/angle_sdk_omp.cpp +++ b/src/OPENMP/angle_spica_omp.cpp @@ -17,32 +17,32 @@ ------------------------------------------------------------------------- */ #include "omp_compat.h" -#include "angle_sdk_omp.h" +#include "angle_spica_omp.h" #include #include "atom.h" #include "neighbor.h" #include "comm.h" #include "force.h" -#include "lj_sdk_common.h" +#include "lj_spica_common.h" #include "suffix.h" using namespace LAMMPS_NS; -using namespace LJSDKParms; +using namespace LJSPICAParms; #define SMALL 0.001 /* ---------------------------------------------------------------------- */ -AngleSDKOMP::AngleSDKOMP(class LAMMPS *lmp) - : AngleSDK(lmp), ThrOMP(lmp,THR_ANGLE) +AngleSPICAOMP::AngleSPICAOMP(class LAMMPS *lmp) + : AngleSPICA(lmp), ThrOMP(lmp,THR_ANGLE) { suffix_flag |= Suffix::OMP; } /* ---------------------------------------------------------------------- */ -void AngleSDKOMP::compute(int eflag, int vflag) +void AngleSPICAOMP::compute(int eflag, int vflag) { ev_init(eflag,vflag); @@ -81,7 +81,7 @@ void AngleSDKOMP::compute(int eflag, int vflag) } template -void AngleSDKOMP::eval(int nfrom, int nto, ThrData * const thr) +void AngleSPICAOMP::eval(int nfrom, int nto, ThrData * const thr) { int i1,i2,i3,n,type; double delx1,dely1,delz1,delx2,dely2,delz2,delx3,dely3,delz3; @@ -171,6 +171,13 @@ void AngleSDKOMP::eval(int nfrom, int nto, ThrData * const thr) f13 = r6inv*(lj1[type1][type3]*r6inv - lj2[type1][type3]); if (EFLAG) e13 = r6inv*(lj3[type1][type3]*r6inv - lj4[type1][type3]); + + } else if (ljt == LJ12_5) { + const double r5inv = r2inv*r2inv*sqrt(r2inv); + const double r7inv = r5inv*r2inv; + + f13 = r5inv*(lj1[type1][type3]*r7inv - lj2[type1][type3]); + if (EFLAG) e13 = r5inv*(lj3[type1][type3]*r7inv - lj4[type1][type3]); } // make sure energy is 0.0 at the cutoff. diff --git a/src/OPENMP/angle_sdk_omp.h b/src/OPENMP/angle_spica_omp.h similarity index 82% rename from src/OPENMP/angle_sdk_omp.h rename to src/OPENMP/angle_spica_omp.h index c4d12787f9..a6186c3f5e 100644 --- a/src/OPENMP/angle_sdk_omp.h +++ b/src/OPENMP/angle_spica_omp.h @@ -17,22 +17,23 @@ #ifdef ANGLE_CLASS // clang-format off -AngleStyle(sdk/omp,AngleSDKOMP); +AngleStyle(spica/omp,AngleSPICAOMP); +AngleStyle(sdk/omp,AngleSPICAOMP); // clang-format on #else -#ifndef LMP_ANGLE_SDK_OMP_H -#define LMP_ANGLE_SDK_OMP_H +#ifndef LMP_ANGLE_SPICA_OMP_H +#define LMP_ANGLE_SPICA_OMP_H -#include "angle_sdk.h" +#include "angle_spica.h" #include "thr_omp.h" namespace LAMMPS_NS { -class AngleSDKOMP : public AngleSDK, public ThrOMP { +class AngleSPICAOMP : public AngleSPICA, public ThrOMP { public: - AngleSDKOMP(class LAMMPS *lmp); + AngleSPICAOMP(class LAMMPS *lmp); void compute(int, int) override; private: diff --git a/src/OPENMP/pair_lj_sdk_coul_long_omp.cpp b/src/OPENMP/pair_lj_spica_coul_long_omp.cpp similarity index 89% rename from src/OPENMP/pair_lj_sdk_coul_long_omp.cpp rename to src/OPENMP/pair_lj_spica_coul_long_omp.cpp index fff5d17b13..a0c90d872c 100644 --- a/src/OPENMP/pair_lj_sdk_coul_long_omp.cpp +++ b/src/OPENMP/pair_lj_spica_coul_long_omp.cpp @@ -13,8 +13,8 @@ Contributing author: Axel Kohlmeyer (Temple U) ------------------------------------------------------------------------- */ -#include "pair_lj_sdk_coul_long_omp.h" -#include "lj_sdk_common.h" +#include "pair_lj_spica_coul_long_omp.h" +#include "lj_spica_common.h" #include "atom.h" #include "comm.h" @@ -26,11 +26,11 @@ #include "omp_compat.h" using namespace LAMMPS_NS; -using namespace LJSDKParms; +using namespace LJSPICAParms; /* ---------------------------------------------------------------------- */ -PairLJSDKCoulLongOMP::PairLJSDKCoulLongOMP(LAMMPS *lmp) : - PairLJSDKCoulLong(lmp), ThrOMP(lmp, THR_PAIR) +PairLJSPICACoulLongOMP::PairLJSPICACoulLongOMP(LAMMPS *lmp) : + PairLJSPICACoulLong(lmp), ThrOMP(lmp, THR_PAIR) { suffix_flag |= Suffix::OMP; respa_enable = 0; @@ -38,7 +38,7 @@ PairLJSDKCoulLongOMP::PairLJSDKCoulLongOMP(LAMMPS *lmp) : /* ---------------------------------------------------------------------- */ -void PairLJSDKCoulLongOMP::compute(int eflag, int vflag) +void PairLJSPICACoulLongOMP::compute(int eflag, int vflag) { ev_init(eflag,vflag); @@ -78,7 +78,7 @@ void PairLJSDKCoulLongOMP::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ template -void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr) +void PairLJSPICACoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr) { const auto * _noalias const x = (dbl3_t *) atom->x[0]; @@ -195,6 +195,15 @@ void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr) if (EFLAG) evdwl = r6inv*(lj3[itype][jtype]*r6inv - lj4[itype][jtype]) - offset[itype][jtype]; + + } else if (ljt == LJ12_5) { + const double r5inv = r2inv*r2inv*sqrt(r2inv); + const double r7inv = r5inv*r2inv; + forcelj = r5inv*(lj1[itype][jtype]*r7inv + - lj2[itype][jtype]); + if (EFLAG) + evdwl = r5inv*(lj3[itype][jtype]*r7inv + - lj4[itype][jtype]) - offset[itype][jtype]; } if (sbindex) { @@ -228,10 +237,10 @@ void PairLJSDKCoulLongOMP::eval_thr(int iifrom, int iito, ThrData * const thr) /* ---------------------------------------------------------------------- */ -double PairLJSDKCoulLongOMP::memory_usage() +double PairLJSPICACoulLongOMP::memory_usage() { double bytes = memory_usage_thr(); - bytes += PairLJSDKCoulLong::memory_usage(); + bytes += PairLJSPICACoulLong::memory_usage(); return bytes; } diff --git a/src/OPENMP/pair_lj_sdk_coul_long_omp.h b/src/OPENMP/pair_lj_spica_coul_long_omp.h similarity index 77% rename from src/OPENMP/pair_lj_sdk_coul_long_omp.h rename to src/OPENMP/pair_lj_spica_coul_long_omp.h index d19139de26..0cc7c588cd 100644 --- a/src/OPENMP/pair_lj_sdk_coul_long_omp.h +++ b/src/OPENMP/pair_lj_spica_coul_long_omp.h @@ -17,22 +17,23 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(lj/sdk/coul/long/omp,PairLJSDKCoulLongOMP); +PairStyle(lj/spica/coul/long/omp,PairLJSPICACoulLongOMP); +PairStyle(lj/sdk/coul/long/omp,PairLJSPICACoulLongOMP); // clang-format on #else -#ifndef LMP_PAIR_LJ_SDK_COUL_LONG_OMP_H -#define LMP_PAIR_LJ_SDK_COUL_LONG_OMP_H +#ifndef LMP_PAIR_LJ_SPICA_COUL_LONG_OMP_H +#define LMP_PAIR_LJ_SPICA_COUL_LONG_OMP_H -#include "pair_lj_sdk_coul_long.h" +#include "pair_lj_spica_coul_long.h" #include "thr_omp.h" namespace LAMMPS_NS { -class PairLJSDKCoulLongOMP : public PairLJSDKCoulLong, public ThrOMP { +class PairLJSPICACoulLongOMP : public PairLJSPICACoulLong, public ThrOMP { public: - PairLJSDKCoulLongOMP(class LAMMPS *); + PairLJSPICACoulLongOMP(class LAMMPS *); void compute(int, int) override; double memory_usage() override; diff --git a/src/OPENMP/pair_lj_sdk_coul_msm_omp.cpp b/src/OPENMP/pair_lj_spica_coul_msm_omp.cpp similarity index 89% rename from src/OPENMP/pair_lj_sdk_coul_msm_omp.cpp rename to src/OPENMP/pair_lj_spica_coul_msm_omp.cpp index 53c058fba1..b353361abe 100644 --- a/src/OPENMP/pair_lj_sdk_coul_msm_omp.cpp +++ b/src/OPENMP/pair_lj_spica_coul_msm_omp.cpp @@ -14,8 +14,8 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include "pair_lj_sdk_coul_msm_omp.h" -#include "lj_sdk_common.h" +#include "pair_lj_spica_coul_msm_omp.h" +#include "lj_spica_common.h" #include "atom.h" #include "comm.h" @@ -29,11 +29,11 @@ #include "omp_compat.h" using namespace LAMMPS_NS; -using namespace LJSDKParms; +using namespace LJSPICAParms; /* ---------------------------------------------------------------------- */ -PairLJSDKCoulMSMOMP::PairLJSDKCoulMSMOMP(LAMMPS *lmp) : - PairLJSDKCoulMSM(lmp), ThrOMP(lmp, THR_PAIR) +PairLJSPICACoulMSMOMP::PairLJSPICACoulMSMOMP(LAMMPS *lmp) : + PairLJSPICACoulMSM(lmp), ThrOMP(lmp, THR_PAIR) { suffix_flag |= Suffix::OMP; respa_enable = 0; @@ -41,7 +41,7 @@ PairLJSDKCoulMSMOMP::PairLJSDKCoulMSMOMP(LAMMPS *lmp) : /* ---------------------------------------------------------------------- */ -void PairLJSDKCoulMSMOMP::compute(int eflag, int vflag) +void PairLJSPICACoulMSMOMP::compute(int eflag, int vflag) { if (force->kspace->scalar_pressure_flag) error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' " @@ -85,7 +85,7 @@ void PairLJSDKCoulMSMOMP::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ template -void PairLJSDKCoulMSMOMP::eval_msm_thr(int iifrom, int iito, ThrData * const thr) +void PairLJSPICACoulMSMOMP::eval_msm_thr(int iifrom, int iito, ThrData * const thr) { const double * const * const x = atom->x; @@ -194,6 +194,15 @@ void PairLJSDKCoulMSMOMP::eval_msm_thr(int iifrom, int iito, ThrData * const thr if (EFLAG) evdwl = r6inv*(lj3[itype][jtype]*r6inv - lj4[itype][jtype]) - offset[itype][jtype]; + + } else if (ljt == LJ12_5) { + const double r5inv = r2inv*r2inv*sqrt(r2inv); + const double r7inv = r5inv*r2inv; + forcelj = r5inv*(lj1[itype][jtype]*r7inv + - lj2[itype][jtype]); + if (EFLAG) + evdwl = r5inv*(lj3[itype][jtype]*r7inv + - lj4[itype][jtype]) - offset[itype][jtype]; } if (sbindex) { @@ -227,10 +236,10 @@ void PairLJSDKCoulMSMOMP::eval_msm_thr(int iifrom, int iito, ThrData * const thr /* ---------------------------------------------------------------------- */ -double PairLJSDKCoulMSMOMP::memory_usage() +double PairLJSPICACoulMSMOMP::memory_usage() { double bytes = memory_usage_thr(); - bytes += PairLJSDKCoulMSM::memory_usage(); + bytes += PairLJSPICACoulMSM::memory_usage(); return bytes; } diff --git a/src/OPENMP/pair_lj_sdk_coul_msm_omp.h b/src/OPENMP/pair_lj_spica_coul_msm_omp.h similarity index 77% rename from src/OPENMP/pair_lj_sdk_coul_msm_omp.h rename to src/OPENMP/pair_lj_spica_coul_msm_omp.h index 9bcde691d0..b84bf35db8 100644 --- a/src/OPENMP/pair_lj_sdk_coul_msm_omp.h +++ b/src/OPENMP/pair_lj_spica_coul_msm_omp.h @@ -17,22 +17,23 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(lj/sdk/coul/msm/omp,PairLJSDKCoulMSMOMP); +PairStyle(lj/spica/coul/msm/omp,PairLJSPICACoulMSMOMP); +PairStyle(lj/sdk/coul/msm/omp,PairLJSPICACoulMSMOMP); // clang-format on #else -#ifndef LMP_PAIR_LJ_SDK_COUL_MSM_OMP_H -#define LMP_PAIR_LJ_SDK_COUL_MSM_OMP_H +#ifndef LMP_PAIR_LJ_SPICA_COUL_MSM_OMP_H +#define LMP_PAIR_LJ_SPICA_COUL_MSM_OMP_H -#include "pair_lj_sdk_coul_msm.h" +#include "pair_lj_spica_coul_msm.h" #include "thr_omp.h" namespace LAMMPS_NS { -class PairLJSDKCoulMSMOMP : public PairLJSDKCoulMSM, public ThrOMP { +class PairLJSPICACoulMSMOMP : public PairLJSPICACoulMSM, public ThrOMP { public: - PairLJSDKCoulMSMOMP(class LAMMPS *); + PairLJSPICACoulMSMOMP(class LAMMPS *); void compute(int, int) override; double memory_usage() override; diff --git a/src/OPENMP/pair_lj_sdk_omp.cpp b/src/OPENMP/pair_lj_spica_omp.cpp similarity index 87% rename from src/OPENMP/pair_lj_sdk_omp.cpp rename to src/OPENMP/pair_lj_spica_omp.cpp index 909bb73fc8..054c5b7d44 100644 --- a/src/OPENMP/pair_lj_sdk_omp.cpp +++ b/src/OPENMP/pair_lj_spica_omp.cpp @@ -14,8 +14,8 @@ This style is a simplified re-implementation of the CG/CMM pair style ------------------------------------------------------------------------- */ -#include "pair_lj_sdk_omp.h" -#include "lj_sdk_common.h" +#include "pair_lj_spica_omp.h" +#include "lj_spica_common.h" #include "atom.h" #include "comm.h" @@ -27,12 +27,12 @@ #include "omp_compat.h" using namespace LAMMPS_NS; -using namespace LJSDKParms; +using namespace LJSPICAParms; /* ---------------------------------------------------------------------- */ -PairLJSDKOMP::PairLJSDKOMP(LAMMPS *lmp) : - PairLJSDK(lmp), ThrOMP(lmp, THR_PAIR) +PairLJSPICAOMP::PairLJSPICAOMP(LAMMPS *lmp) : + PairLJSPICA(lmp), ThrOMP(lmp, THR_PAIR) { suffix_flag |= Suffix::OMP; respa_enable = 0; @@ -40,7 +40,7 @@ PairLJSDKOMP::PairLJSDKOMP(LAMMPS *lmp) : /* ---------------------------------------------------------------------- */ -void PairLJSDKOMP::compute(int eflag, int vflag) +void PairLJSPICAOMP::compute(int eflag, int vflag) { ev_init(eflag,vflag); @@ -80,7 +80,7 @@ void PairLJSDKOMP::compute(int eflag, int vflag) /* ---------------------------------------------------------------------- */ template -void PairLJSDKOMP::eval_thr(int iifrom, int iito, ThrData * const thr) +void PairLJSPICAOMP::eval_thr(int iifrom, int iito, ThrData * const thr) { int i,j,ii,jj,jtype; double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair; @@ -153,6 +153,15 @@ void PairLJSDKOMP::eval_thr(int iifrom, int iito, ThrData * const thr) if (EFLAG) evdwl = r6inv*(lj3[itype][jtype]*r6inv - lj4[itype][jtype]) - offset[itype][jtype]; + + } else if (ljt == LJ12_5) { + const double r5inv = r2inv*r2inv*sqrt(r2inv); + const double r7inv = r5inv*r2inv; + forcelj = r5inv*(lj1[itype][jtype]*r7inv + - lj2[itype][jtype]); + if (EFLAG) + evdwl = r5inv*(lj3[itype][jtype]*r7inv + - lj4[itype][jtype]) - offset[itype][jtype]; } else continue; fpair = factor_lj*forcelj*r2inv; @@ -179,10 +188,10 @@ void PairLJSDKOMP::eval_thr(int iifrom, int iito, ThrData * const thr) /* ---------------------------------------------------------------------- */ -double PairLJSDKOMP::memory_usage() +double PairLJSPICAOMP::memory_usage() { double bytes = memory_usage_thr(); - bytes += PairLJSDK::memory_usage(); + bytes += PairLJSPICA::memory_usage(); return bytes; } diff --git a/src/OPENMP/pair_lj_sdk_omp.h b/src/OPENMP/pair_lj_spica_omp.h similarity index 81% rename from src/OPENMP/pair_lj_sdk_omp.h rename to src/OPENMP/pair_lj_spica_omp.h index 1ef27f6fb6..34a5b357dd 100644 --- a/src/OPENMP/pair_lj_sdk_omp.h +++ b/src/OPENMP/pair_lj_spica_omp.h @@ -17,22 +17,23 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(lj/sdk/omp,PairLJSDKOMP); +PairStyle(lj/spica/omp,PairLJSPICAOMP); +PairStyle(lj/sdk/omp,PairLJSPICAOMP); // clang-format on #else -#ifndef LMP_PAIR_LJ_SDK_OMP_H -#define LMP_PAIR_LJ_SDK_OMP_H +#ifndef LMP_PAIR_LJ_SPICA_OMP_H +#define LMP_PAIR_LJ_SPICA_OMP_H -#include "pair_lj_sdk.h" +#include "pair_lj_spica.h" #include "thr_omp.h" namespace LAMMPS_NS { -class PairLJSDKOMP : public PairLJSDK, public ThrOMP { +class PairLJSPICAOMP : public PairLJSPICA, public ThrOMP { public: - PairLJSDKOMP(class LAMMPS *); + PairLJSPICAOMP(class LAMMPS *); void compute(int, int) override; double memory_usage() override; diff --git a/src/OPENMP/thr_omp.cpp b/src/OPENMP/thr_omp.cpp index 01f12ed17d..95392b17a4 100644 --- a/src/OPENMP/thr_omp.cpp +++ b/src/OPENMP/thr_omp.cpp @@ -1042,7 +1042,7 @@ void ThrOMP::ev_tally_thr(Angle * const angle, const int i, const int j, const i } /* ---------------------------------------------------------------------- - tally energy and virial from 1-3 repulsion of SDK angle into accumulators + tally energy and virial from 1-3 repulsion of SPICA angle into accumulators ------------------------------------------------------------------------- */ void ThrOMP::ev_tally13_thr(Angle * const angle, const int i1, const int i3, From b5e70ebc81b88c5ea850fdbb47df36fff1323cf7 Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Fri, 8 Jul 2022 18:23:10 +0900 Subject: [PATCH 21/72] added a FF name SPICA to tools/kate/lammps.xml and tools/moltemplate/README.txt --- tools/kate/lammps.xml | 7 +++++++ tools/moltemplate/README.txt | 2 +- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/tools/kate/lammps.xml b/tools/kate/lammps.xml index 0d8ba0fda4..d97b5cc8d3 100644 --- a/tools/kate/lammps.xml +++ b/tools/kate/lammps.xml @@ -394,6 +394,8 @@ edip eff/cut gauss/cut + lj/spica + lj/spica/coul/long lj/sdk lj/sdk/coul/long lj/sf @@ -517,6 +519,10 @@ lj/gromacs/coul/gromacs/omp lj/gromacs/cuda lj/gromacs/omp + lj/spica/gpu + lj/spica/omp + lj/spica/coul/long/gpu + lj/spica/coul/long/omp lj/sdk/gpu lj/sdk/omp lj/sdk/coul/long/gpu @@ -596,6 +602,7 @@ table + spica sdk cosine/shift cosine/shift/exp diff --git a/tools/moltemplate/README.txt b/tools/moltemplate/README.txt index 97f68a85de..c33554b14d 100644 --- a/tools/moltemplate/README.txt +++ b/tools/moltemplate/README.txt @@ -9,7 +9,7 @@ cross-platform, text-based molecule and topology builder for LAMMPS. Moltemplate was originally conceived for building custom coarse-grained molecular models, but it has since been generalized for all-atom simulations as well. It currently supports the OPLS, COMPASS, AMBER(GAFF,GAFF2), -MARTINI, SDK, LOPLS(2015), and TraPPE(1998) force fields, and includes +MARTINI, SPICA(SDK), LOPLS(2015), and TraPPE(1998) force fields, and includes (New force fields and examples are added continually through user contributions). From 099992f9c2a2c91f1c588371c7bf26d8e1d817c8 Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Fri, 8 Jul 2022 18:41:50 +0900 Subject: [PATCH 22/72] changed file and style names for lj/spica in unittest/force-styles/tests. --- .../tests/{mol-pair-lj_sdk.yaml => mol-pair-lj_spica.yaml} | 4 ++-- ...lj_sdk_coul_long.yaml => mol-pair-lj_spica_coul_long.yaml} | 4 ++-- ...r-lj_sdk_coul_msm.yaml => mol-pair-lj_spica_coul_msm.yaml} | 4 ++-- ...l_msm_table.yaml => mol-pair-lj_spica_coul_msm_table.yaml} | 4 ++-- ..._sdk_coul_table.yaml => mol-pair-lj_spica_coul_table.yaml} | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) rename unittest/force-styles/tests/{mol-pair-lj_sdk.yaml => mol-pair-lj_spica.yaml} (99%) rename unittest/force-styles/tests/{mol-pair-lj_sdk_coul_long.yaml => mol-pair-lj_spica_coul_long.yaml} (98%) rename unittest/force-styles/tests/{mol-pair-lj_sdk_coul_msm.yaml => mol-pair-lj_spica_coul_msm.yaml} (98%) rename unittest/force-styles/tests/{mol-pair-lj_sdk_coul_msm_table.yaml => mol-pair-lj_spica_coul_msm_table.yaml} (98%) rename unittest/force-styles/tests/{mol-pair-lj_sdk_coul_table.yaml => mol-pair-lj_spica_coul_table.yaml} (98%) diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk.yaml b/unittest/force-styles/tests/mol-pair-lj_spica.yaml similarity index 99% rename from unittest/force-styles/tests/mol-pair-lj_sdk.yaml rename to unittest/force-styles/tests/mol-pair-lj_spica.yaml index 74f8b1d80d..10d0602934 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_spica.yaml @@ -5,12 +5,12 @@ epsilon: 5e-14 skip_tests: prerequisites: ! | atom full - pair lj/sdk + pair lj/spica pre_commands: ! | variable write_data_pair index ij post_commands: ! "" input_file: in.fourmol -pair_style: lj/sdk 8.0 +pair_style: lj/spica 8.0 pair_coeff: ! | 1 1 lj9_6 0.02 2.5 1 2 lj9_6 0.01 1.58114 diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_long.yaml b/unittest/force-styles/tests/mol-pair-lj_spica_coul_long.yaml similarity index 98% rename from unittest/force-styles/tests/mol-pair-lj_sdk_coul_long.yaml rename to unittest/force-styles/tests/mol-pair-lj_spica_coul_long.yaml index 8decb35c5b..7f03b7b063 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_long.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_spica_coul_long.yaml @@ -5,7 +5,7 @@ epsilon: 5e-14 skip_tests: prerequisites: ! | atom full - pair lj/sdk/coul/long + pair lj/spica/coul/long kspace ewald pre_commands: ! | variable write_data_pair index ij @@ -15,7 +15,7 @@ post_commands: ! | kspace_modify gewald 0.3 kspace_modify compute no input_file: in.fourmol -pair_style: lj/sdk/coul/long 8.0 +pair_style: lj/spica/coul/long 8.0 pair_coeff: ! | 1 1 lj9_6 0.02 2.5 1 2 lj9_6 0.01 1.58114 diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml b/unittest/force-styles/tests/mol-pair-lj_spica_coul_msm.yaml similarity index 98% rename from unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml rename to unittest/force-styles/tests/mol-pair-lj_spica_coul_msm.yaml index e0e0629d10..64ec316de4 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_spica_coul_msm.yaml @@ -5,7 +5,7 @@ epsilon: 5e-14 skip_tests: prerequisites: ! | atom full - pair lj/sdk/coul/long + pair lj/spica/coul/long kspace ewald pre_commands: ! | variable write_data_pair index ij @@ -16,7 +16,7 @@ post_commands: ! | kspace_modify cutoff/adjust no kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol -pair_style: lj/sdk/coul/msm 12.0 +pair_style: lj/spica/coul/msm 12.0 pair_coeff: ! | 1 1 lj9_6 0.02 2.5 1 2 lj9_6 0.01 1.58114 diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml b/unittest/force-styles/tests/mol-pair-lj_spica_coul_msm_table.yaml similarity index 98% rename from unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml rename to unittest/force-styles/tests/mol-pair-lj_spica_coul_msm_table.yaml index 035838fc1d..e7448e8337 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_msm_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_spica_coul_msm_table.yaml @@ -5,7 +5,7 @@ epsilon: 5e-14 skip_tests: gpu prerequisites: ! | atom full - pair lj/sdk/coul/long + pair lj/spica/coul/long kspace ewald pre_commands: ! | variable write_data_pair index ij @@ -16,7 +16,7 @@ post_commands: ! | kspace_modify cutoff/adjust no kspace_modify pressure/scalar no # required for OPENMP with msm input_file: in.fourmol -pair_style: lj/sdk/coul/msm 12.0 +pair_style: lj/spica/coul/msm 12.0 pair_coeff: ! | 1 1 lj9_6 0.02 2.5 1 2 lj9_6 0.01 1.58114 diff --git a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_table.yaml b/unittest/force-styles/tests/mol-pair-lj_spica_coul_table.yaml similarity index 98% rename from unittest/force-styles/tests/mol-pair-lj_sdk_coul_table.yaml rename to unittest/force-styles/tests/mol-pair-lj_spica_coul_table.yaml index 108460d616..3d1468b16c 100644 --- a/unittest/force-styles/tests/mol-pair-lj_sdk_coul_table.yaml +++ b/unittest/force-styles/tests/mol-pair-lj_spica_coul_table.yaml @@ -5,7 +5,7 @@ epsilon: 5e-14 skip_tests: gpu prerequisites: ! | atom full - pair lj/sdk/coul/long + pair lj/spica/coul/long kspace ewald pre_commands: ! | variable write_data_pair index ij @@ -15,7 +15,7 @@ post_commands: ! | kspace_modify gewald 0.3 kspace_modify compute no input_file: in.fourmol -pair_style: lj/sdk/coul/long 8.0 +pair_style: lj/spica/coul/long 8.0 pair_coeff: ! | 1 1 lj9_6 0.02 2.5 1 2 lj9_6 0.01 1.58114 From ec45c57181afc032879e0fb1cd4965f30e613aeb Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Fri, 8 Jul 2022 22:00:34 +0900 Subject: [PATCH 23/72] changed reference paper info. --- src/CG-SPICA/README | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/CG-SPICA/README b/src/CG-SPICA/README index 621ee18a39..cbef4ef2c9 100644 --- a/src/CG-SPICA/README +++ b/src/CG-SPICA/README @@ -11,9 +11,9 @@ parametrization of the SPICA (formerly called SDK) and the pSPICA force fields, to simulate biological or soft material systems. For details about the force fields using this implementation, see the following papers: - SDK - Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007). - SPICA - Seo, Shinoda, J Chem Theory Comput, 15, 762 (2019). - pSPICA - Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782 (2020). + SDK - Shinoda, DeVane, Klein, Mol Sim, 33, 27-36 (2007). + SPICA - Seo, Shinoda, J Chem Theory Comput, 15, 762-774 (2019). + pSPICA - Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782-793 (2020). Summary information on these force fields can be found at this web site: https://www.spica-ff.org From 7b7ae55238e380979035f642b339b155c3cb9595 Mon Sep 17 00:00:00 2001 From: Vaibhav Palkar Date: Fri, 8 Jul 2022 15:37:42 -0400 Subject: [PATCH 24/72] small fix, idcreate and idbreak are already deleted in destructor now --- src/MISC/pair_srp_react.cpp | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/MISC/pair_srp_react.cpp b/src/MISC/pair_srp_react.cpp index b302a9a509..f486aa33b7 100644 --- a/src/MISC/pair_srp_react.cpp +++ b/src/MISC/pair_srp_react.cpp @@ -205,7 +205,6 @@ void PairSRPREACT::init_style() arg0[0] = (char *) "bond/break"; arg0[1] = c0; f_srp->modify_params(2, arg0); - delete[] idbreak; } // if using fix bond/create, set id of fix bond/create in fix srp @@ -215,7 +214,6 @@ void PairSRPREACT::init_style() arg0[0] = (char *) "bond/create"; arg0[1] = c0; f_srp->modify_params(2, arg0); - delete[] idcreate; } // bond particles do not contribute to energy or virial From aa11935e88d0776e71bfae8fb4055a4711ce5ff9 Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Mon, 11 Jul 2022 11:38:31 +0900 Subject: [PATCH 25/72] updated .gitignore and Purge.list, and author info, and added URL to the SPICA web. --- doc/src/Packages_details.rst | 5 ++++- doc/src/pair_spica.rst | 1 + src/.gitignore | 18 +++++++++--------- src/CG-SPICA/README | 11 ++++------- src/Purge.list | 24 ++++++++++++++++++++++++ 5 files changed, 42 insertions(+), 17 deletions(-) diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 24a8cc11b9..d1b69740ce 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -376,7 +376,9 @@ Several pair styles and an angle style which implement the coarse-grained SPICA (formerly called SDK) model which enables simulation of biological or soft material systems. -**Author:** Axel Kohlmeyer (Temple U). +**Original Author:** Axel Kohlmeyer (Temple U). + +**Maintainers:** Yusuke Miyazaki and Wataru Shinoda (Okayama U). **Supporting info:** @@ -386,6 +388,7 @@ simulation of biological or soft material systems. * :doc:`angle_style spica ` * examples/PACKAGES/cgspica * https://www.lammps.org/pictures.html#cg +* https://www.spica-ff.org/ ---------- diff --git a/doc/src/pair_spica.rst b/doc/src/pair_spica.rst index 9bd6ee069c..eac44ad0f2 100644 --- a/doc/src/pair_spica.rst +++ b/doc/src/pair_spica.rst @@ -82,6 +82,7 @@ given by as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in :ref:`(Shinoda) `, :ref:`(DeVane) `, :ref:`(Seo) `, and :ref:`(Miyazaki) `. Rc is the cutoff. +Summary information on these force fields can be found at https://www.spica-ff.org Style *lj/spica/coul/long* computes the adds Coulombic interactions with an additional damping factor applied so it can be used in diff --git a/src/.gitignore b/src/.gitignore index 4c1cf49b3b..b783a07892 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -409,8 +409,8 @@ /angle_mm3.h /angle_quartic.cpp /angle_quartic.h -/angle_sdk.cpp -/angle_sdk.h +/angle_spica.cpp +/angle_spica.h /angle_table.cpp /angle_table.h /atom_vec_angle.cpp @@ -990,7 +990,7 @@ /improper_umbrella.h /interlayer_taper.h /kissfft.h -/lj_sdk_common.h +/lj_spica_common.h /math_complex.h /math_vector.h /message.cpp @@ -1218,12 +1218,12 @@ /pair_lj_long_tip4p_long.h /pair_lj_cut_tgpu.cpp /pair_lj_cut_tgpu.h -/pair_lj_sdk.cpp -/pair_lj_sdk.h -/pair_lj_sdk_coul_long.cpp -/pair_lj_sdk_coul_long.h -/pair_lj_sdk_coul_msm.cpp -/pair_lj_sdk_coul_msm.h +/pair_lj_spica.cpp +/pair_lj_spica.h +/pair_lj_spica_coul_long.cpp +/pair_lj_spica_coul_long.h +/pair_lj_spica_coul_msm.cpp +/pair_lj_spica_coul_msm.h /pair_lj_sf_dipole_sf.cpp /pair_lj_sf_dipole_sf.h /pair_lj_switch3_coulgauss_long.cpp diff --git a/src/CG-SPICA/README b/src/CG-SPICA/README index cbef4ef2c9..1ba2274e57 100644 --- a/src/CG-SPICA/README +++ b/src/CG-SPICA/README @@ -38,18 +38,15 @@ style, since the number of charged atom types is usually small. To exploit this property, the use of the kspace_style pppm/cg is recommended over regular pppm. -The person who created this package is Axel Kohlmeyer at Temple U -(akohlmey at gmail.com). Contact him directly if you have questions. - -The person who added a new function type (LJ12_5) to this package is -Yusuke Miyazaki at Okayama U (ymiyazaki93 at gmail.com). Contact him -if you have questions about his code. +Original Author: Axel Kohlmeyer (akohlmey at gmail.com) at Temple U . +Maintainers : Yusuke Miyazaki (ymiyazaki93 at gmail.com) and + Wataru Shinoda (shinoda at okayama-u.ac.jp) at Okayama U. +Contact them if you have questions about his code. --------------------------------- Thanks for contributions, support and testing goes to -Wataru Shinoda (Okayama University) Russell DeVane (Procter & Gamble) Michael L. Klein (Temple University, Philadelphia) Balasubramanian Sundaram (JNCASR, Bangalore) diff --git a/src/Purge.list b/src/Purge.list index a2fa9f1165..5b838be535 100644 --- a/src/Purge.list +++ b/src/Purge.list @@ -51,6 +51,30 @@ lmpinstalledpkgs.h lmpgitversion.h mliap_model_python_couple.cpp mliap_model_python_couple.h +# renamed on 11 July 2022 +lj_sdk_common.h +angle_sdk.cpp +pair_lj_sdk.cpp +pair_lj_sdk_coul_msm.cpp +pair_lj_sdk_coul_long.h +pair_lj_sdk_coul_msm.h +angle_sdk.h +pair_lj_sdk.h +pair_lj_sdk_coul_long.cpp +pair_lj_sdk_kokkos.h +pair_lj_sdk_kokkos.cpp +pair_lj_sdk_gpu.cpp +pair_lj_sdk_gpu.h +pair_lj_sdk_coul_long_gpu.cpp +pair_lj_sdk_coul_long_gpu.h +pair_lj_sdk_omp.h +pair_lj_sdk_coul_msm_omp.cpp +pair_lj_sdk_coul_long_omp.h +angle_sdk_omp.cpp +pair_lj_sdk_omp.cpp +pair_lj_sdk_coul_msm_omp.h +pair_lj_sdk_coul_long_omp.cpp +angle_sdk_omp.h # removed on 8 April 2022 fix_client_md.cpp fix_client_md.h From 35afe94ec1a13231b695adece214d1500da9f00d Mon Sep 17 00:00:00 2001 From: yskmiyazaki Date: Mon, 11 Jul 2022 11:52:45 +0900 Subject: [PATCH 26/72] fixed a line in CG-SPICA/README --- src/CG-SPICA/README | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/CG-SPICA/README b/src/CG-SPICA/README index 1ba2274e57..50f56ce5e8 100644 --- a/src/CG-SPICA/README +++ b/src/CG-SPICA/README @@ -41,7 +41,7 @@ recommended over regular pppm. Original Author: Axel Kohlmeyer (akohlmey at gmail.com) at Temple U . Maintainers : Yusuke Miyazaki (ymiyazaki93 at gmail.com) and Wataru Shinoda (shinoda at okayama-u.ac.jp) at Okayama U. -Contact them if you have questions about his code. +Contact them if you have questions. --------------------------------- From b55cf30cb85ac0e7320d7a5e4ac51f1bf074b51d Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Wed, 13 Jul 2022 11:39:30 -0400 Subject: [PATCH 27/72] Update Errors_messages.rst --- doc/src/Errors_messages.rst | 118 ++++++++++++++++++------------------ 1 file changed, 59 insertions(+), 59 deletions(-) diff --git a/doc/src/Errors_messages.rst b/doc/src/Errors_messages.rst index 4e216828d3..4f4cda32e5 100644 --- a/doc/src/Errors_messages.rst +++ b/doc/src/Errors_messages.rst @@ -476,65 +476,6 @@ Doc page with :doc:`WARNING messages ` *Bonds defined but no bond types* The data file header lists bonds but no bond types. -*Bond/react: Cannot use fix bond/react with non-molecular systems* - Only systems with bonds that can be changed can be used. Atom_style - template does not qualify. - -*Bond/react: Invalid template atom ID in map file* - Atom IDs in molecule templates range from 1 to the number of atoms in the template. - -*Bond/react: Rmax cutoff is longer than pairwise cutoff* - This is not allowed because bond creation is done using the pairwise - neighbor list. - -*Bond/react: Molecule template ID for fix bond/react does not exist* - A valid molecule template must have been created with the molecule - command. - -*Bond/react: Reaction templates must contain the same number of atoms* - There should be a one-to-one correspondence between atoms in the - pre-reacted and post-reacted templates, as specified by the map file. - -*Bond/react: Unknown section in map file* - Please ensure reaction map files are properly formatted. - -*Bond/react: Atom/Bond type affected by reaction too close to template edge* - This means an atom which changes type or connectivity during the - reaction is too close to an 'edge' atom defined in the map - file. This could cause incorrect assignment of bonds, angle, etc. - Generally, this means you must include more atoms in your templates, - such that there are at least two atoms between each atom involved in - the reaction and an edge atom. - -*Bond/react: Fix bond/react needs ghost atoms from farther away* - This is because a processor needs to map the entire unreacted - molecule template onto simulation atoms it knows about. The - comm_modify cutoff command can be used to extend the communication - range. - -*Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted* - Self-explanatory. - -*Bond/react: First neighbors of chiral atoms must be of mutually different types* - Self-explanatory. - -*Bond/react: Chiral atoms must have exactly four first neighbors* - Self-explanatory. - -*Bond/react: Molecule template 'Coords' section required for chiralIDs keyword* - The coordinates of atoms in the pre-reacted template are used to determine - chirality. - -*Bond/react special bond generation overflow* - The number of special bonds per-atom created by a reaction exceeds the - system setting. See the read_data or create_box command for how to - specify this value. - -*Bond/react topology/atom exceed system topology/atom* - The number of bonds, angles etc per-atom created by a reaction exceeds - the system setting. See the read_data or create_box command for how to - specify this value. - *Both restart files must use % or neither* Self-explanatory. @@ -3521,6 +3462,65 @@ Doc page with :doc:`WARNING messages ` acquire needed info, The comm_modify cutoff command can be used to extend the communication range. +*Fix bond/react: Cannot use fix bond/react with non-molecular systems* + Only systems with bonds that can be changed can be used. Atom_style + template does not qualify. + +*Fix bond/react: Invalid template atom ID in map file* + Atom IDs in molecule templates range from 1 to the number of atoms in the template. + +*Fix bond/react: Rmax cutoff is longer than pairwise cutoff* + This is not allowed because bond creation is done using the pairwise + neighbor list. + +*Fix bond/react: Molecule template ID for fix bond/react does not exist* + A valid molecule template must have been created with the molecule + command. + +*Fix bond/react: Reaction templates must contain the same number of atoms* + There should be a one-to-one correspondence between atoms in the + pre-reacted and post-reacted templates, as specified by the map file. + +*Fix bond/react: Unknown section in map file* + Please ensure reaction map files are properly formatted. + +*Fix bond/react: Atom/Bond type affected by reaction too close to template edge* + This means an atom which changes type or connectivity during the + reaction is too close to an 'edge' atom defined in the map + file. This could cause incorrect assignment of bonds, angle, etc. + Generally, this means you must include more atoms in your templates, + such that there are at least two atoms between each atom involved in + the reaction and an edge atom. + +*Fix bond/react: Fix bond/react needs ghost atoms from farther away* + This is because a processor needs to map the entire unreacted + molecule template onto simulation atoms it knows about. The + comm_modify cutoff command can be used to extend the communication + range. + +*Fix bond/react: A deleted atom cannot remain bonded to an atom that is not deleted* + Self-explanatory. + +*Fix bond/react: First neighbors of chiral atoms must be of mutually different types* + Self-explanatory. + +*Fix bond/react: Chiral atoms must have exactly four first neighbors* + Self-explanatory. + +*Fix bond/react: Molecule template 'Coords' section required for chiralIDs keyword* + The coordinates of atoms in the pre-reacted template are used to determine + chirality. + +*Fix bond/react special bond generation overflow* + The number of special bonds per-atom created by a reaction exceeds the + system setting. See the read_data or create_box command for how to + specify this value. + +*Fix bond/react topology/atom exceed system topology/atom* + The number of bonds, angles etc per-atom created by a reaction exceeds + the system setting. See the read_data or create_box command for how to + specify this value. + *Fix bond/swap cannot use dihedral or improper styles* These styles cannot be defined when using this fix. From e41976e17efd689496174125329dc40f3641f8e0 Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Wed, 13 Jul 2022 11:51:50 -0400 Subject: [PATCH 28/72] Update Errors_warnings.rst --- doc/src/Errors_warnings.rst | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst index ab06ac523c..f488eaaa88 100644 --- a/doc/src/Errors_warnings.rst +++ b/doc/src/Errors_warnings.rst @@ -68,14 +68,6 @@ Doc page with :doc:`ERROR messages ` length, multiplying by the number of bonds in the interaction (e.g. 3 for a dihedral) and adding a small amount of stretch. -*Bond/react: Atom affected by reaction too close to template edge* - This means an atom which changes type or connectivity during the - reaction is too close to an 'edge' atom defined in the superimpose - file. This could cause incorrect assignment of bonds, angle, etc. - Generally, this means you must include more atoms in your templates, - such that there are at least two atoms between each atom involved in - the reaction and an edge atom. - *Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero* Self-explanatory. @@ -206,12 +198,20 @@ Doc page with :doc:`ERROR messages ` *Fix SRD walls overlap but fix srd overlap not set* You likely want to set this in your input script. -* Fix bond/create is used multiple times or with fix bond/break - may not work as expected* +*Fix bond/create is used multiple times or with fix bond/break - may not work as expected* When using fix bond/create multiple times or in combination with fix bond/break, the individual fix instances do not share information about changes they made at the same time step and thus it may result in unexpected behavior. +*Fix bond/react: Atom affected by reaction too close to template edge* + This means an atom which changes type or connectivity during the + reaction is too close to an 'edge' atom defined in the superimpose + file. This could cause incorrect assignment of bonds, angle, etc. + Generally, this means you must include more atoms in your templates, + such that there are at least two atoms between each atom involved in + the reaction and an edge atom. + *Fix bond/swap will ignore defined angles* See the page for fix bond/swap for more info on this restriction. @@ -810,4 +810,3 @@ This will most likely cause errors in kinetic fluctuations. *Using pair tail corrections with pair_modify compute no* The tail corrections will thus not be computed. - From df2e16cc2307620f0e645fdd4c342837e05931f8 Mon Sep 17 00:00:00 2001 From: AkosSeres Date: Thu, 14 Jul 2022 16:57:19 +0200 Subject: [PATCH 29/72] Fix bug in vtk dump --- src/VTK/dump_vtk.cpp | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/src/VTK/dump_vtk.cpp b/src/VTK/dump_vtk.cpp index 51c6632b78..57de0ac0de 100644 --- a/src/VTK/dump_vtk.cpp +++ b/src/VTK/dump_vtk.cpp @@ -334,13 +334,15 @@ int DumpVTK::count() // un-choose if not in region - auto region = domain->get_region_by_id(idregion); - if (region) { - region->prematch(); - double **x = atom->x; - for (i = 0; i < nlocal; i++) - if (choose[i] && region->match(x[i][0],x[i][1],x[i][2]) == 0) - choose[i] = 0; + if(idregion != nullptr){ + auto region = domain->get_region_by_id(idregion); + if (region) { + region->prematch(); + double **x = atom->x; + for (i = 0; i < nlocal; i++) + if (choose[i] && region->match(x[i][0],x[i][1],x[i][2]) == 0) + choose[i] = 0; + } } // un-choose if any threshold criterion isn't met From 5b0313f758137bd8112335b4e16bc4df89771a71 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 14 Jul 2022 19:13:49 -0400 Subject: [PATCH 30/72] cosmetic --- src/VTK/dump_vtk.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/VTK/dump_vtk.cpp b/src/VTK/dump_vtk.cpp index 57de0ac0de..f346badfb5 100644 --- a/src/VTK/dump_vtk.cpp +++ b/src/VTK/dump_vtk.cpp @@ -334,7 +334,7 @@ int DumpVTK::count() // un-choose if not in region - if(idregion != nullptr){ + if (idregion) { auto region = domain->get_region_by_id(idregion); if (region) { region->prematch(); From 4c7825e5c7ad29dec09a5de51064ed5ea1d6d9bc Mon Sep 17 00:00:00 2001 From: jtclemm Date: Fri, 15 Jul 2022 09:20:07 -0600 Subject: [PATCH 31/72] Inverting if statements --- src/GRANULAR/compute_contact_atom.cpp | 49 +++++++++++++-------------- 1 file changed, 24 insertions(+), 25 deletions(-) diff --git a/src/GRANULAR/compute_contact_atom.cpp b/src/GRANULAR/compute_contact_atom.cpp index a502630fd4..91511f57ec 100644 --- a/src/GRANULAR/compute_contact_atom.cpp +++ b/src/GRANULAR/compute_contact_atom.cpp @@ -133,34 +133,33 @@ void ComputeContactAtom::compute_peratom() i = ilist[ii]; // Only proceed if i is either part of the compute group or will contribute to contacts - if ((mask[i] & groupbit) || (mask[i] & jgroupbit)) { - xtmp = x[i][0]; - ytmp = x[i][1]; - ztmp = x[i][2]; - radi = radius[i]; - jlist = firstneigh[i]; - jnum = numneigh[i]; + if (! (mask[i] & groupbit) && ! (mask[i] & jgroupbit)) continue; - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - j &= NEIGHMASK; + xtmp = x[i][0]; + ytmp = x[i][1]; + ztmp = x[i][2]; + radi = radius[i]; + jlist = firstneigh[i]; + jnum = numneigh[i]; - // Only tally for atoms in compute group (groupbit) if neighbor is in group2 (jgroupbit) - update_i_flag = (mask[i] & groupbit) && (mask[j] & jgroupbit); - update_j_flag = (mask[j] & groupbit) && (mask[i] & jgroupbit); + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + j &= NEIGHMASK; - if (update_i_flag || update_j_flag) { - delx = xtmp - x[j][0]; - dely = ytmp - x[j][1]; - delz = ztmp - x[j][2]; - rsq = delx * delx + dely * dely + delz * delz; - radsum = radi + radius[j]; - radsumsq = radsum * radsum; - if (rsq <= radsumsq) { - if (update_i_flag) contact[i] += 1.0; - if (update_j_flag) contact[j] += 1.0; - } - } + // Only tally for atoms in compute group (groupbit) if neighbor is in group2 (jgroupbit) + update_i_flag = (mask[i] & groupbit) && (mask[j] & jgroupbit); + update_j_flag = (mask[j] & groupbit) && (mask[i] & jgroupbit); + if (! update_i_flag && ! update_j_flag) continue; + + delx = xtmp - x[j][0]; + dely = ytmp - x[j][1]; + delz = ztmp - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + radsum = radi + radius[j]; + radsumsq = radsum * radsum; + if (rsq <= radsumsq) { + if (update_i_flag) contact[i] += 1.0; + if (update_j_flag) contact[j] += 1.0; } } } From d05c4b529aae5550bd7a426eeed9a3ba3ae63981 Mon Sep 17 00:00:00 2001 From: Taylor Barnes Date: Fri, 15 Jul 2022 15:22:07 +0000 Subject: [PATCH 32/72] Add natoms check to mdi/qm fix --- src/MDI/fix_mdi_qm.cpp | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/src/MDI/fix_mdi_qm.cpp b/src/MDI/fix_mdi_qm.cpp index bc2a3843ce..62b71cd5f6 100644 --- a/src/MDI/fix_mdi_qm.cpp +++ b/src/MDI/fix_mdi_qm.cpp @@ -246,11 +246,22 @@ void FixMDIQM::init() int ierr = MDI_Check_command_exists("@DEFAULT", ">NATOMS", mdicomm, &natoms_exists); if (ierr) error->all(FLERR, "MDI: >NATOMS command check"); if ( natoms_exists ) { + ierr = MDI_Send_command(">NATOMS", mdicomm); if (ierr) error->all(FLERR, "MDI: >NATOMS command"); int n = static_cast (atom->natoms); ierr = MDI_Send(&n, 1, MDI_INT, mdicomm); if (ierr) error->all(FLERR, "MDI: >NATOMS data"); + + } else { // confirm that the engine's NATOMS is correct + + ierr = MDI_Send_command("all(FLERR, "MDI: all(FLERR, "MDI: natoms ) error->all(FLERR, "MDI: Engine has the wrong number of atoms, and does not support the >NATOMS command."); + } int elements_exists; @@ -369,6 +380,9 @@ void FixMDIQM::post_force(int vflag) if (ierr) error->all(FLERR, "MDI: all(FLERR, "MDI: Date: Fri, 15 Jul 2022 12:16:15 -0400 Subject: [PATCH 33/72] whitespace --- doc/src/pair_spica.rst | 10 +++++----- src/CG-SPICA/README | 6 +++--- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/doc/src/pair_spica.rst b/doc/src/pair_spica.rst index eac44ad0f2..74a069d8a2 100644 --- a/doc/src/pair_spica.rst +++ b/doc/src/pair_spica.rst @@ -71,7 +71,7 @@ given by E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^4 \right] \qquad r < r_c \\ - E = & \frac{12}{7}\left(\frac{12}{5}\right)^{\left(\frac{5}{7}\right)} \epsilon + E = & \frac{12}{7}\left(\frac{12}{5}\right)^{\left(\frac{5}{7}\right)} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^5 \right] \qquad r < r_c \\ @@ -79,8 +79,8 @@ given by \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c -as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in -:ref:`(Shinoda) `, :ref:`(DeVane) `, :ref:`(Seo) `, and :ref:`(Miyazaki) `. +as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in +:ref:`(Shinoda) `, :ref:`(DeVane) `, :ref:`(Seo) `, and :ref:`(Miyazaki) `. Rc is the cutoff. Summary information on these force fields can be found at https://www.spica-ff.org @@ -119,8 +119,8 @@ specified since a Coulombic cutoff cannot be specified for an individual I,J type pair. All type pairs use the same global Coulombic cutoff specified in the pair_style command. -The original implementation of the above styles are -style *lj/sdk*, *lj/sdk/coul/long*, and *lj/sdk/coul/msm*, +The original implementation of the above styles are +style *lj/sdk*, *lj/sdk/coul/long*, and *lj/sdk/coul/msm*, and available for backward compatibility. ---------- diff --git a/src/CG-SPICA/README b/src/CG-SPICA/README index 50f56ce5e8..8a84a735a8 100644 --- a/src/CG-SPICA/README +++ b/src/CG-SPICA/README @@ -38,9 +38,9 @@ style, since the number of charged atom types is usually small. To exploit this property, the use of the kspace_style pppm/cg is recommended over regular pppm. -Original Author: Axel Kohlmeyer (akohlmey at gmail.com) at Temple U . -Maintainers : Yusuke Miyazaki (ymiyazaki93 at gmail.com) and - Wataru Shinoda (shinoda at okayama-u.ac.jp) at Okayama U. +Original Author: Axel Kohlmeyer (akohlmey at gmail.com) at Temple U . +Maintainers : Yusuke Miyazaki (ymiyazaki93 at gmail.com) and + Wataru Shinoda (shinoda at okayama-u.ac.jp) at Okayama U. Contact them if you have questions. --------------------------------- From 8b1734d4c3db10aab43e41576c4bdc834aba1fc5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 15 Jul 2022 12:18:15 -0400 Subject: [PATCH 34/72] whitespace --- src/GRANULAR/compute_contact_atom.h | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/GRANULAR/compute_contact_atom.h b/src/GRANULAR/compute_contact_atom.h index 04157b5455..5262c1b29b 100644 --- a/src/GRANULAR/compute_contact_atom.h +++ b/src/GRANULAR/compute_contact_atom.h @@ -37,10 +37,10 @@ class ComputeContactAtom : public Compute { private: int nmax; - + char *group2; - int jgroup, jgroupbit; - + int jgroup, jgroupbit; + class NeighList *list; double *contact; }; From 2f3115372d4970a853bae2bb602bd8feb536782d Mon Sep 17 00:00:00 2001 From: Taylor Barnes Date: Fri, 15 Jul 2022 20:00:44 +0000 Subject: [PATCH 35/72] Remove debug lines from fix_mdi_qm.cpp --- src/MDI/fix_mdi_qm.cpp | 3 --- 1 file changed, 3 deletions(-) diff --git a/src/MDI/fix_mdi_qm.cpp b/src/MDI/fix_mdi_qm.cpp index 62b71cd5f6..12bd6938aa 100644 --- a/src/MDI/fix_mdi_qm.cpp +++ b/src/MDI/fix_mdi_qm.cpp @@ -380,9 +380,6 @@ void FixMDIQM::post_force(int vflag) if (ierr) error->all(FLERR, "MDI: all(FLERR, "MDI: Date: Fri, 15 Jul 2022 14:47:45 -0600 Subject: [PATCH 36/72] add a table with list of dump styles --- doc/src/Commands_all.rst | 1 + doc/src/Commands_bond.rst | 1 + doc/src/Commands_compute.rst | 1 + doc/src/Commands_dump.rst | 56 ++++++++++++++++++++++++++++++++++++ doc/src/Commands_fix.rst | 1 + doc/src/Commands_kspace.rst | 1 + doc/src/Commands_pair.rst | 1 + 7 files changed, 62 insertions(+) create mode 100644 doc/src/Commands_dump.rst diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst index a868ad84fc..5e309c3ed0 100644 --- a/doc/src/Commands_all.rst +++ b/doc/src/Commands_all.rst @@ -10,6 +10,7 @@ * :ref:`Dihedral styles ` * :ref:`Improper styles ` * :doc:`KSpace styles ` + * :doc:`Dump styles ` General commands ================ diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst index dcedbb72b4..e230426ab9 100644 --- a/doc/src/Commands_bond.rst +++ b/doc/src/Commands_bond.rst @@ -10,6 +10,7 @@ * :ref:`Dihedral styles ` * :ref:`Improper styles ` * :doc:`KSpace styles ` + * :doc:`Dump styles ` .. _bond: diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst index bb0c3e9c2a..682a75f201 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -10,6 +10,7 @@ * :ref:`Dihedral styles ` * :ref:`Improper styles ` * :doc:`KSpace styles ` + * :doc:`Dump styles ` Compute commands ================ diff --git a/doc/src/Commands_dump.rst b/doc/src/Commands_dump.rst new file mode 100644 index 0000000000..2867a2194d --- /dev/null +++ b/doc/src/Commands_dump.rst @@ -0,0 +1,56 @@ +.. table_from_list:: + :columns: 3 + + * :doc:`General commands ` + * :doc:`Fix styles ` + * :doc:`Compute styles ` + * :doc:`Pair styles ` + * :ref:`Bond styles ` + * :ref:`Angle styles ` + * :ref:`Dihedral styles ` + * :ref:`Improper styles ` + * :doc:`KSpace styles ` + * :doc:`Dump styles ` + +Dump commands +============= + +An alphabetic list of all LAMMPS :doc:`dump ` commands. + +.. table_from_list:: + :columns: 5 + + * :doc:`atom ` + * :doc:`atom/adios ` + * :doc:`atom/gz ` + * :doc:`atom/mpiio ` + * :doc:`atom/zstd ` + * :doc:`cfg ` + * :doc:`cfg/gz ` + * :doc:`cfg/mpiio ` + * :doc:`cfg/uef ` + * :doc:`cfg/zstd ` + * :doc:`custom ` + * :doc:`custom/adios ` + * :doc:`custom/gz ` + * :doc:`custom/mpiio ` + * :doc:`custom/zstd ` + * :doc:`dcd ` + * :doc:`deprecated ` + * :doc:`h5md ` + * :doc:`image ` + * :doc:`local ` + * :doc:`local/gz ` + * :doc:`local/zstd ` + * :doc:`molfile ` + * :doc:`movie ` + * :doc:`netcdf ` + * :doc:`netcdf/mpiio ` + * :doc:`vtk ` + * :doc:`xtc ` + * :doc:`xyz ` + * :doc:`xyz/gz ` + * :doc:`xyz/mpiio ` + * :doc:`xyz/zstd ` + * :doc:`yaml ` + diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index 4e40523c44..cb61cbe17b 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -10,6 +10,7 @@ * :ref:`Dihedral styles ` * :ref:`Improper styles ` * :doc:`KSpace styles ` + * :doc:`Dump styles ` Fix commands ============ diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst index 0f64338415..088789e321 100644 --- a/doc/src/Commands_kspace.rst +++ b/doc/src/Commands_kspace.rst @@ -10,6 +10,7 @@ * :ref:`Dihedral styles ` * :ref:`Improper styles ` * :doc:`KSpace styles ` + * :doc:`Dump styles ` KSpace solvers ============== diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index f9ddecc590..7f14132c9b 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -10,6 +10,7 @@ * :ref:`Dihedral styles ` * :ref:`Improper styles ` * :doc:`KSpace styles ` + * :doc:`Dump styles ` Pair_style potentials ====================== From c8ca8fb2d60165444f3ffb3e0429e01007ac711f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 15 Jul 2022 17:51:36 -0400 Subject: [PATCH 37/72] properly integrate the new file into the document toctree --- doc/src/Commands.rst | 1 + doc/src/Commands_dump.rst | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/doc/src/Commands.rst b/doc/src/Commands.rst index 72a98159ff..32920b75fb 100644 --- a/doc/src/Commands.rst +++ b/doc/src/Commands.rst @@ -21,6 +21,7 @@ commands in it are used to define a LAMMPS simulation. Commands_pair Commands_bond Commands_kspace + Commands_dump .. toctree:: :maxdepth: 1 diff --git a/doc/src/Commands_dump.rst b/doc/src/Commands_dump.rst index 2867a2194d..12dd7b2321 100644 --- a/doc/src/Commands_dump.rst +++ b/doc/src/Commands_dump.rst @@ -15,7 +15,7 @@ Dump commands ============= -An alphabetic list of all LAMMPS :doc:`dump ` commands. +An alphabetic list of all LAMMPS :doc:`dump ` commands. .. table_from_list:: :columns: 5 From 698d3b06a58b596c2da7c76ffaad911b66377558 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 15 Jul 2022 21:23:08 -0400 Subject: [PATCH 38/72] update style checker script to also check dump styles --- doc/utils/check-styles.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py index 47d3dd5e3b..82de537863 100755 --- a/doc/utils/check-styles.py +++ b/doc/utils/check-styles.py @@ -60,7 +60,7 @@ reader = {} region = {} total = 0 -index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style)\s+([a-zA-Z0-9/_]+)$") +index_pattern = re.compile(r"^.. index:: (compute|fix|pair_style|angle_style|bond_style|dihedral_style|improper_style|kspace_style|dump)\s+([a-zA-Z0-9/_]+)$") style_pattern = re.compile(r"(.+)Style\((.+),(.+)\)") upper = re.compile("[A-Z]+") gpu = re.compile("(.+)/gpu$") @@ -84,7 +84,8 @@ def load_index_entries_in_file(path): def load_index_entries(): index = {'compute': set(), 'fix': set(), 'pair_style': set(), 'angle_style': set(), - 'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(), 'kspace_style': set()} + 'bond_style': set(), 'dihedral_style': set(), 'improper_style': set(), + 'kspace_style': set(), 'dump': set()} rst_files = glob(os.path.join(doc_dir, '*.rst')) for f in rst_files: for command_type, style in load_index_entries_in_file(f): @@ -277,6 +278,7 @@ counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) ` counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) `",improper,'Improper',suffix=True) counter += check_style('improper_style.rst', doc_dir, ":doc:`(.+) ` -",improper,'Improper',suffix=False) counter += check_style('Commands_kspace.rst', doc_dir, ":doc:`(.+) `",kspace,'KSpace',suffix=True) +counter += check_style('Commands_dump.rst', doc_dir, ":doc:`(.+) `",dump,'Dump',suffix=True) if counter: print(f"Found {counter} issue(s) with style lists") @@ -290,6 +292,7 @@ counter += check_style_index("bond_style", bond, index["bond_style"]) counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"]) counter += check_style_index("improper_style", improper, index["improper_style"]) counter += check_style_index("kspace_style", kspace, index["kspace_style"]) +counter += check_style_index("dump", dump, index["dump"]) counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm']) if counter: From b28f8bc70ea0939e5be46d6df5e2f105a287ea2d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 15 Jul 2022 21:23:26 -0400 Subject: [PATCH 39/72] add missing index entries for dump style --- doc/src/dump.rst | 22 ++++++++++++++++++++++ doc/src/dump_image.rst | 1 + doc/src/dump_netcdf.rst | 1 + 3 files changed, 24 insertions(+) diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 843d2e4883..fb291a2bc3 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -1,4 +1,26 @@ .. index:: dump +.. index:: dump atom +.. index:: dump cfg +.. index:: dump custom +.. index:: dump dcd +.. index:: dump local +.. index:: dump xtc +.. index:: dump yaml +.. index:: dump xyz +.. index:: dump atom/gz +.. index:: dump cfg/gz +.. index:: dump custom/gz +.. index:: dump local/gz +.. index:: dump xyz/gz +.. index:: dump atom/mpiio +.. index:: dump cfg/mpiio +.. index:: dump custom/mpiio +.. index:: dump xyz/mpiio +.. index:: dump atom/zstd +.. index:: dump cfg/zstd +.. index:: dump custom/zstd +.. index:: dump xyz/zstd +.. index:: dump local/zstd dump command ============ diff --git a/doc/src/dump_image.rst b/doc/src/dump_image.rst index 0aeab34f60..9b16a7c133 100644 --- a/doc/src/dump_image.rst +++ b/doc/src/dump_image.rst @@ -1,4 +1,5 @@ .. index:: dump image +.. index:: dump movie dump image command ================== diff --git a/doc/src/dump_netcdf.rst b/doc/src/dump_netcdf.rst index d53a0a3b12..04790f4986 100644 --- a/doc/src/dump_netcdf.rst +++ b/doc/src/dump_netcdf.rst @@ -1,4 +1,5 @@ .. index:: dump netcdf +.. index:: dump netcdf/mpiio dump netcdf command =================== From db9731bf3bb3c1e8997f20f5507ccaac36e92c6b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 15 Jul 2022 22:58:49 -0400 Subject: [PATCH 40/72] also index dump styles --- doc/src/Manual.rst | 1 + doc/src/dumps.rst | 8 ++++++++ 2 files changed, 9 insertions(+) create mode 100644 doc/src/dumps.rst diff --git a/doc/src/Manual.rst b/doc/src/Manual.rst index 3d7c7ad8dd..962810181f 100644 --- a/doc/src/Manual.rst +++ b/doc/src/Manual.rst @@ -110,6 +110,7 @@ Command Reference angles dihedrals impropers + dumps fix_modify_atc_commands Bibliography diff --git a/doc/src/dumps.rst b/doc/src/dumps.rst new file mode 100644 index 0000000000..4a8f387338 --- /dev/null +++ b/doc/src/dumps.rst @@ -0,0 +1,8 @@ +Dump Styles +############### + +.. toctree:: + :maxdepth: 1 + :glob: + + dump* From a829d607ce87a78eac5c6fca7f466f28a725be9e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 12 Jul 2022 00:38:20 -0400 Subject: [PATCH 41/72] work around issues with Intel compilers compiling the GPU package --- src/GPU/fix_gpu.cpp | 2 +- src/GPU/fix_nh_gpu.cpp | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/GPU/fix_gpu.cpp b/src/GPU/fix_gpu.cpp index 85b4f8e0e9..3ca57133a9 100644 --- a/src/GPU/fix_gpu.cpp +++ b/src/GPU/fix_gpu.cpp @@ -275,7 +275,7 @@ void FixGPU::init() // also disallow GPU neighbor lists for hybrid styles if (force->pair_match("^hybrid",0) != nullptr) { - auto hybrid = dynamic_cast( force->pair); + auto hybrid = dynamic_cast(force->pair); for (int i = 0; i < hybrid->nstyles; i++) if (!utils::strmatch(hybrid->keywords[i],"/gpu$")) force->pair->no_virial_fdotr_compute = 1; diff --git a/src/GPU/fix_nh_gpu.cpp b/src/GPU/fix_nh_gpu.cpp index e90be98d6b..53999fe52c 100644 --- a/src/GPU/fix_nh_gpu.cpp +++ b/src/GPU/fix_nh_gpu.cpp @@ -77,7 +77,7 @@ void FixNHGPU::remap() double oldlo,oldhi; double expfac; - auto * _noalias const x = (dbl3_t *) atom->x[0]; + dbl3_t * _noalias const x = (dbl3_t *) atom->x[0]; int *mask = atom->mask; int nlocal = atom->nlocal; double *h = domain->h; @@ -414,7 +414,7 @@ void FixNHGPU::nh_v_press() return; } - auto * _noalias const v = (dbl3_t *)atom->v[0]; + dbl3_t * _noalias const v = (dbl3_t *)atom->v[0]; int *mask = atom->mask; int nlocal = atom->nlocal; if (igroup == atom->firstgroup) nlocal = atom->nfirst; From 9e1685211b1f3c6295758d7f413b14b8c801c7b3 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 15 Jul 2022 05:39:17 -0400 Subject: [PATCH 42/72] allow ramp(x,y) to be used in between runs (returning x) and avoid division by zero on run 0 --- doc/src/variable.rst | 4 +++- src/variable.cpp | 37 +++++++++++++++++++++++++------------ 2 files changed, 28 insertions(+), 13 deletions(-) diff --git a/doc/src/variable.rst b/doc/src/variable.rst index 9f76f78f45..ceaa4d7245 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -685,7 +685,9 @@ of a run, according to this formula: The run begins on startstep and ends on stopstep. Startstep and stopstep can span multiple runs, using the *start* and *stop* keywords of the :doc:`run ` command. See the :doc:`run ` command for -details of how to do this. +details of how to do this. If called in between runs or during a +:doc:`run 0 ` command, the ramp(x,y) function will return the +value of x. The stagger(x,y) function uses the current timestep to generate a new timestep. X,y > 0 and x > y are required. The generated timesteps diff --git a/src/variable.cpp b/src/variable.cpp index 878066f466..574aa26c86 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -2561,9 +2561,14 @@ double Variable::collapse_tree(Tree *tree) arg2 = collapse_tree(tree->second); if (tree->first->type != VALUE || tree->second->type != VALUE) return 0.0; tree->type = VALUE; - double delta = update->ntimestep - update->beginstep; - if (delta != 0.0) delta /= update->endstep - update->beginstep; - tree->value = arg1 + delta*(arg2-arg1); + if (update->whichflag == 0) { + tree->value = arg1; + } else { + double delta = update->ntimestep - update->beginstep; + if ((delta != 0.0) && (update->beginstep != update->endstep)) + delta /= update->endstep - update->beginstep; + tree->value = arg1 + delta*(arg2-arg1); + } return tree->value; } @@ -2935,9 +2940,14 @@ double Variable::eval_tree(Tree *tree, int i) if (tree->type == RAMP) { arg1 = eval_tree(tree->first,i); arg2 = eval_tree(tree->second,i); - double delta = update->ntimestep - update->beginstep; - if (delta != 0.0) delta /= update->endstep - update->beginstep; - arg = arg1 + delta*(arg2-arg1); + if (update->whichflag == 0) { + arg = arg1; + } else { + double delta = update->ntimestep - update->beginstep; + if ((delta != 0.0) && (update->beginstep != update->endstep)) + delta /= update->endstep - update->beginstep; + arg = arg1 + delta*(arg2-arg1); + } return arg; } @@ -3445,14 +3455,17 @@ int Variable::math_function(char *word, char *contents, Tree **tree, Tree **tree } else if (strcmp(word,"ramp") == 0) { if (narg != 2) print_var_error(FLERR,"Invalid math function in variable formula",ivar); - if (update->whichflag == 0) - print_var_error(FLERR,"Cannot use ramp in variable formula between runs",ivar); if (tree) newtree->type = RAMP; else { - double delta = update->ntimestep - update->beginstep; - if (delta != 0.0) delta /= update->endstep - update->beginstep; - double value = value1 + delta*(value2-value1); - argstack[nargstack++] = value; + if (update->whichflag == 0) { + argstack[nargstack++] = value1; + } else { + double delta = update->ntimestep - update->beginstep; + if ((delta != 0.0) && (update->beginstep != update->endstep)) + delta /= update->endstep - update->beginstep; + double value = value1 + delta*(value2-value1); + argstack[nargstack++] = value; + } } } else if (strcmp(word,"stagger") == 0) { From 51e3428286f14b78d8b3ffcae2ada276e4116718 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 15 Jul 2022 17:52:10 -0400 Subject: [PATCH 43/72] add false positive --- doc/utils/sphinx-config/false_positives.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 7231c8a7e2..9f6edbec4c 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -3742,6 +3742,7 @@ wallstyle walltime Waltham Waroquier +Wataru wavepacket wB Wbody From d51069b3633dbe2106b6921010637c95f02d7ef0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 15 Jul 2022 19:05:56 -0400 Subject: [PATCH 44/72] fix cut-n-paste typo --- src/variable.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/variable.cpp b/src/variable.cpp index 574aa26c86..8b25b06f9c 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -3638,7 +3638,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree, Tree **tree print_var_error(FLERR,"Invalid math function in variable formula",ivar); if (update->whichflag == 0) print_var_error(FLERR,"Cannot use swiggle in variable formula between runs",ivar); - if (tree) newtree->type = CWIGGLE; + if (tree) newtree->type = SWIGGLE; else { if (values[0] == 0.0) print_var_error(FLERR,"Invalid math function in variable formula",ivar); From 34aca71258de53af3d9e40a422c4f22001a457f9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 15 Jul 2022 22:30:40 -0400 Subject: [PATCH 45/72] disallow use of variable functions vdisplace(), swiggle(), and cwiggle() with fix dt/reset --- doc/src/variable.rst | 14 ++++++++------ src/variable.cpp | 30 +++++++++++++++--------------- 2 files changed, 23 insertions(+), 21 deletions(-) diff --git a/doc/src/variable.rst b/doc/src/variable.rst index ceaa4d7245..d484e0a2dd 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -783,10 +783,11 @@ according to this formula: where dt = the timestep size. The run begins on startstep. Startstep can span multiple runs, using -the *start* keyword of the :doc:`run ` command. See the -:doc:`run ` command for details of how to do this. Note that the +the *start* keyword of the :doc:`run ` command. See the :doc:`run +` command for details of how to do this. Note that the :doc:`thermo_style ` keyword elaplong = -timestep-startstep. +timestep-startstep. This function may not be used in combination with +:doc:`fix dt/reset `. The swiggle(x,y,z) and cwiggle(x,y,z) functions each take 3 arguments: x = value0, y = amplitude, z = period. They use the elapsed time to @@ -801,10 +802,11 @@ run, according to one of these formulas, where omega = 2 PI / period: where dt = the timestep size. The run begins on startstep. Startstep can span multiple runs, using -the *start* keyword of the :doc:`run ` command. See the -:doc:`run ` command for details of how to do this. Note that the +the *start* keyword of the :doc:`run ` command. See the :doc:`run +` command for details of how to do this. Note that the :doc:`thermo_style ` keyword elaplong = -timestep-startstep. +timestep-startstep. These functions may not be used in combination with +:doc:`fix dt/reset `. ---------- diff --git a/src/variable.cpp b/src/variable.cpp index 8b25b06f9c..84ab0d69ae 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -2735,7 +2735,7 @@ double Variable::collapse_tree(Tree *tree) tree->extra[0]->type != VALUE) return 0.0; tree->type = VALUE; if (arg3 == 0.0) - error->one(FLERR,"Invalid math function in variable formula"); + error->one(FLERR,"Invalid swiggle(x,y,z) function in variable formula: z must be > 0"); double delta = update->ntimestep - update->beginstep; double omega = 2.0*MY_PI/arg3; tree->value = arg1 + arg2*sin(omega*delta*update->dt); @@ -2750,7 +2750,7 @@ double Variable::collapse_tree(Tree *tree) tree->extra[0]->type != VALUE) return 0.0; tree->type = VALUE; if (arg3 == 0.0) - error->one(FLERR,"Invalid math function in variable formula"); + error->one(FLERR,"Invalid cwiggle(x,y,z) function in variable formula: z must be > 0"); double delta = update->ntimestep - update->beginstep; double omega = 2.0*MY_PI/arg3; tree->value = arg1 + arg2*(1.0-cos(omega*delta*update->dt)); @@ -3064,7 +3064,7 @@ double Variable::eval_tree(Tree *tree, int i) arg2 = eval_tree(tree->second,i); arg3 = eval_tree(tree->extra[0],i); if (arg3 == 0.0) - error->one(FLERR,"Invalid math function in variable formula"); + error->one(FLERR,"Invalid swiggle(x,y,z) function in variable formula: z must be > 0"); double delta = update->ntimestep - update->beginstep; double omega = 2.0*MY_PI/arg3; arg = arg1 + arg2*sin(omega*delta*update->dt); @@ -3076,7 +3076,7 @@ double Variable::eval_tree(Tree *tree, int i) arg2 = eval_tree(tree->second,i); arg3 = eval_tree(tree->extra[0],i); if (arg3 == 0.0) - error->one(FLERR,"Invalid math function in variable formula"); + error->one(FLERR,"Invalid cwiggle(x,y,z) function in variable formula: z must be > 0"); double delta = update->ntimestep - update->beginstep; double omega = 2.0*MY_PI/arg3; arg = arg1 + arg2*(1.0-cos(omega*delta*update->dt)); @@ -3623,9 +3623,9 @@ int Variable::math_function(char *word, char *contents, Tree **tree, Tree **tree } else if (strcmp(word,"vdisplace") == 0) { if (narg != 2) - print_var_error(FLERR,"Invalid math function in variable formula",ivar); - if (update->whichflag == 0) - print_var_error(FLERR,"Cannot use vdisplace in variable formula between runs",ivar); + print_var_error(FLERR,"Invalid vdisplace function in variable formula: must have 2 arguments",ivar); + if (modify->get_fix_by_style("dt/reset").size() > 0) + print_var_error(FLERR,"Must not use vdisplace(x,y) function with fix dt/reset",ivar); if (tree) newtree->type = VDISPLACE; else { double delta = update->ntimestep - update->beginstep; @@ -3635,13 +3635,13 @@ int Variable::math_function(char *word, char *contents, Tree **tree, Tree **tree } else if (strcmp(word,"swiggle") == 0) { if (narg != 3) - print_var_error(FLERR,"Invalid math function in variable formula",ivar); - if (update->whichflag == 0) - print_var_error(FLERR,"Cannot use swiggle in variable formula between runs",ivar); + print_var_error(FLERR,"Invalid swiggle function in variable formula: must have 3 arguments",ivar); + if (modify->get_fix_by_style("dt/reset").size() > 0) + print_var_error(FLERR,"Must not use swiggle(x,y,z) function with fix dt/reset",ivar); if (tree) newtree->type = SWIGGLE; else { if (values[0] == 0.0) - print_var_error(FLERR,"Invalid math function in variable formula",ivar); + print_var_error(FLERR,"Invalid swiggle(x,y,z) function in variable formula: z must be > 0",ivar); double delta = update->ntimestep - update->beginstep; double omega = 2.0*MY_PI/values[0]; double value = value1 + value2*sin(omega*delta*update->dt); @@ -3650,13 +3650,13 @@ int Variable::math_function(char *word, char *contents, Tree **tree, Tree **tree } else if (strcmp(word,"cwiggle") == 0) { if (narg != 3) - print_var_error(FLERR,"Invalid math function in variable formula",ivar); - if (update->whichflag == 0) - print_var_error(FLERR,"Cannot use cwiggle in variable formula between runs",ivar); + print_var_error(FLERR,"Invalid cwiggle function in variable formula: must have 3 arguments",ivar); + if (modify->get_fix_by_style("dt/reset").size() > 0) + print_var_error(FLERR,"Must not use cwiggle(x,y,z) function with fix dt/reset",ivar); if (tree) newtree->type = CWIGGLE; else { if (values[0] == 0.0) - print_var_error(FLERR,"Invalid math function in variable formula",ivar); + print_var_error(FLERR,"Invalid cwiggle(x,y,z) function in variable formula: z must be > 0",ivar); double delta = update->ntimestep - update->beginstep; double omega = 2.0*MY_PI/values[0]; double value = value1 + value2*(1.0-cos(omega*delta*update->dt)); From 6689a20754f0b5818324282d6c10e5f5fb45ef92 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 16 Jul 2022 06:10:56 -0400 Subject: [PATCH 46/72] clarify --- doc/src/variable.rst | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 deletions(-) diff --git a/doc/src/variable.rst b/doc/src/variable.rst index d484e0a2dd..d5c05a205e 100644 --- a/doc/src/variable.rst +++ b/doc/src/variable.rst @@ -785,8 +785,11 @@ where dt = the timestep size. The run begins on startstep. Startstep can span multiple runs, using the *start* keyword of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. Note that the -:doc:`thermo_style ` keyword elaplong = -timestep-startstep. This function may not be used in combination with +:doc:`thermo_style ` keyword elaplong = timestep-startstep. +If used between runs this function will return +the value according to the end of the last run or the value of x if +used before *any* runs. This function assumes the length of the time +step does not change and thus may not be used in combination with :doc:`fix dt/reset `. The swiggle(x,y,z) and cwiggle(x,y,z) functions each take 3 arguments: @@ -804,8 +807,11 @@ where dt = the timestep size. The run begins on startstep. Startstep can span multiple runs, using the *start* keyword of the :doc:`run ` command. See the :doc:`run ` command for details of how to do this. Note that the -:doc:`thermo_style ` keyword elaplong = -timestep-startstep. These functions may not be used in combination with +:doc:`thermo_style ` keyword elaplong = timestep-startstep. +If used between runs these functions will return +the value according to the end of the last run or the value of x if +used before *any* runs. These functions assume the length of the time +step does not change and thus may not be used in combination with :doc:`fix dt/reset `. ---------- From e856bb23643cd9fa5cf04f5c3cd2c2cad574c931 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 16 Jul 2022 06:23:09 -0400 Subject: [PATCH 47/72] silence static code analysis warnings about integer overflows --- src/ML-SNAP/compute_grid.cpp | 6 +++--- src/ML-SNAP/compute_grid_local.cpp | 2 +- src/ML-SNAP/compute_sna_grid.cpp | 2 +- src/fix_store.cpp | 10 +++++----- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/src/ML-SNAP/compute_grid.cpp b/src/ML-SNAP/compute_grid.cpp index 7a5ffe1e24..bedd8a04f4 100644 --- a/src/ML-SNAP/compute_grid.cpp +++ b/src/ML-SNAP/compute_grid.cpp @@ -235,8 +235,8 @@ void ComputeGrid::set_grid_local() double ComputeGrid::memory_usage() { - double nbytes = size_array_rows * size_array_cols * sizeof(double); // grid - nbytes += size_array_rows * size_array_cols * sizeof(double); // gridall - nbytes += size_array_cols * ngridlocal * sizeof(double); // gridlocal + double nbytes = (double) size_array_rows * size_array_cols * sizeof(double); // grid + nbytes += (double) size_array_rows * size_array_cols * sizeof(double); // gridall + nbytes += (double) size_array_cols * ngridlocal * sizeof(double); // gridlocal return nbytes; } diff --git a/src/ML-SNAP/compute_grid_local.cpp b/src/ML-SNAP/compute_grid_local.cpp index 48714962ac..0fa9440a02 100644 --- a/src/ML-SNAP/compute_grid_local.cpp +++ b/src/ML-SNAP/compute_grid_local.cpp @@ -265,6 +265,6 @@ void ComputeGridLocal::assign_coords() double ComputeGridLocal::memory_usage() { - int nbytes = size_local_rows * size_local_cols * sizeof(double); // gridlocal + double nbytes = (double) size_local_rows * size_local_cols * sizeof(double); // gridlocal return nbytes; } diff --git a/src/ML-SNAP/compute_sna_grid.cpp b/src/ML-SNAP/compute_sna_grid.cpp index 497390f99a..dbce35ae08 100644 --- a/src/ML-SNAP/compute_sna_grid.cpp +++ b/src/ML-SNAP/compute_sna_grid.cpp @@ -292,7 +292,7 @@ void ComputeSNAGrid::compute_array() } } - memset(&grid[0][0], 0, size_array_rows * size_array_cols * sizeof(double)); + memset(&grid[0][0], 0, sizeof(double) * size_array_rows * size_array_cols); for (int iz = nzlo; iz <= nzhi; iz++) for (int iy = nylo; iy <= nyhi; iy++) diff --git a/src/fix_store.cpp b/src/fix_store.cpp index a80c9b0b56..b94f573376 100644 --- a/src/fix_store.cpp +++ b/src/fix_store.cpp @@ -77,7 +77,7 @@ vstore(nullptr), astore(nullptr), rbuf(nullptr) else if (narg == 6) arrayflag = 1; else tensorflag = 1; nvalues = n2*n3; - nbytes = n2*n3 * sizeof(double); + nbytes = nvalues * sizeof(double); } vstore = nullptr; @@ -194,7 +194,7 @@ void FixStore::write_restart(FILE *fp) rbuf[0] = n1; rbuf[1] = n2; if (vecflag) memcpy(&rbuf[2],vstore,n1*sizeof(double)); - else if (arrayflag) memcpy(&rbuf[2],&astore[0][0],n1*n2*sizeof(double)); + else if (arrayflag) memcpy(&rbuf[2],&astore[0][0],sizeof(double)*n1*n2); int n = n1*n2 + 2; if (comm->me == 0) { @@ -391,8 +391,8 @@ int FixStore::size_restart(int /*nlocal*/) double FixStore::memory_usage() { - double bytes = 0.0; - if (flavor == GLOBAL) bytes += n1*n2 * sizeof(double); - if (flavor == PERATOM) bytes += atom->nmax*n2*n3 * sizeof(double); + double bytes = (double) n1 * n2; + if (flavor == GLOBAL) bytes *= sizeof(double); + if (flavor == PERATOM) bytes *= atom->nmax * sizeof(double); return bytes; } From a9c072488a849f2a3600965115cb501bdb571219 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 17 Jul 2022 11:42:28 -0400 Subject: [PATCH 48/72] fix cut-n-paste error and improve error message --- src/dump.cpp | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/dump.cpp b/src/dump.cpp index 22750ed05c..9a8bac052a 100644 --- a/src/dump.cpp +++ b/src/dump.cpp @@ -1151,7 +1151,8 @@ void Dump::modify_params(int narg, char **arg) } } if ((icol < 0) || (icol >= (int)keyword_user.size())) - error->all(FLERR, "Illegal thermo_modify command"); + error->all(FLERR, "Incorrect dump_modify arguments: {} {} {}", + arg[iarg], arg[iarg+1], arg[iarg+2]); keyword_user[icol] = arg[iarg+2]; iarg += 3; } From 34cb0b704715cb8b48295870614c22d09b9a18bf Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 17 Jul 2022 11:46:19 -0400 Subject: [PATCH 49/72] add support for dump_modify colname to dump local --- src/dump_local.cpp | 39 +++++++++++++++++++++++++++++---------- src/dump_local.h | 3 ++- 2 files changed, 31 insertions(+), 11 deletions(-) diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 012e8b95dd..5fad243e74 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -34,9 +34,9 @@ using namespace LAMMPS_NS; DumpLocal::DumpLocal(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg), - label(nullptr), vtype(nullptr), vformat(nullptr), columns(nullptr), field2index(nullptr), - argindex(nullptr), id_compute(nullptr), compute(nullptr), id_fix(nullptr), fix(nullptr), - pack_choice(nullptr) + label(nullptr), vtype(nullptr), vformat(nullptr), columns(nullptr), columns_default(nullptr), + field2index(nullptr), argindex(nullptr), id_compute(nullptr), compute(nullptr), + id_fix(nullptr), fix(nullptr), pack_choice(nullptr) { if (narg == 5) error->all(FLERR,"No dump local arguments specified"); @@ -87,25 +87,30 @@ DumpLocal::DumpLocal(LAMMPS *lmp, int narg, char **arg) : // setup format strings vformat = new char*[size_one]; - std::string fdefault; + std::string cols; + for (int i = 0; i < size_one; i++) { - if (vtype[i] == Dump::INT) fdefault += "%d "; - else if (vtype[i] == Dump::DOUBLE) fdefault += "%g "; + if (vtype[i] == Dump::INT) cols += "%d "; + else if (vtype[i] == Dump::DOUBLE) cols += "%g "; vformat[i] = nullptr; } - format_default = utils::strdup(fdefault); + cols.resize(cols.size()-1); + format_default = utils::strdup(cols); format_column_user = new char*[size_one]; for (int i = 0; i < size_one; i++) format_column_user[i] = nullptr; // setup column string - std::string cols; + cols.clear(); + keyword_user.resize(nfield); for (int iarg = 0; iarg < nfield; iarg++) { + key2col[earg[iarg]] = iarg; + keyword_user[iarg].clear(); + if (cols.size()) cols += " "; cols += earg[iarg]; - cols += " "; } - columns = utils::strdup(cols); + columns_default = utils::strdup(cols); // setup default label string @@ -143,6 +148,7 @@ DumpLocal::~DumpLocal() delete[] format_column_user; delete[] columns; + delete[] columns_default; delete[] label; } @@ -150,6 +156,19 @@ DumpLocal::~DumpLocal() void DumpLocal::init_style() { + // assemble ITEMS: column string from defaults and user values + + delete[] columns; + std::string combined; + int icol = 0; + for (auto item : utils::split_words(columns_default)) { + if (combined.size()) combined += " "; + if (keyword_user[icol].size()) combined += keyword_user[icol]; + else combined += item; + ++icol; + } + columns = utils::strdup(combined); + if (sort_flag && sortcol == 0) error->all(FLERR,"Dump local cannot sort by atom ID"); diff --git a/src/dump_local.h b/src/dump_local.h index 160ff87f0a..ae49d6c479 100644 --- a/src/dump_local.h +++ b/src/dump_local.h @@ -37,7 +37,8 @@ class DumpLocal : public Dump { int *vtype; // type of each vector (INT, DOUBLE) char **vformat; // format string for each vector element - char *columns; // column labels + char *columns; // column labels + char *columns_default; int nfield; // # of keywords listed by user From 7232261ceafd6e8408ae63236d9d515c7f9fc845 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 17 Jul 2022 12:13:05 -0400 Subject: [PATCH 50/72] correct unit tests for dump local --- unittest/formats/test_dump_local.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/unittest/formats/test_dump_local.cpp b/unittest/formats/test_dump_local.cpp index c548427201..ead071743c 100644 --- a/unittest/formats/test_dump_local.cpp +++ b/unittest/formats/test_dump_local.cpp @@ -89,7 +89,7 @@ TEST_F(DumpLocalTest, run0) ASSERT_EQ(utils::split_words(lines[5]).size(), 2); ASSERT_EQ(utils::split_words(lines[6]).size(), 2); ASSERT_EQ(utils::split_words(lines[7]).size(), 2); - ASSERT_THAT(lines[8], Eq("ITEM: ENTRIES index c_comp[1] ")); + ASSERT_THAT(lines[8], Eq("ITEM: ENTRIES index c_comp[1]")); ASSERT_EQ(utils::split_words(lines[9]).size(), 2); ASSERT_THAT(lines[9], Eq("1 1.18765 ")); delete_file(dump_file); @@ -103,7 +103,7 @@ TEST_F(DumpLocalTest, label_run0) ASSERT_FILE_EXISTS(dump_file); auto lines = read_lines(dump_file); ASSERT_THAT(lines[2], Eq("ITEM: NUMBER OF ELEMENTS")); - ASSERT_THAT(lines[8], Eq("ITEM: ELEMENTS index c_comp[1] ")); + ASSERT_THAT(lines[8], Eq("ITEM: ELEMENTS index c_comp[1]")); delete_file(dump_file); } @@ -178,7 +178,7 @@ TEST_F(DumpLocalTest, no_buffer_run0) ASSERT_EQ(utils::split_words(lines[5]).size(), 2); ASSERT_EQ(utils::split_words(lines[6]).size(), 2); ASSERT_EQ(utils::split_words(lines[7]).size(), 2); - ASSERT_THAT(lines[8], Eq("ITEM: ENTRIES index c_comp[1] ")); + ASSERT_THAT(lines[8], Eq("ITEM: ENTRIES index c_comp[1]")); ASSERT_EQ(utils::split_words(lines[9]).size(), 2); ASSERT_THAT(lines[9], Eq("1 1.18765 ")); delete_file(dump_file); From 3685d6974ad7b88258b1f7b9b5b857c3e2b31d8b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 18 Jul 2022 14:01:18 -0400 Subject: [PATCH 51/72] reorder initializers to silence compiler warning --- src/pair_hybrid.cpp | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp index 375423c321..2ea749a3a3 100644 --- a/src/pair_hybrid.cpp +++ b/src/pair_hybrid.cpp @@ -33,9 +33,9 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairHybrid::PairHybrid(LAMMPS *lmp) : Pair(lmp), - styles(nullptr), keywords(nullptr), multiple(nullptr), nmap(nullptr), - map(nullptr), special_lj(nullptr), special_coul(nullptr), compute_tally(nullptr), cutmax_style(nullptr) +PairHybrid::PairHybrid(LAMMPS *lmp) : + Pair(lmp), styles(nullptr), cutmax_style(nullptr), keywords(nullptr), multiple(nullptr), + nmap(nullptr), map(nullptr), special_lj(nullptr), special_coul(nullptr), compute_tally(nullptr) { nstyles = 0; From 0ac8dce7b479b466238d018c1c1a933e0ea287ae Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 18 Jul 2022 14:00:53 -0400 Subject: [PATCH 52/72] strip off -pendantic-errors flag when compiling with nvcc_wrapper to fix error compiling ML-PACE --- lib/kokkos/bin/nvcc_wrapper | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/lib/kokkos/bin/nvcc_wrapper b/lib/kokkos/bin/nvcc_wrapper index 8c168412e7..fd2b92c4d0 100755 --- a/lib/kokkos/bin/nvcc_wrapper +++ b/lib/kokkos/bin/nvcc_wrapper @@ -306,13 +306,13 @@ do -A) ;; - #strip of -std=c++98 due to nvcc warnings and Tribits will place both -std=c++11 and -std=c++98 + #strip off -std=c++98 due to nvcc warnings and Tribits will place both -std=c++11 and -std=c++98 -std=c++98|--std=c++98) ;; - #strip of pedantic because it produces endless warnings about #LINE added by the preprocessor - -pedantic|-Wpedantic|-ansi) + #strip off pedantic because it produces endless warnings about #LINE added by the preprocessor + -pedantic|-pedantic-errors|-Wpedantic|-ansi) ;; - #strip of -Woverloaded-virtual to avoid "cc1: warning: command line option ‘-Woverloaded-virtual’ is valid for C++/ObjC++ but not for C" + #strip off -Woverloaded-virtual to avoid "cc1: warning: command line option ‘-Woverloaded-virtual’ is valid for C++/ObjC++ but not for C" -Woverloaded-virtual) ;; #strip -Xcompiler because we add it From ed73c21a2104dfbfe02719422e924ab8f22c5633 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 19 Jul 2022 13:25:05 -0400 Subject: [PATCH 53/72] Set path to python interpreter when running in a virtual environment --- cmake/CMakeLists.txt | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 669bff1533..cf8e54b995 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -154,6 +154,19 @@ endif() ######################################################################## # User input options # ######################################################################## +# set path to python interpreter and thus enforcing python version if +# when in a virtual environment and PYTHON_EXECUTABLE is not set on command line +if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE) + if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows") + set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe") + else() + set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python") + endif() + set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}") + message(STATUS "Running in virtual environment: $ENV{VIRTUAL_ENV}\n" + " Setting Python interpreter to: ${PYTHON_EXECUTABLE}") +endif() + set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically") mark_as_advanced(LAMMPS_MACHINE) if(LAMMPS_MACHINE) From b6550886577dedce2b6cde74526f3b81655dbd57 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 19 Jul 2022 13:26:50 -0400 Subject: [PATCH 54/72] adjust search for python interpreter so it is consistent with manual --- cmake/CMakeLists.txt | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index cf8e54b995..a9b46671d8 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -795,9 +795,13 @@ if(BUILD_SHARED_LIBS) set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6) find_package(PythonInterp) # Deprecated since version 3.12 if(PYTHONINTERP_FOUND) - set(Python_EXECUTABLE ${PYTHON_EXECUTABLE}) + set(Python_EXECUTABLE ${PYTHON_EXECUTABLE}) endif() else() + # backward compatibility + if(PYTHON_EXECUTABLE) + set(Python_EXECUTABLE ${PYTHON_EXECUTABLE}) + endif() find_package(Python COMPONENTS Interpreter) endif() if(BUILD_IS_MULTI_CONFIG) @@ -830,11 +834,17 @@ endif() ############################################################################### if(BUILD_SHARED_LIBS OR PKG_PYTHON) if(CMAKE_VERSION VERSION_LESS 3.12) + # adjust so we find Python 3 versions before Python 2 on old systems with old CMake + set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6) find_package(PythonInterp) # Deprecated since version 3.12 if(PYTHONINTERP_FOUND) - set(Python_EXECUTABLE ${PYTHON_EXECUTABLE}) + set(Python_EXECUTABLE ${PYTHON_EXECUTABLE}) endif() else() + # backward compatibility + if(PYTHON_EXECUTABLE) + set(Python_EXECUTABLE ${PYTHON_EXECUTABLE}) + endif() find_package(Python COMPONENTS Interpreter) endif() if(Python_EXECUTABLE) From 5eec9da8fe4386c4ae027dc4e9340e105ebb5391 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 19 Jul 2022 13:28:43 -0400 Subject: [PATCH 55/72] make search for python libraries consistent with search for python interpreter - apply same semantics of selecting the interpreter than the main cmake script - make certain that we search for the interpreter first - when searching for the library find the version matching the interpreter - error out when library version and interpreter version does not match --- cmake/Modules/Packages/MDI.cmake | 13 +++++++++++++ cmake/Modules/Packages/PYTHON.cmake | 20 ++++++++++++++++++++ 2 files changed, 33 insertions(+) diff --git a/cmake/Modules/Packages/MDI.cmake b/cmake/Modules/Packages/MDI.cmake index 1a14d5273a..d873c8f6d1 100644 --- a/cmake/Modules/Packages/MDI.cmake +++ b/cmake/Modules/Packages/MDI.cmake @@ -26,8 +26,21 @@ if(DOWNLOAD_MDI) # detect if we have python development support and thus can enable python plugins set(MDI_USE_PYTHON_PLUGINS OFF) if(CMAKE_VERSION VERSION_LESS 3.12) + if(NOT PYTHON_VERSION_STRING) + set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6) + # search for interpreter first, so we have a consistent library + find_package(PythonInterp) # Deprecated since version 3.12 + if(PYTHONINTERP_FOUND) + set(Python_EXECUTABLE ${PYTHON_EXECUTABLE}) + endif() + endif() + # search for the library matching the selected interpreter + set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}) find_package(PythonLibs QUIET) # Deprecated since version 3.12 if(PYTHONLIBS_FOUND) + if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING)) + message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}") + endif() set(MDI_USE_PYTHON_PLUGINS ON) endif() else() diff --git a/cmake/Modules/Packages/PYTHON.cmake b/cmake/Modules/Packages/PYTHON.cmake index c94db88073..4a2925fe31 100644 --- a/cmake/Modules/Packages/PYTHON.cmake +++ b/cmake/Modules/Packages/PYTHON.cmake @@ -1,8 +1,28 @@ if(CMAKE_VERSION VERSION_LESS 3.12) + if(NOT PYTHON_VERSION_STRING) + set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6) + # search for interpreter first, so we have a consistent library + find_package(PythonInterp) # Deprecated since version 3.12 + if(PYTHONINTERP_FOUND) + set(Python_EXECUTABLE ${PYTHON_EXECUTABLE}) + endif() + endif() + # search for the library matching the selected interpreter + set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}) find_package(PythonLibs REQUIRED) # Deprecated since version 3.12 + if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING)) + message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}") + endif() target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIRS}) target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARIES}) else() + if(NOT Python_INTERPRETER) + # backward compatibility + if(PYTHON_EXECUTABLE) + set(Python_EXECUTABLE ${PYTHON_EXECUTABLE}) + endif() + find_package(Python COMPONENTS Interpreter) + endif() find_package(Python REQUIRED COMPONENTS Interpreter Development) target_link_libraries(lammps PRIVATE Python::Python) endif() From 3c99a6b5c41af1f35ff790198f49b68b828d09f2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 20 Jul 2022 17:01:44 -0400 Subject: [PATCH 56/72] Correctly handle the dependency of pair style (and fix) srp/react on the MC package --- cmake/CMakeLists.txt | 2 +- cmake/Modules/Packages/MISC.cmake | 13 ++++++++ src/Depend.sh | 4 +++ src/MISC/Install.sh | 55 +++++++++++++++++++++++++++++++ 4 files changed, 73 insertions(+), 1 deletion(-) create mode 100644 cmake/Modules/Packages/MISC.cmake create mode 100644 src/MISC/Install.sh diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index a9b46671d8..ac7f88f939 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -648,7 +648,7 @@ endif() # packages which selectively include variants based on enabled styles # e.g. accelerator packages ###################################################################### -foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH PHONON QEQ OPENMP KOKKOS OPT INTEL GPU) +foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU) if(PKG_${PKG_WITH_INCL}) include(Packages/${PKG_WITH_INCL}) endif() diff --git a/cmake/Modules/Packages/MISC.cmake b/cmake/Modules/Packages/MISC.cmake new file mode 100644 index 0000000000..38207835a0 --- /dev/null +++ b/cmake/Modules/Packages/MISC.cmake @@ -0,0 +1,13 @@ +# pair style and fix srp/react depend on the fixes bond/break and bond/create from the MC package +if(NOT PKG_MC) + get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX) + list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MISC/fix_srp_react.h) + set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}") + get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR) + list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/MISC/pair_srp_react.h) + set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}") + get_target_property(LAMMPS_SOURCES lammps SOURCES) + list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MISC/fix_srp_react.cpp) + list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MISC/pair_srp_react.cpp) + set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}") +endif() diff --git a/src/Depend.sh b/src/Depend.sh index 5dd903f0bc..90dfdbba7a 100755 --- a/src/Depend.sh +++ b/src/Depend.sh @@ -128,6 +128,10 @@ if (test $1 = "MANYBODY") then depend OPENMP fi +if (test $1 = "MC") then + depend MISC +fi + if (test $1 = "MEAM") then depend KOKKOS fi diff --git a/src/MISC/Install.sh b/src/MISC/Install.sh new file mode 100644 index 0000000000..b6ba8a13fe --- /dev/null +++ b/src/MISC/Install.sh @@ -0,0 +1,55 @@ +# Install/Uninstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update + +mode=$1 + +# enforce using portable C locale +LC_ALL=C +export LC_ALL + +# arg1 = file, arg2 = file it depends on + +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} + +# package files without dependencies +action bond_special.cpp +action bond_special.h +action compute_viscosity_cos.cpp +action compute_viscosity_cos.h +action fix_accelerate_cos.cpp +action fix_accelerate_cos.h +action fix_imd.cpp +action fix_imd.h +action fix_ipi.cpp +action fix_ipi.h +action fix_srp.cpp +action fix_srp.h +action pair_agni.cpp +action pair_agni.h +action pair_list.cpp +action pair_list.h +action pair_srp.cpp +action pair_srp.h +action pair_tracker.cpp +action pair_tracker.h + +# package files with dependencies +action pair_srp_react.cpp fix_bond_break.h +action pair_srp_react.h fix_bond_break.h +action fix_srp_react.cpp fix_bond_break.h +action fix_srp_react.h fix_bond_break.h From 00cecceab77989e57445a089b722c018302f4d69 Mon Sep 17 00:00:00 2001 From: Paulius Velesko Date: Thu, 21 Jul 2022 03:55:53 +0000 Subject: [PATCH 57/72] gitignore --- .gitignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.gitignore b/.gitignore index bd2d0ea705..0cc211ab09 100644 --- a/.gitignore +++ b/.gitignore @@ -55,3 +55,4 @@ out/RelWithDebInfo out/Release out/x86 out/x64 +benchmark/* From bf65b4720f26d5b2dc90d1076a3ff7379784774d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 21 Jul 2022 05:20:11 -0400 Subject: [PATCH 58/72] add more BLAS/LAPACK functions to support LATTE package --- lib/linalg/zdrot.f | 153 ++++++++++++++ lib/linalg/zheevd.f | 395 ++++++++++++++++++++++++++++++++++++ lib/linalg/zlacpy.f | 156 ++++++++++++++ lib/linalg/zlacrm.f | 182 +++++++++++++++++ lib/linalg/zlaed0.f | 368 +++++++++++++++++++++++++++++++++ lib/linalg/zlaed7.f | 382 +++++++++++++++++++++++++++++++++++ lib/linalg/zlaed8.f | 483 ++++++++++++++++++++++++++++++++++++++++++++ lib/linalg/zstedc.f | 483 ++++++++++++++++++++++++++++++++++++++++++++ lib/linalg/zunm2l.f | 278 +++++++++++++++++++++++++ lib/linalg/zunm2r.f | 283 ++++++++++++++++++++++++++ lib/linalg/zunmql.f | 336 ++++++++++++++++++++++++++++++ lib/linalg/zunmqr.f | 337 +++++++++++++++++++++++++++++++ lib/linalg/zunmtr.f | 307 ++++++++++++++++++++++++++++ 13 files changed, 4143 insertions(+) create mode 100644 lib/linalg/zdrot.f create mode 100644 lib/linalg/zheevd.f create mode 100644 lib/linalg/zlacpy.f create mode 100644 lib/linalg/zlacrm.f create mode 100644 lib/linalg/zlaed0.f create mode 100644 lib/linalg/zlaed7.f create mode 100644 lib/linalg/zlaed8.f create mode 100644 lib/linalg/zstedc.f create mode 100644 lib/linalg/zunm2l.f create mode 100644 lib/linalg/zunm2r.f create mode 100644 lib/linalg/zunmql.f create mode 100644 lib/linalg/zunmqr.f create mode 100644 lib/linalg/zunmtr.f diff --git a/lib/linalg/zdrot.f b/lib/linalg/zdrot.f new file mode 100644 index 0000000000..3145561d67 --- /dev/null +++ b/lib/linalg/zdrot.f @@ -0,0 +1,153 @@ +*> \brief \b ZDROT +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +* Definition: +* =========== +* +* SUBROUTINE ZDROT( N, ZX, INCX, ZY, INCY, C, S ) +* +* .. Scalar Arguments .. +* INTEGER INCX, INCY, N +* DOUBLE PRECISION C, S +* .. +* .. Array Arguments .. +* COMPLEX*16 ZX( * ), ZY( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> Applies a plane rotation, where the cos and sin (c and s) are real +*> and the vectors cx and cy are complex. +*> jack dongarra, linpack, 3/11/78. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> On entry, N specifies the order of the vectors cx and cy. +*> N must be at least zero. +*> \endverbatim +*> +*> \param[in,out] ZX +*> \verbatim +*> ZX is COMPLEX*16 array, dimension at least +*> ( 1 + ( N - 1 )*abs( INCX ) ). +*> Before entry, the incremented array ZX must contain the n +*> element vector cx. On exit, ZX is overwritten by the updated +*> vector cx. +*> \endverbatim +*> +*> \param[in] INCX +*> \verbatim +*> INCX is INTEGER +*> On entry, INCX specifies the increment for the elements of +*> ZX. INCX must not be zero. +*> \endverbatim +*> +*> \param[in,out] ZY +*> \verbatim +*> ZY is COMPLEX*16 array, dimension at least +*> ( 1 + ( N - 1 )*abs( INCY ) ). +*> Before entry, the incremented array ZY must contain the n +*> element vector cy. On exit, ZY is overwritten by the updated +*> vector cy. +*> \endverbatim +*> +*> \param[in] INCY +*> \verbatim +*> INCY is INTEGER +*> On entry, INCY specifies the increment for the elements of +*> ZY. INCY must not be zero. +*> \endverbatim +*> +*> \param[in] C +*> \verbatim +*> C is DOUBLE PRECISION +*> On entry, C specifies the cosine, cos. +*> \endverbatim +*> +*> \param[in] S +*> \verbatim +*> S is DOUBLE PRECISION +*> On entry, S specifies the sine, sin. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup complex16_blas_level1 +* +* ===================================================================== + SUBROUTINE ZDROT( N, ZX, INCX, ZY, INCY, C, S ) +* +* -- Reference BLAS level1 routine -- +* -- Reference BLAS is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + INTEGER INCX, INCY, N + DOUBLE PRECISION C, S +* .. +* .. Array Arguments .. + COMPLEX*16 ZX( * ), ZY( * ) +* .. +* +* ===================================================================== +* +* .. Local Scalars .. + INTEGER I, IX, IY + COMPLEX*16 CTEMP +* .. +* .. Executable Statements .. +* + IF( N.LE.0 ) + $ RETURN + IF( INCX.EQ.1 .AND. INCY.EQ.1 ) THEN +* +* code for both increments equal to 1 +* + DO I = 1, N + CTEMP = C*ZX( I ) + S*ZY( I ) + ZY( I ) = C*ZY( I ) - S*ZX( I ) + ZX( I ) = CTEMP + END DO + ELSE +* +* code for unequal increments or equal increments not equal +* to 1 +* + IX = 1 + IY = 1 + IF( INCX.LT.0 ) + $ IX = ( -N+1 )*INCX + 1 + IF( INCY.LT.0 ) + $ IY = ( -N+1 )*INCY + 1 + DO I = 1, N + CTEMP = C*ZX( IX ) + S*ZY( IY ) + ZY( IY ) = C*ZY( IY ) - S*ZX( IX ) + ZX( IX ) = CTEMP + IX = IX + INCX + IY = IY + INCY + END DO + END IF + RETURN +* +* End of ZDROT +* + END diff --git a/lib/linalg/zheevd.f b/lib/linalg/zheevd.f new file mode 100644 index 0000000000..7f58c7f726 --- /dev/null +++ b/lib/linalg/zheevd.f @@ -0,0 +1,395 @@ +*> \brief ZHEEVD computes the eigenvalues and, optionally, the left and/or right eigenvectors for HE matrices +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download ZHEEVD + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE ZHEEVD( JOBZ, UPLO, N, A, LDA, W, WORK, LWORK, RWORK, +* LRWORK, IWORK, LIWORK, INFO ) +* +* .. Scalar Arguments .. +* CHARACTER JOBZ, UPLO +* INTEGER INFO, LDA, LIWORK, LRWORK, LWORK, N +* .. +* .. Array Arguments .. +* INTEGER IWORK( * ) +* DOUBLE PRECISION RWORK( * ), W( * ) +* COMPLEX*16 A( LDA, * ), WORK( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> ZHEEVD computes all eigenvalues and, optionally, eigenvectors of a +*> complex Hermitian matrix A. If eigenvectors are desired, it uses a +*> divide and conquer algorithm. +*> +*> The divide and conquer algorithm makes very mild assumptions about +*> floating point arithmetic. It will work on machines with a guard +*> digit in add/subtract, or on those binary machines without guard +*> digits which subtract like the Cray X-MP, Cray Y-MP, Cray C-90, or +*> Cray-2. It could conceivably fail on hexadecimal or decimal machines +*> without guard digits, but we know of none. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] JOBZ +*> \verbatim +*> JOBZ is CHARACTER*1 +*> = 'N': Compute eigenvalues only; +*> = 'V': Compute eigenvalues and eigenvectors. +*> \endverbatim +*> +*> \param[in] UPLO +*> \verbatim +*> UPLO is CHARACTER*1 +*> = 'U': Upper triangle of A is stored; +*> = 'L': Lower triangle of A is stored. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The order of the matrix A. N >= 0. +*> \endverbatim +*> +*> \param[in,out] A +*> \verbatim +*> A is COMPLEX*16 array, dimension (LDA, N) +*> On entry, the Hermitian matrix A. If UPLO = 'U', the +*> leading N-by-N upper triangular part of A contains the +*> upper triangular part of the matrix A. If UPLO = 'L', +*> the leading N-by-N lower triangular part of A contains +*> the lower triangular part of the matrix A. +*> On exit, if JOBZ = 'V', then if INFO = 0, A contains the +*> orthonormal eigenvectors of the matrix A. +*> If JOBZ = 'N', then on exit the lower triangle (if UPLO='L') +*> or the upper triangle (if UPLO='U') of A, including the +*> diagonal, is destroyed. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. LDA >= max(1,N). +*> \endverbatim +*> +*> \param[out] W +*> \verbatim +*> W is DOUBLE PRECISION array, dimension (N) +*> If INFO = 0, the eigenvalues in ascending order. +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is COMPLEX*16 array, dimension (MAX(1,LWORK)) +*> On exit, if INFO = 0, WORK(1) returns the optimal LWORK. +*> \endverbatim +*> +*> \param[in] LWORK +*> \verbatim +*> LWORK is INTEGER +*> The length of the array WORK. +*> If N <= 1, LWORK must be at least 1. +*> If JOBZ = 'N' and N > 1, LWORK must be at least N + 1. +*> If JOBZ = 'V' and N > 1, LWORK must be at least 2*N + N**2. +*> +*> If LWORK = -1, then a workspace query is assumed; the routine +*> only calculates the optimal sizes of the WORK, RWORK and +*> IWORK arrays, returns these values as the first entries of +*> the WORK, RWORK and IWORK arrays, and no error message +*> related to LWORK or LRWORK or LIWORK is issued by XERBLA. +*> \endverbatim +*> +*> \param[out] RWORK +*> \verbatim +*> RWORK is DOUBLE PRECISION array, +*> dimension (LRWORK) +*> On exit, if INFO = 0, RWORK(1) returns the optimal LRWORK. +*> \endverbatim +*> +*> \param[in] LRWORK +*> \verbatim +*> LRWORK is INTEGER +*> The dimension of the array RWORK. +*> If N <= 1, LRWORK must be at least 1. +*> If JOBZ = 'N' and N > 1, LRWORK must be at least N. +*> If JOBZ = 'V' and N > 1, LRWORK must be at least +*> 1 + 5*N + 2*N**2. +*> +*> If LRWORK = -1, then a workspace query is assumed; the +*> routine only calculates the optimal sizes of the WORK, RWORK +*> and IWORK arrays, returns these values as the first entries +*> of the WORK, RWORK and IWORK arrays, and no error message +*> related to LWORK or LRWORK or LIWORK is issued by XERBLA. +*> \endverbatim +*> +*> \param[out] IWORK +*> \verbatim +*> IWORK is INTEGER array, dimension (MAX(1,LIWORK)) +*> On exit, if INFO = 0, IWORK(1) returns the optimal LIWORK. +*> \endverbatim +*> +*> \param[in] LIWORK +*> \verbatim +*> LIWORK is INTEGER +*> The dimension of the array IWORK. +*> If N <= 1, LIWORK must be at least 1. +*> If JOBZ = 'N' and N > 1, LIWORK must be at least 1. +*> If JOBZ = 'V' and N > 1, LIWORK must be at least 3 + 5*N. +*> +*> If LIWORK = -1, then a workspace query is assumed; the +*> routine only calculates the optimal sizes of the WORK, RWORK +*> and IWORK arrays, returns these values as the first entries +*> of the WORK, RWORK and IWORK arrays, and no error message +*> related to LWORK or LRWORK or LIWORK is issued by XERBLA. +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit +*> < 0: if INFO = -i, the i-th argument had an illegal value +*> > 0: if INFO = i and JOBZ = 'N', then the algorithm failed +*> to converge; i off-diagonal elements of an intermediate +*> tridiagonal form did not converge to zero; +*> if INFO = i and JOBZ = 'V', then the algorithm failed +*> to compute an eigenvalue while working on the submatrix +*> lying in rows and columns INFO/(N+1) through +*> mod(INFO,N+1). +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup complex16HEeigen +* +*> \par Further Details: +* ===================== +*> +*> Modified description of INFO. Sven, 16 Feb 05. +* +*> \par Contributors: +* ================== +*> +*> Jeff Rutter, Computer Science Division, University of California +*> at Berkeley, USA +*> +* ===================================================================== + SUBROUTINE ZHEEVD( JOBZ, UPLO, N, A, LDA, W, WORK, LWORK, RWORK, + $ LRWORK, IWORK, LIWORK, INFO ) +* +* -- LAPACK driver routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + CHARACTER JOBZ, UPLO + INTEGER INFO, LDA, LIWORK, LRWORK, LWORK, N +* .. +* .. Array Arguments .. + INTEGER IWORK( * ) + DOUBLE PRECISION RWORK( * ), W( * ) + COMPLEX*16 A( LDA, * ), WORK( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO, ONE + PARAMETER ( ZERO = 0.0D0, ONE = 1.0D0 ) + COMPLEX*16 CONE + PARAMETER ( CONE = ( 1.0D0, 0.0D0 ) ) +* .. +* .. Local Scalars .. + LOGICAL LOWER, LQUERY, WANTZ + INTEGER IINFO, IMAX, INDE, INDRWK, INDTAU, INDWK2, + $ INDWRK, ISCALE, LIOPT, LIWMIN, LLRWK, LLWORK, + $ LLWRK2, LOPT, LROPT, LRWMIN, LWMIN + DOUBLE PRECISION ANRM, BIGNUM, EPS, RMAX, RMIN, SAFMIN, SIGMA, + $ SMLNUM +* .. +* .. External Functions .. + LOGICAL LSAME + INTEGER ILAENV + DOUBLE PRECISION DLAMCH, ZLANHE + EXTERNAL LSAME, ILAENV, DLAMCH, ZLANHE +* .. +* .. External Subroutines .. + EXTERNAL DSCAL, DSTERF, XERBLA, ZHETRD, ZLACPY, ZLASCL, + $ ZSTEDC, ZUNMTR +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX, SQRT +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + WANTZ = LSAME( JOBZ, 'V' ) + LOWER = LSAME( UPLO, 'L' ) + LQUERY = ( LWORK.EQ.-1 .OR. LRWORK.EQ.-1 .OR. LIWORK.EQ.-1 ) +* + INFO = 0 + IF( .NOT.( WANTZ .OR. LSAME( JOBZ, 'N' ) ) ) THEN + INFO = -1 + ELSE IF( .NOT.( LOWER .OR. LSAME( UPLO, 'U' ) ) ) THEN + INFO = -2 + ELSE IF( N.LT.0 ) THEN + INFO = -3 + ELSE IF( LDA.LT.MAX( 1, N ) ) THEN + INFO = -5 + END IF +* + IF( INFO.EQ.0 ) THEN + IF( N.LE.1 ) THEN + LWMIN = 1 + LRWMIN = 1 + LIWMIN = 1 + LOPT = LWMIN + LROPT = LRWMIN + LIOPT = LIWMIN + ELSE + IF( WANTZ ) THEN + LWMIN = 2*N + N*N + LRWMIN = 1 + 5*N + 2*N**2 + LIWMIN = 3 + 5*N + ELSE + LWMIN = N + 1 + LRWMIN = N + LIWMIN = 1 + END IF + LOPT = MAX( LWMIN, N + + $ N*ILAENV( 1, 'ZHETRD', UPLO, N, -1, -1, -1 ) ) + LROPT = LRWMIN + LIOPT = LIWMIN + END IF + WORK( 1 ) = LOPT + RWORK( 1 ) = LROPT + IWORK( 1 ) = LIOPT +* + IF( LWORK.LT.LWMIN .AND. .NOT.LQUERY ) THEN + INFO = -8 + ELSE IF( LRWORK.LT.LRWMIN .AND. .NOT.LQUERY ) THEN + INFO = -10 + ELSE IF( LIWORK.LT.LIWMIN .AND. .NOT.LQUERY ) THEN + INFO = -12 + END IF + END IF +* + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'ZHEEVD', -INFO ) + RETURN + ELSE IF( LQUERY ) THEN + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 ) + $ RETURN +* + IF( N.EQ.1 ) THEN + W( 1 ) = DBLE( A( 1, 1 ) ) + IF( WANTZ ) + $ A( 1, 1 ) = CONE + RETURN + END IF +* +* Get machine constants. +* + SAFMIN = DLAMCH( 'Safe minimum' ) + EPS = DLAMCH( 'Precision' ) + SMLNUM = SAFMIN / EPS + BIGNUM = ONE / SMLNUM + RMIN = SQRT( SMLNUM ) + RMAX = SQRT( BIGNUM ) +* +* Scale matrix to allowable range, if necessary. +* + ANRM = ZLANHE( 'M', UPLO, N, A, LDA, RWORK ) + ISCALE = 0 + IF( ANRM.GT.ZERO .AND. ANRM.LT.RMIN ) THEN + ISCALE = 1 + SIGMA = RMIN / ANRM + ELSE IF( ANRM.GT.RMAX ) THEN + ISCALE = 1 + SIGMA = RMAX / ANRM + END IF + IF( ISCALE.EQ.1 ) + $ CALL ZLASCL( UPLO, 0, 0, ONE, SIGMA, N, N, A, LDA, INFO ) +* +* Call ZHETRD to reduce Hermitian matrix to tridiagonal form. +* + INDE = 1 + INDTAU = 1 + INDWRK = INDTAU + N + INDRWK = INDE + N + INDWK2 = INDWRK + N*N + LLWORK = LWORK - INDWRK + 1 + LLWRK2 = LWORK - INDWK2 + 1 + LLRWK = LRWORK - INDRWK + 1 + CALL ZHETRD( UPLO, N, A, LDA, W, RWORK( INDE ), WORK( INDTAU ), + $ WORK( INDWRK ), LLWORK, IINFO ) +* +* For eigenvalues only, call DSTERF. For eigenvectors, first call +* ZSTEDC to generate the eigenvector matrix, WORK(INDWRK), of the +* tridiagonal matrix, then call ZUNMTR to multiply it to the +* Householder transformations represented as Householder vectors in +* A. +* + IF( .NOT.WANTZ ) THEN + CALL DSTERF( N, W, RWORK( INDE ), INFO ) + ELSE + CALL ZSTEDC( 'I', N, W, RWORK( INDE ), WORK( INDWRK ), N, + $ WORK( INDWK2 ), LLWRK2, RWORK( INDRWK ), LLRWK, + $ IWORK, LIWORK, INFO ) + CALL ZUNMTR( 'L', UPLO, 'N', N, N, A, LDA, WORK( INDTAU ), + $ WORK( INDWRK ), N, WORK( INDWK2 ), LLWRK2, IINFO ) + CALL ZLACPY( 'A', N, N, WORK( INDWRK ), N, A, LDA ) + END IF +* +* If matrix was scaled, then rescale eigenvalues appropriately. +* + IF( ISCALE.EQ.1 ) THEN + IF( INFO.EQ.0 ) THEN + IMAX = N + ELSE + IMAX = INFO - 1 + END IF + CALL DSCAL( IMAX, ONE / SIGMA, W, 1 ) + END IF +* + WORK( 1 ) = LOPT + RWORK( 1 ) = LROPT + IWORK( 1 ) = LIOPT +* + RETURN +* +* End of ZHEEVD +* + END diff --git a/lib/linalg/zlacpy.f b/lib/linalg/zlacpy.f new file mode 100644 index 0000000000..06017509e0 --- /dev/null +++ b/lib/linalg/zlacpy.f @@ -0,0 +1,156 @@ +*> \brief \b ZLACPY copies all or part of one two-dimensional array to another. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download ZLACPY + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE ZLACPY( UPLO, M, N, A, LDA, B, LDB ) +* +* .. Scalar Arguments .. +* CHARACTER UPLO +* INTEGER LDA, LDB, M, N +* .. +* .. Array Arguments .. +* COMPLEX*16 A( LDA, * ), B( LDB, * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> ZLACPY copies all or part of a two-dimensional matrix A to another +*> matrix B. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] UPLO +*> \verbatim +*> UPLO is CHARACTER*1 +*> Specifies the part of the matrix A to be copied to B. +*> = 'U': Upper triangular part +*> = 'L': Lower triangular part +*> Otherwise: All of the matrix A +*> \endverbatim +*> +*> \param[in] M +*> \verbatim +*> M is INTEGER +*> The number of rows of the matrix A. M >= 0. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The number of columns of the matrix A. N >= 0. +*> \endverbatim +*> +*> \param[in] A +*> \verbatim +*> A is COMPLEX*16 array, dimension (LDA,N) +*> The m by n matrix A. If UPLO = 'U', only the upper trapezium +*> is accessed; if UPLO = 'L', only the lower trapezium is +*> accessed. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. LDA >= max(1,M). +*> \endverbatim +*> +*> \param[out] B +*> \verbatim +*> B is COMPLEX*16 array, dimension (LDB,N) +*> On exit, B = A in the locations specified by UPLO. +*> \endverbatim +*> +*> \param[in] LDB +*> \verbatim +*> LDB is INTEGER +*> The leading dimension of the array B. LDB >= max(1,M). +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup complex16OTHERauxiliary +* +* ===================================================================== + SUBROUTINE ZLACPY( UPLO, M, N, A, LDA, B, LDB ) +* +* -- LAPACK auxiliary routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + CHARACTER UPLO + INTEGER LDA, LDB, M, N +* .. +* .. Array Arguments .. + COMPLEX*16 A( LDA, * ), B( LDB, * ) +* .. +* +* ===================================================================== +* +* .. Local Scalars .. + INTEGER I, J +* .. +* .. External Functions .. + LOGICAL LSAME + EXTERNAL LSAME +* .. +* .. Intrinsic Functions .. + INTRINSIC MIN +* .. +* .. Executable Statements .. +* + IF( LSAME( UPLO, 'U' ) ) THEN + DO 20 J = 1, N + DO 10 I = 1, MIN( J, M ) + B( I, J ) = A( I, J ) + 10 CONTINUE + 20 CONTINUE +* + ELSE IF( LSAME( UPLO, 'L' ) ) THEN + DO 40 J = 1, N + DO 30 I = J, M + B( I, J ) = A( I, J ) + 30 CONTINUE + 40 CONTINUE +* + ELSE + DO 60 J = 1, N + DO 50 I = 1, M + B( I, J ) = A( I, J ) + 50 CONTINUE + 60 CONTINUE + END IF +* + RETURN +* +* End of ZLACPY +* + END diff --git a/lib/linalg/zlacrm.f b/lib/linalg/zlacrm.f new file mode 100644 index 0000000000..ce8b9b02c5 --- /dev/null +++ b/lib/linalg/zlacrm.f @@ -0,0 +1,182 @@ +*> \brief \b ZLACRM multiplies a complex matrix by a square real matrix. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download ZLACRM + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE ZLACRM( M, N, A, LDA, B, LDB, C, LDC, RWORK ) +* +* .. Scalar Arguments .. +* INTEGER LDA, LDB, LDC, M, N +* .. +* .. Array Arguments .. +* DOUBLE PRECISION B( LDB, * ), RWORK( * ) +* COMPLEX*16 A( LDA, * ), C( LDC, * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> ZLACRM performs a very simple matrix-matrix multiplication: +*> C := A * B, +*> where A is M by N and complex; B is N by N and real; +*> C is M by N and complex. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] M +*> \verbatim +*> M is INTEGER +*> The number of rows of the matrix A and of the matrix C. +*> M >= 0. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The number of columns and rows of the matrix B and +*> the number of columns of the matrix C. +*> N >= 0. +*> \endverbatim +*> +*> \param[in] A +*> \verbatim +*> A is COMPLEX*16 array, dimension (LDA, N) +*> On entry, A contains the M by N matrix A. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. LDA >=max(1,M). +*> \endverbatim +*> +*> \param[in] B +*> \verbatim +*> B is DOUBLE PRECISION array, dimension (LDB, N) +*> On entry, B contains the N by N matrix B. +*> \endverbatim +*> +*> \param[in] LDB +*> \verbatim +*> LDB is INTEGER +*> The leading dimension of the array B. LDB >=max(1,N). +*> \endverbatim +*> +*> \param[out] C +*> \verbatim +*> C is COMPLEX*16 array, dimension (LDC, N) +*> On exit, C contains the M by N matrix C. +*> \endverbatim +*> +*> \param[in] LDC +*> \verbatim +*> LDC is INTEGER +*> The leading dimension of the array C. LDC >=max(1,N). +*> \endverbatim +*> +*> \param[out] RWORK +*> \verbatim +*> RWORK is DOUBLE PRECISION array, dimension (2*M*N) +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup complex16OTHERauxiliary +* +* ===================================================================== + SUBROUTINE ZLACRM( M, N, A, LDA, B, LDB, C, LDC, RWORK ) +* +* -- LAPACK auxiliary routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + INTEGER LDA, LDB, LDC, M, N +* .. +* .. Array Arguments .. + DOUBLE PRECISION B( LDB, * ), RWORK( * ) + COMPLEX*16 A( LDA, * ), C( LDC, * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ONE, ZERO + PARAMETER ( ONE = 1.0D0, ZERO = 0.0D0 ) +* .. +* .. Local Scalars .. + INTEGER I, J, L +* .. +* .. Intrinsic Functions .. + INTRINSIC DBLE, DCMPLX, DIMAG +* .. +* .. External Subroutines .. + EXTERNAL DGEMM +* .. +* .. Executable Statements .. +* +* Quick return if possible. +* + IF( ( M.EQ.0 ) .OR. ( N.EQ.0 ) ) + $ RETURN +* + DO 20 J = 1, N + DO 10 I = 1, M + RWORK( ( J-1 )*M+I ) = DBLE( A( I, J ) ) + 10 CONTINUE + 20 CONTINUE +* + L = M*N + 1 + CALL DGEMM( 'N', 'N', M, N, N, ONE, RWORK, M, B, LDB, ZERO, + $ RWORK( L ), M ) + DO 40 J = 1, N + DO 30 I = 1, M + C( I, J ) = RWORK( L+( J-1 )*M+I-1 ) + 30 CONTINUE + 40 CONTINUE +* + DO 60 J = 1, N + DO 50 I = 1, M + RWORK( ( J-1 )*M+I ) = DIMAG( A( I, J ) ) + 50 CONTINUE + 60 CONTINUE + CALL DGEMM( 'N', 'N', M, N, N, ONE, RWORK, M, B, LDB, ZERO, + $ RWORK( L ), M ) + DO 80 J = 1, N + DO 70 I = 1, M + C( I, J ) = DCMPLX( DBLE( C( I, J ) ), + $ RWORK( L+( J-1 )*M+I-1 ) ) + 70 CONTINUE + 80 CONTINUE +* + RETURN +* +* End of ZLACRM +* + END diff --git a/lib/linalg/zlaed0.f b/lib/linalg/zlaed0.f new file mode 100644 index 0000000000..c4deac037a --- /dev/null +++ b/lib/linalg/zlaed0.f @@ -0,0 +1,368 @@ +*> \brief \b ZLAED0 used by ZSTEDC. Computes all eigenvalues and corresponding eigenvectors of an unreduced symmetric tridiagonal matrix using the divide and conquer method. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download ZLAED0 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE ZLAED0( QSIZ, N, D, E, Q, LDQ, QSTORE, LDQS, RWORK, +* IWORK, INFO ) +* +* .. Scalar Arguments .. +* INTEGER INFO, LDQ, LDQS, N, QSIZ +* .. +* .. Array Arguments .. +* INTEGER IWORK( * ) +* DOUBLE PRECISION D( * ), E( * ), RWORK( * ) +* COMPLEX*16 Q( LDQ, * ), QSTORE( LDQS, * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> Using the divide and conquer method, ZLAED0 computes all eigenvalues +*> of a symmetric tridiagonal matrix which is one diagonal block of +*> those from reducing a dense or band Hermitian matrix and +*> corresponding eigenvectors of the dense or band matrix. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] QSIZ +*> \verbatim +*> QSIZ is INTEGER +*> The dimension of the unitary matrix used to reduce +*> the full matrix to tridiagonal form. QSIZ >= N if ICOMPQ = 1. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The dimension of the symmetric tridiagonal matrix. N >= 0. +*> \endverbatim +*> +*> \param[in,out] D +*> \verbatim +*> D is DOUBLE PRECISION array, dimension (N) +*> On entry, the diagonal elements of the tridiagonal matrix. +*> On exit, the eigenvalues in ascending order. +*> \endverbatim +*> +*> \param[in,out] E +*> \verbatim +*> E is DOUBLE PRECISION array, dimension (N-1) +*> On entry, the off-diagonal elements of the tridiagonal matrix. +*> On exit, E has been destroyed. +*> \endverbatim +*> +*> \param[in,out] Q +*> \verbatim +*> Q is COMPLEX*16 array, dimension (LDQ,N) +*> On entry, Q must contain an QSIZ x N matrix whose columns +*> unitarily orthonormal. It is a part of the unitary matrix +*> that reduces the full dense Hermitian matrix to a +*> (reducible) symmetric tridiagonal matrix. +*> \endverbatim +*> +*> \param[in] LDQ +*> \verbatim +*> LDQ is INTEGER +*> The leading dimension of the array Q. LDQ >= max(1,N). +*> \endverbatim +*> +*> \param[out] IWORK +*> \verbatim +*> IWORK is INTEGER array, +*> the dimension of IWORK must be at least +*> 6 + 6*N + 5*N*lg N +*> ( lg( N ) = smallest integer k +*> such that 2^k >= N ) +*> \endverbatim +*> +*> \param[out] RWORK +*> \verbatim +*> RWORK is DOUBLE PRECISION array, +*> dimension (1 + 3*N + 2*N*lg N + 3*N**2) +*> ( lg( N ) = smallest integer k +*> such that 2^k >= N ) +*> \endverbatim +*> +*> \param[out] QSTORE +*> \verbatim +*> QSTORE is COMPLEX*16 array, dimension (LDQS, N) +*> Used to store parts of +*> the eigenvector matrix when the updating matrix multiplies +*> take place. +*> \endverbatim +*> +*> \param[in] LDQS +*> \verbatim +*> LDQS is INTEGER +*> The leading dimension of the array QSTORE. +*> LDQS >= max(1,N). +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit. +*> < 0: if INFO = -i, the i-th argument had an illegal value. +*> > 0: The algorithm failed to compute an eigenvalue while +*> working on the submatrix lying in rows and columns +*> INFO/(N+1) through mod(INFO,N+1). +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup complex16OTHERcomputational +* +* ===================================================================== + SUBROUTINE ZLAED0( QSIZ, N, D, E, Q, LDQ, QSTORE, LDQS, RWORK, + $ IWORK, INFO ) +* +* -- LAPACK computational routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + INTEGER INFO, LDQ, LDQS, N, QSIZ +* .. +* .. Array Arguments .. + INTEGER IWORK( * ) + DOUBLE PRECISION D( * ), E( * ), RWORK( * ) + COMPLEX*16 Q( LDQ, * ), QSTORE( LDQS, * ) +* .. +* +* ===================================================================== +* +* Warning: N could be as big as QSIZ! +* +* .. Parameters .. + DOUBLE PRECISION TWO + PARAMETER ( TWO = 2.D+0 ) +* .. +* .. Local Scalars .. + INTEGER CURLVL, CURPRB, CURR, I, IGIVCL, IGIVNM, + $ IGIVPT, INDXQ, IPERM, IPRMPT, IQ, IQPTR, IWREM, + $ J, K, LGN, LL, MATSIZ, MSD2, SMLSIZ, SMM1, + $ SPM1, SPM2, SUBMAT, SUBPBS, TLVLS + DOUBLE PRECISION TEMP +* .. +* .. External Subroutines .. + EXTERNAL DCOPY, DSTEQR, XERBLA, ZCOPY, ZLACRM, ZLAED7 +* .. +* .. External Functions .. + INTEGER ILAENV + EXTERNAL ILAENV +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, DBLE, INT, LOG, MAX +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 +* +* IF( ICOMPQ .LT. 0 .OR. ICOMPQ .GT. 2 ) THEN +* INFO = -1 +* ELSE IF( ( ICOMPQ .EQ. 1 ) .AND. ( QSIZ .LT. MAX( 0, N ) ) ) +* $ THEN + IF( QSIZ.LT.MAX( 0, N ) ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( LDQ.LT.MAX( 1, N ) ) THEN + INFO = -6 + ELSE IF( LDQS.LT.MAX( 1, N ) ) THEN + INFO = -8 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'ZLAED0', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 ) + $ RETURN +* + SMLSIZ = ILAENV( 9, 'ZLAED0', ' ', 0, 0, 0, 0 ) +* +* Determine the size and placement of the submatrices, and save in +* the leading elements of IWORK. +* + IWORK( 1 ) = N + SUBPBS = 1 + TLVLS = 0 + 10 CONTINUE + IF( IWORK( SUBPBS ).GT.SMLSIZ ) THEN + DO 20 J = SUBPBS, 1, -1 + IWORK( 2*J ) = ( IWORK( J )+1 ) / 2 + IWORK( 2*J-1 ) = IWORK( J ) / 2 + 20 CONTINUE + TLVLS = TLVLS + 1 + SUBPBS = 2*SUBPBS + GO TO 10 + END IF + DO 30 J = 2, SUBPBS + IWORK( J ) = IWORK( J ) + IWORK( J-1 ) + 30 CONTINUE +* +* Divide the matrix into SUBPBS submatrices of size at most SMLSIZ+1 +* using rank-1 modifications (cuts). +* + SPM1 = SUBPBS - 1 + DO 40 I = 1, SPM1 + SUBMAT = IWORK( I ) + 1 + SMM1 = SUBMAT - 1 + D( SMM1 ) = D( SMM1 ) - ABS( E( SMM1 ) ) + D( SUBMAT ) = D( SUBMAT ) - ABS( E( SMM1 ) ) + 40 CONTINUE +* + INDXQ = 4*N + 3 +* +* Set up workspaces for eigenvalues only/accumulate new vectors +* routine +* + TEMP = LOG( DBLE( N ) ) / LOG( TWO ) + LGN = INT( TEMP ) + IF( 2**LGN.LT.N ) + $ LGN = LGN + 1 + IF( 2**LGN.LT.N ) + $ LGN = LGN + 1 + IPRMPT = INDXQ + N + 1 + IPERM = IPRMPT + N*LGN + IQPTR = IPERM + N*LGN + IGIVPT = IQPTR + N + 2 + IGIVCL = IGIVPT + N*LGN +* + IGIVNM = 1 + IQ = IGIVNM + 2*N*LGN + IWREM = IQ + N**2 + 1 +* Initialize pointers + DO 50 I = 0, SUBPBS + IWORK( IPRMPT+I ) = 1 + IWORK( IGIVPT+I ) = 1 + 50 CONTINUE + IWORK( IQPTR ) = 1 +* +* Solve each submatrix eigenproblem at the bottom of the divide and +* conquer tree. +* + CURR = 0 + DO 70 I = 0, SPM1 + IF( I.EQ.0 ) THEN + SUBMAT = 1 + MATSIZ = IWORK( 1 ) + ELSE + SUBMAT = IWORK( I ) + 1 + MATSIZ = IWORK( I+1 ) - IWORK( I ) + END IF + LL = IQ - 1 + IWORK( IQPTR+CURR ) + CALL DSTEQR( 'I', MATSIZ, D( SUBMAT ), E( SUBMAT ), + $ RWORK( LL ), MATSIZ, RWORK, INFO ) + CALL ZLACRM( QSIZ, MATSIZ, Q( 1, SUBMAT ), LDQ, RWORK( LL ), + $ MATSIZ, QSTORE( 1, SUBMAT ), LDQS, + $ RWORK( IWREM ) ) + IWORK( IQPTR+CURR+1 ) = IWORK( IQPTR+CURR ) + MATSIZ**2 + CURR = CURR + 1 + IF( INFO.GT.0 ) THEN + INFO = SUBMAT*( N+1 ) + SUBMAT + MATSIZ - 1 + RETURN + END IF + K = 1 + DO 60 J = SUBMAT, IWORK( I+1 ) + IWORK( INDXQ+J ) = K + K = K + 1 + 60 CONTINUE + 70 CONTINUE +* +* Successively merge eigensystems of adjacent submatrices +* into eigensystem for the corresponding larger matrix. +* +* while ( SUBPBS > 1 ) +* + CURLVL = 1 + 80 CONTINUE + IF( SUBPBS.GT.1 ) THEN + SPM2 = SUBPBS - 2 + DO 90 I = 0, SPM2, 2 + IF( I.EQ.0 ) THEN + SUBMAT = 1 + MATSIZ = IWORK( 2 ) + MSD2 = IWORK( 1 ) + CURPRB = 0 + ELSE + SUBMAT = IWORK( I ) + 1 + MATSIZ = IWORK( I+2 ) - IWORK( I ) + MSD2 = MATSIZ / 2 + CURPRB = CURPRB + 1 + END IF +* +* Merge lower order eigensystems (of size MSD2 and MATSIZ - MSD2) +* into an eigensystem of size MATSIZ. ZLAED7 handles the case +* when the eigenvectors of a full or band Hermitian matrix (which +* was reduced to tridiagonal form) are desired. +* +* I am free to use Q as a valuable working space until Loop 150. +* + CALL ZLAED7( MATSIZ, MSD2, QSIZ, TLVLS, CURLVL, CURPRB, + $ D( SUBMAT ), QSTORE( 1, SUBMAT ), LDQS, + $ E( SUBMAT+MSD2-1 ), IWORK( INDXQ+SUBMAT ), + $ RWORK( IQ ), IWORK( IQPTR ), IWORK( IPRMPT ), + $ IWORK( IPERM ), IWORK( IGIVPT ), + $ IWORK( IGIVCL ), RWORK( IGIVNM ), + $ Q( 1, SUBMAT ), RWORK( IWREM ), + $ IWORK( SUBPBS+1 ), INFO ) + IF( INFO.GT.0 ) THEN + INFO = SUBMAT*( N+1 ) + SUBMAT + MATSIZ - 1 + RETURN + END IF + IWORK( I / 2+1 ) = IWORK( I+2 ) + 90 CONTINUE + SUBPBS = SUBPBS / 2 + CURLVL = CURLVL + 1 + GO TO 80 + END IF +* +* end while +* +* Re-merge the eigenvalues/vectors which were deflated at the final +* merge step. +* + DO 100 I = 1, N + J = IWORK( INDXQ+I ) + RWORK( I ) = D( J ) + CALL ZCOPY( QSIZ, QSTORE( 1, J ), 1, Q( 1, I ), 1 ) + 100 CONTINUE + CALL DCOPY( N, RWORK, 1, D, 1 ) +* + RETURN +* +* End of ZLAED0 +* + END diff --git a/lib/linalg/zlaed7.f b/lib/linalg/zlaed7.f new file mode 100644 index 0000000000..83f32d8b81 --- /dev/null +++ b/lib/linalg/zlaed7.f @@ -0,0 +1,382 @@ +*> \brief \b ZLAED7 used by ZSTEDC. Computes the updated eigensystem of a diagonal matrix after modification by a rank-one symmetric matrix. Used when the original matrix is dense. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download ZLAED7 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE ZLAED7( N, CUTPNT, QSIZ, TLVLS, CURLVL, CURPBM, D, Q, +* LDQ, RHO, INDXQ, QSTORE, QPTR, PRMPTR, PERM, +* GIVPTR, GIVCOL, GIVNUM, WORK, RWORK, IWORK, +* INFO ) +* +* .. Scalar Arguments .. +* INTEGER CURLVL, CURPBM, CUTPNT, INFO, LDQ, N, QSIZ, +* $ TLVLS +* DOUBLE PRECISION RHO +* .. +* .. Array Arguments .. +* INTEGER GIVCOL( 2, * ), GIVPTR( * ), INDXQ( * ), +* $ IWORK( * ), PERM( * ), PRMPTR( * ), QPTR( * ) +* DOUBLE PRECISION D( * ), GIVNUM( 2, * ), QSTORE( * ), RWORK( * ) +* COMPLEX*16 Q( LDQ, * ), WORK( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> ZLAED7 computes the updated eigensystem of a diagonal +*> matrix after modification by a rank-one symmetric matrix. This +*> routine is used only for the eigenproblem which requires all +*> eigenvalues and optionally eigenvectors of a dense or banded +*> Hermitian matrix that has been reduced to tridiagonal form. +*> +*> T = Q(in) ( D(in) + RHO * Z*Z**H ) Q**H(in) = Q(out) * D(out) * Q**H(out) +*> +*> where Z = Q**Hu, u is a vector of length N with ones in the +*> CUTPNT and CUTPNT + 1 th elements and zeros elsewhere. +*> +*> The eigenvectors of the original matrix are stored in Q, and the +*> eigenvalues are in D. The algorithm consists of three stages: +*> +*> The first stage consists of deflating the size of the problem +*> when there are multiple eigenvalues or if there is a zero in +*> the Z vector. For each such occurrence the dimension of the +*> secular equation problem is reduced by one. This stage is +*> performed by the routine DLAED2. +*> +*> The second stage consists of calculating the updated +*> eigenvalues. This is done by finding the roots of the secular +*> equation via the routine DLAED4 (as called by SLAED3). +*> This routine also calculates the eigenvectors of the current +*> problem. +*> +*> The final stage consists of computing the updated eigenvectors +*> directly using the updated eigenvalues. The eigenvectors for +*> the current problem are multiplied with the eigenvectors from +*> the overall problem. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The dimension of the symmetric tridiagonal matrix. N >= 0. +*> \endverbatim +*> +*> \param[in] CUTPNT +*> \verbatim +*> CUTPNT is INTEGER +*> Contains the location of the last eigenvalue in the leading +*> sub-matrix. min(1,N) <= CUTPNT <= N. +*> \endverbatim +*> +*> \param[in] QSIZ +*> \verbatim +*> QSIZ is INTEGER +*> The dimension of the unitary matrix used to reduce +*> the full matrix to tridiagonal form. QSIZ >= N. +*> \endverbatim +*> +*> \param[in] TLVLS +*> \verbatim +*> TLVLS is INTEGER +*> The total number of merging levels in the overall divide and +*> conquer tree. +*> \endverbatim +*> +*> \param[in] CURLVL +*> \verbatim +*> CURLVL is INTEGER +*> The current level in the overall merge routine, +*> 0 <= curlvl <= tlvls. +*> \endverbatim +*> +*> \param[in] CURPBM +*> \verbatim +*> CURPBM is INTEGER +*> The current problem in the current level in the overall +*> merge routine (counting from upper left to lower right). +*> \endverbatim +*> +*> \param[in,out] D +*> \verbatim +*> D is DOUBLE PRECISION array, dimension (N) +*> On entry, the eigenvalues of the rank-1-perturbed matrix. +*> On exit, the eigenvalues of the repaired matrix. +*> \endverbatim +*> +*> \param[in,out] Q +*> \verbatim +*> Q is COMPLEX*16 array, dimension (LDQ,N) +*> On entry, the eigenvectors of the rank-1-perturbed matrix. +*> On exit, the eigenvectors of the repaired tridiagonal matrix. +*> \endverbatim +*> +*> \param[in] LDQ +*> \verbatim +*> LDQ is INTEGER +*> The leading dimension of the array Q. LDQ >= max(1,N). +*> \endverbatim +*> +*> \param[in] RHO +*> \verbatim +*> RHO is DOUBLE PRECISION +*> Contains the subdiagonal element used to create the rank-1 +*> modification. +*> \endverbatim +*> +*> \param[out] INDXQ +*> \verbatim +*> INDXQ is INTEGER array, dimension (N) +*> This contains the permutation which will reintegrate the +*> subproblem just solved back into sorted order, +*> ie. D( INDXQ( I = 1, N ) ) will be in ascending order. +*> \endverbatim +*> +*> \param[out] IWORK +*> \verbatim +*> IWORK is INTEGER array, dimension (4*N) +*> \endverbatim +*> +*> \param[out] RWORK +*> \verbatim +*> RWORK is DOUBLE PRECISION array, +*> dimension (3*N+2*QSIZ*N) +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is COMPLEX*16 array, dimension (QSIZ*N) +*> \endverbatim +*> +*> \param[in,out] QSTORE +*> \verbatim +*> QSTORE is DOUBLE PRECISION array, dimension (N**2+1) +*> Stores eigenvectors of submatrices encountered during +*> divide and conquer, packed together. QPTR points to +*> beginning of the submatrices. +*> \endverbatim +*> +*> \param[in,out] QPTR +*> \verbatim +*> QPTR is INTEGER array, dimension (N+2) +*> List of indices pointing to beginning of submatrices stored +*> in QSTORE. The submatrices are numbered starting at the +*> bottom left of the divide and conquer tree, from left to +*> right and bottom to top. +*> \endverbatim +*> +*> \param[in] PRMPTR +*> \verbatim +*> PRMPTR is INTEGER array, dimension (N lg N) +*> Contains a list of pointers which indicate where in PERM a +*> level's permutation is stored. PRMPTR(i+1) - PRMPTR(i) +*> indicates the size of the permutation and also the size of +*> the full, non-deflated problem. +*> \endverbatim +*> +*> \param[in] PERM +*> \verbatim +*> PERM is INTEGER array, dimension (N lg N) +*> Contains the permutations (from deflation and sorting) to be +*> applied to each eigenblock. +*> \endverbatim +*> +*> \param[in] GIVPTR +*> \verbatim +*> GIVPTR is INTEGER array, dimension (N lg N) +*> Contains a list of pointers which indicate where in GIVCOL a +*> level's Givens rotations are stored. GIVPTR(i+1) - GIVPTR(i) +*> indicates the number of Givens rotations. +*> \endverbatim +*> +*> \param[in] GIVCOL +*> \verbatim +*> GIVCOL is INTEGER array, dimension (2, N lg N) +*> Each pair of numbers indicates a pair of columns to take place +*> in a Givens rotation. +*> \endverbatim +*> +*> \param[in] GIVNUM +*> \verbatim +*> GIVNUM is DOUBLE PRECISION array, dimension (2, N lg N) +*> Each number indicates the S value to be used in the +*> corresponding Givens rotation. +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit. +*> < 0: if INFO = -i, the i-th argument had an illegal value. +*> > 0: if INFO = 1, an eigenvalue did not converge +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup complex16OTHERcomputational +* +* ===================================================================== + SUBROUTINE ZLAED7( N, CUTPNT, QSIZ, TLVLS, CURLVL, CURPBM, D, Q, + $ LDQ, RHO, INDXQ, QSTORE, QPTR, PRMPTR, PERM, + $ GIVPTR, GIVCOL, GIVNUM, WORK, RWORK, IWORK, + $ INFO ) +* +* -- LAPACK computational routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + INTEGER CURLVL, CURPBM, CUTPNT, INFO, LDQ, N, QSIZ, + $ TLVLS + DOUBLE PRECISION RHO +* .. +* .. Array Arguments .. + INTEGER GIVCOL( 2, * ), GIVPTR( * ), INDXQ( * ), + $ IWORK( * ), PERM( * ), PRMPTR( * ), QPTR( * ) + DOUBLE PRECISION D( * ), GIVNUM( 2, * ), QSTORE( * ), RWORK( * ) + COMPLEX*16 Q( LDQ, * ), WORK( * ) +* .. +* +* ===================================================================== +* +* .. Local Scalars .. + INTEGER COLTYP, CURR, I, IDLMDA, INDX, + $ INDXC, INDXP, IQ, IW, IZ, K, N1, N2, PTR +* .. +* .. External Subroutines .. + EXTERNAL DLAED9, DLAEDA, DLAMRG, XERBLA, ZLACRM, ZLAED8 +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX, MIN +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 +* +* IF( ICOMPQ.LT.0 .OR. ICOMPQ.GT.1 ) THEN +* INFO = -1 +* ELSE IF( N.LT.0 ) THEN + IF( N.LT.0 ) THEN + INFO = -1 + ELSE IF( MIN( 1, N ).GT.CUTPNT .OR. N.LT.CUTPNT ) THEN + INFO = -2 + ELSE IF( QSIZ.LT.N ) THEN + INFO = -3 + ELSE IF( LDQ.LT.MAX( 1, N ) ) THEN + INFO = -9 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'ZLAED7', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 ) + $ RETURN +* +* The following values are for bookkeeping purposes only. They are +* integer pointers which indicate the portion of the workspace +* used by a particular array in DLAED2 and SLAED3. +* + IZ = 1 + IDLMDA = IZ + N + IW = IDLMDA + N + IQ = IW + N +* + INDX = 1 + INDXC = INDX + N + COLTYP = INDXC + N + INDXP = COLTYP + N +* +* Form the z-vector which consists of the last row of Q_1 and the +* first row of Q_2. +* + PTR = 1 + 2**TLVLS + DO 10 I = 1, CURLVL - 1 + PTR = PTR + 2**( TLVLS-I ) + 10 CONTINUE + CURR = PTR + CURPBM + CALL DLAEDA( N, TLVLS, CURLVL, CURPBM, PRMPTR, PERM, GIVPTR, + $ GIVCOL, GIVNUM, QSTORE, QPTR, RWORK( IZ ), + $ RWORK( IZ+N ), INFO ) +* +* When solving the final problem, we no longer need the stored data, +* so we will overwrite the data from this level onto the previously +* used storage space. +* + IF( CURLVL.EQ.TLVLS ) THEN + QPTR( CURR ) = 1 + PRMPTR( CURR ) = 1 + GIVPTR( CURR ) = 1 + END IF +* +* Sort and Deflate eigenvalues. +* + CALL ZLAED8( K, N, QSIZ, Q, LDQ, D, RHO, CUTPNT, RWORK( IZ ), + $ RWORK( IDLMDA ), WORK, QSIZ, RWORK( IW ), + $ IWORK( INDXP ), IWORK( INDX ), INDXQ, + $ PERM( PRMPTR( CURR ) ), GIVPTR( CURR+1 ), + $ GIVCOL( 1, GIVPTR( CURR ) ), + $ GIVNUM( 1, GIVPTR( CURR ) ), INFO ) + PRMPTR( CURR+1 ) = PRMPTR( CURR ) + N + GIVPTR( CURR+1 ) = GIVPTR( CURR+1 ) + GIVPTR( CURR ) +* +* Solve Secular Equation. +* + IF( K.NE.0 ) THEN + CALL DLAED9( K, 1, K, N, D, RWORK( IQ ), K, RHO, + $ RWORK( IDLMDA ), RWORK( IW ), + $ QSTORE( QPTR( CURR ) ), K, INFO ) + CALL ZLACRM( QSIZ, K, WORK, QSIZ, QSTORE( QPTR( CURR ) ), K, Q, + $ LDQ, RWORK( IQ ) ) + QPTR( CURR+1 ) = QPTR( CURR ) + K**2 + IF( INFO.NE.0 ) THEN + RETURN + END IF +* +* Prepare the INDXQ sorting premutation. +* + N1 = K + N2 = N - K + CALL DLAMRG( N1, N2, D, 1, -1, INDXQ ) + ELSE + QPTR( CURR+1 ) = QPTR( CURR ) + DO 20 I = 1, N + INDXQ( I ) = I + 20 CONTINUE + END IF +* + RETURN +* +* End of ZLAED7 +* + END diff --git a/lib/linalg/zlaed8.f b/lib/linalg/zlaed8.f new file mode 100644 index 0000000000..995a673de9 --- /dev/null +++ b/lib/linalg/zlaed8.f @@ -0,0 +1,483 @@ +*> \brief \b ZLAED8 used by ZSTEDC. Merges eigenvalues and deflates secular equation. Used when the original matrix is dense. +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download ZLAED8 + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE ZLAED8( K, N, QSIZ, Q, LDQ, D, RHO, CUTPNT, Z, DLAMDA, +* Q2, LDQ2, W, INDXP, INDX, INDXQ, PERM, GIVPTR, +* GIVCOL, GIVNUM, INFO ) +* +* .. Scalar Arguments .. +* INTEGER CUTPNT, GIVPTR, INFO, K, LDQ, LDQ2, N, QSIZ +* DOUBLE PRECISION RHO +* .. +* .. Array Arguments .. +* INTEGER GIVCOL( 2, * ), INDX( * ), INDXP( * ), +* $ INDXQ( * ), PERM( * ) +* DOUBLE PRECISION D( * ), DLAMDA( * ), GIVNUM( 2, * ), W( * ), +* $ Z( * ) +* COMPLEX*16 Q( LDQ, * ), Q2( LDQ2, * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> ZLAED8 merges the two sets of eigenvalues together into a single +*> sorted set. Then it tries to deflate the size of the problem. +*> There are two ways in which deflation can occur: when two or more +*> eigenvalues are close together or if there is a tiny element in the +*> Z vector. For each such occurrence the order of the related secular +*> equation problem is reduced by one. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[out] K +*> \verbatim +*> K is INTEGER +*> Contains the number of non-deflated eigenvalues. +*> This is the order of the related secular equation. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The dimension of the symmetric tridiagonal matrix. N >= 0. +*> \endverbatim +*> +*> \param[in] QSIZ +*> \verbatim +*> QSIZ is INTEGER +*> The dimension of the unitary matrix used to reduce +*> the dense or band matrix to tridiagonal form. +*> QSIZ >= N if ICOMPQ = 1. +*> \endverbatim +*> +*> \param[in,out] Q +*> \verbatim +*> Q is COMPLEX*16 array, dimension (LDQ,N) +*> On entry, Q contains the eigenvectors of the partially solved +*> system which has been previously updated in matrix +*> multiplies with other partially solved eigensystems. +*> On exit, Q contains the trailing (N-K) updated eigenvectors +*> (those which were deflated) in its last N-K columns. +*> \endverbatim +*> +*> \param[in] LDQ +*> \verbatim +*> LDQ is INTEGER +*> The leading dimension of the array Q. LDQ >= max( 1, N ). +*> \endverbatim +*> +*> \param[in,out] D +*> \verbatim +*> D is DOUBLE PRECISION array, dimension (N) +*> On entry, D contains the eigenvalues of the two submatrices to +*> be combined. On exit, D contains the trailing (N-K) updated +*> eigenvalues (those which were deflated) sorted into increasing +*> order. +*> \endverbatim +*> +*> \param[in,out] RHO +*> \verbatim +*> RHO is DOUBLE PRECISION +*> Contains the off diagonal element associated with the rank-1 +*> cut which originally split the two submatrices which are now +*> being recombined. RHO is modified during the computation to +*> the value required by DLAED3. +*> \endverbatim +*> +*> \param[in] CUTPNT +*> \verbatim +*> CUTPNT is INTEGER +*> Contains the location of the last eigenvalue in the leading +*> sub-matrix. MIN(1,N) <= CUTPNT <= N. +*> \endverbatim +*> +*> \param[in] Z +*> \verbatim +*> Z is DOUBLE PRECISION array, dimension (N) +*> On input this vector contains the updating vector (the last +*> row of the first sub-eigenvector matrix and the first row of +*> the second sub-eigenvector matrix). The contents of Z are +*> destroyed during the updating process. +*> \endverbatim +*> +*> \param[out] DLAMDA +*> \verbatim +*> DLAMDA is DOUBLE PRECISION array, dimension (N) +*> Contains a copy of the first K eigenvalues which will be used +*> by DLAED3 to form the secular equation. +*> \endverbatim +*> +*> \param[out] Q2 +*> \verbatim +*> Q2 is COMPLEX*16 array, dimension (LDQ2,N) +*> If ICOMPQ = 0, Q2 is not referenced. Otherwise, +*> Contains a copy of the first K eigenvectors which will be used +*> by DLAED7 in a matrix multiply (DGEMM) to update the new +*> eigenvectors. +*> \endverbatim +*> +*> \param[in] LDQ2 +*> \verbatim +*> LDQ2 is INTEGER +*> The leading dimension of the array Q2. LDQ2 >= max( 1, N ). +*> \endverbatim +*> +*> \param[out] W +*> \verbatim +*> W is DOUBLE PRECISION array, dimension (N) +*> This will hold the first k values of the final +*> deflation-altered z-vector and will be passed to DLAED3. +*> \endverbatim +*> +*> \param[out] INDXP +*> \verbatim +*> INDXP is INTEGER array, dimension (N) +*> This will contain the permutation used to place deflated +*> values of D at the end of the array. On output INDXP(1:K) +*> points to the nondeflated D-values and INDXP(K+1:N) +*> points to the deflated eigenvalues. +*> \endverbatim +*> +*> \param[out] INDX +*> \verbatim +*> INDX is INTEGER array, dimension (N) +*> This will contain the permutation used to sort the contents of +*> D into ascending order. +*> \endverbatim +*> +*> \param[in] INDXQ +*> \verbatim +*> INDXQ is INTEGER array, dimension (N) +*> This contains the permutation which separately sorts the two +*> sub-problems in D into ascending order. Note that elements in +*> the second half of this permutation must first have CUTPNT +*> added to their values in order to be accurate. +*> \endverbatim +*> +*> \param[out] PERM +*> \verbatim +*> PERM is INTEGER array, dimension (N) +*> Contains the permutations (from deflation and sorting) to be +*> applied to each eigenblock. +*> \endverbatim +*> +*> \param[out] GIVPTR +*> \verbatim +*> GIVPTR is INTEGER +*> Contains the number of Givens rotations which took place in +*> this subproblem. +*> \endverbatim +*> +*> \param[out] GIVCOL +*> \verbatim +*> GIVCOL is INTEGER array, dimension (2, N) +*> Each pair of numbers indicates a pair of columns to take place +*> in a Givens rotation. +*> \endverbatim +*> +*> \param[out] GIVNUM +*> \verbatim +*> GIVNUM is DOUBLE PRECISION array, dimension (2, N) +*> Each number indicates the S value to be used in the +*> corresponding Givens rotation. +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit. +*> < 0: if INFO = -i, the i-th argument had an illegal value. +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup complex16OTHERcomputational +* +* ===================================================================== + SUBROUTINE ZLAED8( K, N, QSIZ, Q, LDQ, D, RHO, CUTPNT, Z, DLAMDA, + $ Q2, LDQ2, W, INDXP, INDX, INDXQ, PERM, GIVPTR, + $ GIVCOL, GIVNUM, INFO ) +* +* -- LAPACK computational routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + INTEGER CUTPNT, GIVPTR, INFO, K, LDQ, LDQ2, N, QSIZ + DOUBLE PRECISION RHO +* .. +* .. Array Arguments .. + INTEGER GIVCOL( 2, * ), INDX( * ), INDXP( * ), + $ INDXQ( * ), PERM( * ) + DOUBLE PRECISION D( * ), DLAMDA( * ), GIVNUM( 2, * ), W( * ), + $ Z( * ) + COMPLEX*16 Q( LDQ, * ), Q2( LDQ2, * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION MONE, ZERO, ONE, TWO, EIGHT + PARAMETER ( MONE = -1.0D0, ZERO = 0.0D0, ONE = 1.0D0, + $ TWO = 2.0D0, EIGHT = 8.0D0 ) +* .. +* .. Local Scalars .. + INTEGER I, IMAX, J, JLAM, JMAX, JP, K2, N1, N1P1, N2 + DOUBLE PRECISION C, EPS, S, T, TAU, TOL +* .. +* .. External Functions .. + INTEGER IDAMAX + DOUBLE PRECISION DLAMCH, DLAPY2 + EXTERNAL IDAMAX, DLAMCH, DLAPY2 +* .. +* .. External Subroutines .. + EXTERNAL DCOPY, DLAMRG, DSCAL, XERBLA, ZCOPY, ZDROT, + $ ZLACPY +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, MAX, MIN, SQRT +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 +* + IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( QSIZ.LT.N ) THEN + INFO = -3 + ELSE IF( LDQ.LT.MAX( 1, N ) ) THEN + INFO = -5 + ELSE IF( CUTPNT.LT.MIN( 1, N ) .OR. CUTPNT.GT.N ) THEN + INFO = -8 + ELSE IF( LDQ2.LT.MAX( 1, N ) ) THEN + INFO = -12 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'ZLAED8', -INFO ) + RETURN + END IF +* +* Need to initialize GIVPTR to O here in case of quick exit +* to prevent an unspecified code behavior (usually sigfault) +* when IWORK array on entry to *stedc is not zeroed +* (or at least some IWORK entries which used in *laed7 for GIVPTR). +* + GIVPTR = 0 +* +* Quick return if possible +* + IF( N.EQ.0 ) + $ RETURN +* + N1 = CUTPNT + N2 = N - N1 + N1P1 = N1 + 1 +* + IF( RHO.LT.ZERO ) THEN + CALL DSCAL( N2, MONE, Z( N1P1 ), 1 ) + END IF +* +* Normalize z so that norm(z) = 1 +* + T = ONE / SQRT( TWO ) + DO 10 J = 1, N + INDX( J ) = J + 10 CONTINUE + CALL DSCAL( N, T, Z, 1 ) + RHO = ABS( TWO*RHO ) +* +* Sort the eigenvalues into increasing order +* + DO 20 I = CUTPNT + 1, N + INDXQ( I ) = INDXQ( I ) + CUTPNT + 20 CONTINUE + DO 30 I = 1, N + DLAMDA( I ) = D( INDXQ( I ) ) + W( I ) = Z( INDXQ( I ) ) + 30 CONTINUE + I = 1 + J = CUTPNT + 1 + CALL DLAMRG( N1, N2, DLAMDA, 1, 1, INDX ) + DO 40 I = 1, N + D( I ) = DLAMDA( INDX( I ) ) + Z( I ) = W( INDX( I ) ) + 40 CONTINUE +* +* Calculate the allowable deflation tolerance +* + IMAX = IDAMAX( N, Z, 1 ) + JMAX = IDAMAX( N, D, 1 ) + EPS = DLAMCH( 'Epsilon' ) + TOL = EIGHT*EPS*ABS( D( JMAX ) ) +* +* If the rank-1 modifier is small enough, no more needs to be done +* -- except to reorganize Q so that its columns correspond with the +* elements in D. +* + IF( RHO*ABS( Z( IMAX ) ).LE.TOL ) THEN + K = 0 + DO 50 J = 1, N + PERM( J ) = INDXQ( INDX( J ) ) + CALL ZCOPY( QSIZ, Q( 1, PERM( J ) ), 1, Q2( 1, J ), 1 ) + 50 CONTINUE + CALL ZLACPY( 'A', QSIZ, N, Q2( 1, 1 ), LDQ2, Q( 1, 1 ), LDQ ) + RETURN + END IF +* +* If there are multiple eigenvalues then the problem deflates. Here +* the number of equal eigenvalues are found. As each equal +* eigenvalue is found, an elementary reflector is computed to rotate +* the corresponding eigensubspace so that the corresponding +* components of Z are zero in this new basis. +* + K = 0 + K2 = N + 1 + DO 60 J = 1, N + IF( RHO*ABS( Z( J ) ).LE.TOL ) THEN +* +* Deflate due to small z component. +* + K2 = K2 - 1 + INDXP( K2 ) = J + IF( J.EQ.N ) + $ GO TO 100 + ELSE + JLAM = J + GO TO 70 + END IF + 60 CONTINUE + 70 CONTINUE + J = J + 1 + IF( J.GT.N ) + $ GO TO 90 + IF( RHO*ABS( Z( J ) ).LE.TOL ) THEN +* +* Deflate due to small z component. +* + K2 = K2 - 1 + INDXP( K2 ) = J + ELSE +* +* Check if eigenvalues are close enough to allow deflation. +* + S = Z( JLAM ) + C = Z( J ) +* +* Find sqrt(a**2+b**2) without overflow or +* destructive underflow. +* + TAU = DLAPY2( C, S ) + T = D( J ) - D( JLAM ) + C = C / TAU + S = -S / TAU + IF( ABS( T*C*S ).LE.TOL ) THEN +* +* Deflation is possible. +* + Z( J ) = TAU + Z( JLAM ) = ZERO +* +* Record the appropriate Givens rotation +* + GIVPTR = GIVPTR + 1 + GIVCOL( 1, GIVPTR ) = INDXQ( INDX( JLAM ) ) + GIVCOL( 2, GIVPTR ) = INDXQ( INDX( J ) ) + GIVNUM( 1, GIVPTR ) = C + GIVNUM( 2, GIVPTR ) = S + CALL ZDROT( QSIZ, Q( 1, INDXQ( INDX( JLAM ) ) ), 1, + $ Q( 1, INDXQ( INDX( J ) ) ), 1, C, S ) + T = D( JLAM )*C*C + D( J )*S*S + D( J ) = D( JLAM )*S*S + D( J )*C*C + D( JLAM ) = T + K2 = K2 - 1 + I = 1 + 80 CONTINUE + IF( K2+I.LE.N ) THEN + IF( D( JLAM ).LT.D( INDXP( K2+I ) ) ) THEN + INDXP( K2+I-1 ) = INDXP( K2+I ) + INDXP( K2+I ) = JLAM + I = I + 1 + GO TO 80 + ELSE + INDXP( K2+I-1 ) = JLAM + END IF + ELSE + INDXP( K2+I-1 ) = JLAM + END IF + JLAM = J + ELSE + K = K + 1 + W( K ) = Z( JLAM ) + DLAMDA( K ) = D( JLAM ) + INDXP( K ) = JLAM + JLAM = J + END IF + END IF + GO TO 70 + 90 CONTINUE +* +* Record the last eigenvalue. +* + K = K + 1 + W( K ) = Z( JLAM ) + DLAMDA( K ) = D( JLAM ) + INDXP( K ) = JLAM +* + 100 CONTINUE +* +* Sort the eigenvalues and corresponding eigenvectors into DLAMDA +* and Q2 respectively. The eigenvalues/vectors which were not +* deflated go into the first K slots of DLAMDA and Q2 respectively, +* while those which were deflated go into the last N - K slots. +* + DO 110 J = 1, N + JP = INDXP( J ) + DLAMDA( J ) = D( JP ) + PERM( J ) = INDXQ( INDX( JP ) ) + CALL ZCOPY( QSIZ, Q( 1, PERM( J ) ), 1, Q2( 1, J ), 1 ) + 110 CONTINUE +* +* The deflated eigenvalues and their corresponding vectors go back +* into the last N - K slots of D and Q respectively. +* + IF( K.LT.N ) THEN + CALL DCOPY( N-K, DLAMDA( K+1 ), 1, D( K+1 ), 1 ) + CALL ZLACPY( 'A', QSIZ, N-K, Q2( 1, K+1 ), LDQ2, Q( 1, K+1 ), + $ LDQ ) + END IF +* + RETURN +* +* End of ZLAED8 +* + END diff --git a/lib/linalg/zstedc.f b/lib/linalg/zstedc.f new file mode 100644 index 0000000000..74d390af7e --- /dev/null +++ b/lib/linalg/zstedc.f @@ -0,0 +1,483 @@ +*> \brief \b ZSTEDC +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download ZSTEDC + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE ZSTEDC( COMPZ, N, D, E, Z, LDZ, WORK, LWORK, RWORK, +* LRWORK, IWORK, LIWORK, INFO ) +* +* .. Scalar Arguments .. +* CHARACTER COMPZ +* INTEGER INFO, LDZ, LIWORK, LRWORK, LWORK, N +* .. +* .. Array Arguments .. +* INTEGER IWORK( * ) +* DOUBLE PRECISION D( * ), E( * ), RWORK( * ) +* COMPLEX*16 WORK( * ), Z( LDZ, * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> ZSTEDC computes all eigenvalues and, optionally, eigenvectors of a +*> symmetric tridiagonal matrix using the divide and conquer method. +*> The eigenvectors of a full or band complex Hermitian matrix can also +*> be found if ZHETRD or ZHPTRD or ZHBTRD has been used to reduce this +*> matrix to tridiagonal form. +*> +*> This code makes very mild assumptions about floating point +*> arithmetic. It will work on machines with a guard digit in +*> add/subtract, or on those binary machines without guard digits +*> which subtract like the Cray X-MP, Cray Y-MP, Cray C-90, or Cray-2. +*> It could conceivably fail on hexadecimal or decimal machines +*> without guard digits, but we know of none. See DLAED3 for details. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] COMPZ +*> \verbatim +*> COMPZ is CHARACTER*1 +*> = 'N': Compute eigenvalues only. +*> = 'I': Compute eigenvectors of tridiagonal matrix also. +*> = 'V': Compute eigenvectors of original Hermitian matrix +*> also. On entry, Z contains the unitary matrix used +*> to reduce the original matrix to tridiagonal form. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The dimension of the symmetric tridiagonal matrix. N >= 0. +*> \endverbatim +*> +*> \param[in,out] D +*> \verbatim +*> D is DOUBLE PRECISION array, dimension (N) +*> On entry, the diagonal elements of the tridiagonal matrix. +*> On exit, if INFO = 0, the eigenvalues in ascending order. +*> \endverbatim +*> +*> \param[in,out] E +*> \verbatim +*> E is DOUBLE PRECISION array, dimension (N-1) +*> On entry, the subdiagonal elements of the tridiagonal matrix. +*> On exit, E has been destroyed. +*> \endverbatim +*> +*> \param[in,out] Z +*> \verbatim +*> Z is COMPLEX*16 array, dimension (LDZ,N) +*> On entry, if COMPZ = 'V', then Z contains the unitary +*> matrix used in the reduction to tridiagonal form. +*> On exit, if INFO = 0, then if COMPZ = 'V', Z contains the +*> orthonormal eigenvectors of the original Hermitian matrix, +*> and if COMPZ = 'I', Z contains the orthonormal eigenvectors +*> of the symmetric tridiagonal matrix. +*> If COMPZ = 'N', then Z is not referenced. +*> \endverbatim +*> +*> \param[in] LDZ +*> \verbatim +*> LDZ is INTEGER +*> The leading dimension of the array Z. LDZ >= 1. +*> If eigenvectors are desired, then LDZ >= max(1,N). +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is COMPLEX*16 array, dimension (MAX(1,LWORK)) +*> On exit, if INFO = 0, WORK(1) returns the optimal LWORK. +*> \endverbatim +*> +*> \param[in] LWORK +*> \verbatim +*> LWORK is INTEGER +*> The dimension of the array WORK. +*> If COMPZ = 'N' or 'I', or N <= 1, LWORK must be at least 1. +*> If COMPZ = 'V' and N > 1, LWORK must be at least N*N. +*> Note that for COMPZ = 'V', then if N is less than or +*> equal to the minimum divide size, usually 25, then LWORK need +*> only be 1. +*> +*> If LWORK = -1, then a workspace query is assumed; the routine +*> only calculates the optimal sizes of the WORK, RWORK and +*> IWORK arrays, returns these values as the first entries of +*> the WORK, RWORK and IWORK arrays, and no error message +*> related to LWORK or LRWORK or LIWORK is issued by XERBLA. +*> \endverbatim +*> +*> \param[out] RWORK +*> \verbatim +*> RWORK is DOUBLE PRECISION array, dimension (MAX(1,LRWORK)) +*> On exit, if INFO = 0, RWORK(1) returns the optimal LRWORK. +*> \endverbatim +*> +*> \param[in] LRWORK +*> \verbatim +*> LRWORK is INTEGER +*> The dimension of the array RWORK. +*> If COMPZ = 'N' or N <= 1, LRWORK must be at least 1. +*> If COMPZ = 'V' and N > 1, LRWORK must be at least +*> 1 + 3*N + 2*N*lg N + 4*N**2 , +*> where lg( N ) = smallest integer k such +*> that 2**k >= N. +*> If COMPZ = 'I' and N > 1, LRWORK must be at least +*> 1 + 4*N + 2*N**2 . +*> Note that for COMPZ = 'I' or 'V', then if N is less than or +*> equal to the minimum divide size, usually 25, then LRWORK +*> need only be max(1,2*(N-1)). +*> +*> If LRWORK = -1, then a workspace query is assumed; the +*> routine only calculates the optimal sizes of the WORK, RWORK +*> and IWORK arrays, returns these values as the first entries +*> of the WORK, RWORK and IWORK arrays, and no error message +*> related to LWORK or LRWORK or LIWORK is issued by XERBLA. +*> \endverbatim +*> +*> \param[out] IWORK +*> \verbatim +*> IWORK is INTEGER array, dimension (MAX(1,LIWORK)) +*> On exit, if INFO = 0, IWORK(1) returns the optimal LIWORK. +*> \endverbatim +*> +*> \param[in] LIWORK +*> \verbatim +*> LIWORK is INTEGER +*> The dimension of the array IWORK. +*> If COMPZ = 'N' or N <= 1, LIWORK must be at least 1. +*> If COMPZ = 'V' or N > 1, LIWORK must be at least +*> 6 + 6*N + 5*N*lg N. +*> If COMPZ = 'I' or N > 1, LIWORK must be at least +*> 3 + 5*N . +*> Note that for COMPZ = 'I' or 'V', then if N is less than or +*> equal to the minimum divide size, usually 25, then LIWORK +*> need only be 1. +*> +*> If LIWORK = -1, then a workspace query is assumed; the +*> routine only calculates the optimal sizes of the WORK, RWORK +*> and IWORK arrays, returns these values as the first entries +*> of the WORK, RWORK and IWORK arrays, and no error message +*> related to LWORK or LRWORK or LIWORK is issued by XERBLA. +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit. +*> < 0: if INFO = -i, the i-th argument had an illegal value. +*> > 0: The algorithm failed to compute an eigenvalue while +*> working on the submatrix lying in rows and columns +*> INFO/(N+1) through mod(INFO,N+1). +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup complex16OTHERcomputational +* +*> \par Contributors: +* ================== +*> +*> Jeff Rutter, Computer Science Division, University of California +*> at Berkeley, USA +* +* ===================================================================== + SUBROUTINE ZSTEDC( COMPZ, N, D, E, Z, LDZ, WORK, LWORK, RWORK, + $ LRWORK, IWORK, LIWORK, INFO ) +* +* -- LAPACK computational routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + CHARACTER COMPZ + INTEGER INFO, LDZ, LIWORK, LRWORK, LWORK, N +* .. +* .. Array Arguments .. + INTEGER IWORK( * ) + DOUBLE PRECISION D( * ), E( * ), RWORK( * ) + COMPLEX*16 WORK( * ), Z( LDZ, * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + DOUBLE PRECISION ZERO, ONE, TWO + PARAMETER ( ZERO = 0.0D0, ONE = 1.0D0, TWO = 2.0D0 ) +* .. +* .. Local Scalars .. + LOGICAL LQUERY + INTEGER FINISH, I, ICOMPZ, II, J, K, LGN, LIWMIN, LL, + $ LRWMIN, LWMIN, M, SMLSIZ, START + DOUBLE PRECISION EPS, ORGNRM, P, TINY +* .. +* .. External Functions .. + LOGICAL LSAME + INTEGER ILAENV + DOUBLE PRECISION DLAMCH, DLANST + EXTERNAL LSAME, ILAENV, DLAMCH, DLANST +* .. +* .. External Subroutines .. + EXTERNAL DLASCL, DLASET, DSTEDC, DSTEQR, DSTERF, XERBLA, + $ ZLACPY, ZLACRM, ZLAED0, ZSTEQR, ZSWAP +* .. +* .. Intrinsic Functions .. + INTRINSIC ABS, DBLE, INT, LOG, MAX, MOD, SQRT +* .. +* .. Executable Statements .. +* +* Test the input parameters. +* + INFO = 0 + LQUERY = ( LWORK.EQ.-1 .OR. LRWORK.EQ.-1 .OR. LIWORK.EQ.-1 ) +* + IF( LSAME( COMPZ, 'N' ) ) THEN + ICOMPZ = 0 + ELSE IF( LSAME( COMPZ, 'V' ) ) THEN + ICOMPZ = 1 + ELSE IF( LSAME( COMPZ, 'I' ) ) THEN + ICOMPZ = 2 + ELSE + ICOMPZ = -1 + END IF + IF( ICOMPZ.LT.0 ) THEN + INFO = -1 + ELSE IF( N.LT.0 ) THEN + INFO = -2 + ELSE IF( ( LDZ.LT.1 ) .OR. + $ ( ICOMPZ.GT.0 .AND. LDZ.LT.MAX( 1, N ) ) ) THEN + INFO = -6 + END IF +* + IF( INFO.EQ.0 ) THEN +* +* Compute the workspace requirements +* + SMLSIZ = ILAENV( 9, 'ZSTEDC', ' ', 0, 0, 0, 0 ) + IF( N.LE.1 .OR. ICOMPZ.EQ.0 ) THEN + LWMIN = 1 + LIWMIN = 1 + LRWMIN = 1 + ELSE IF( N.LE.SMLSIZ ) THEN + LWMIN = 1 + LIWMIN = 1 + LRWMIN = 2*( N - 1 ) + ELSE IF( ICOMPZ.EQ.1 ) THEN + LGN = INT( LOG( DBLE( N ) ) / LOG( TWO ) ) + IF( 2**LGN.LT.N ) + $ LGN = LGN + 1 + IF( 2**LGN.LT.N ) + $ LGN = LGN + 1 + LWMIN = N*N + LRWMIN = 1 + 3*N + 2*N*LGN + 4*N**2 + LIWMIN = 6 + 6*N + 5*N*LGN + ELSE IF( ICOMPZ.EQ.2 ) THEN + LWMIN = 1 + LRWMIN = 1 + 4*N + 2*N**2 + LIWMIN = 3 + 5*N + END IF + WORK( 1 ) = LWMIN + RWORK( 1 ) = LRWMIN + IWORK( 1 ) = LIWMIN +* + IF( LWORK.LT.LWMIN .AND. .NOT.LQUERY ) THEN + INFO = -8 + ELSE IF( LRWORK.LT.LRWMIN .AND. .NOT.LQUERY ) THEN + INFO = -10 + ELSE IF( LIWORK.LT.LIWMIN .AND. .NOT.LQUERY ) THEN + INFO = -12 + END IF + END IF +* + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'ZSTEDC', -INFO ) + RETURN + ELSE IF( LQUERY ) THEN + RETURN + END IF +* +* Quick return if possible +* + IF( N.EQ.0 ) + $ RETURN + IF( N.EQ.1 ) THEN + IF( ICOMPZ.NE.0 ) + $ Z( 1, 1 ) = ONE + RETURN + END IF +* +* If the following conditional clause is removed, then the routine +* will use the Divide and Conquer routine to compute only the +* eigenvalues, which requires (3N + 3N**2) real workspace and +* (2 + 5N + 2N lg(N)) integer workspace. +* Since on many architectures DSTERF is much faster than any other +* algorithm for finding eigenvalues only, it is used here +* as the default. If the conditional clause is removed, then +* information on the size of workspace needs to be changed. +* +* If COMPZ = 'N', use DSTERF to compute the eigenvalues. +* + IF( ICOMPZ.EQ.0 ) THEN + CALL DSTERF( N, D, E, INFO ) + GO TO 70 + END IF +* +* If N is smaller than the minimum divide size (SMLSIZ+1), then +* solve the problem with another solver. +* + IF( N.LE.SMLSIZ ) THEN +* + CALL ZSTEQR( COMPZ, N, D, E, Z, LDZ, RWORK, INFO ) +* + ELSE +* +* If COMPZ = 'I', we simply call DSTEDC instead. +* + IF( ICOMPZ.EQ.2 ) THEN + CALL DLASET( 'Full', N, N, ZERO, ONE, RWORK, N ) + LL = N*N + 1 + CALL DSTEDC( 'I', N, D, E, RWORK, N, + $ RWORK( LL ), LRWORK-LL+1, IWORK, LIWORK, INFO ) + DO 20 J = 1, N + DO 10 I = 1, N + Z( I, J ) = RWORK( ( J-1 )*N+I ) + 10 CONTINUE + 20 CONTINUE + GO TO 70 + END IF +* +* From now on, only option left to be handled is COMPZ = 'V', +* i.e. ICOMPZ = 1. +* +* Scale. +* + ORGNRM = DLANST( 'M', N, D, E ) + IF( ORGNRM.EQ.ZERO ) + $ GO TO 70 +* + EPS = DLAMCH( 'Epsilon' ) +* + START = 1 +* +* while ( START <= N ) +* + 30 CONTINUE + IF( START.LE.N ) THEN +* +* Let FINISH be the position of the next subdiagonal entry +* such that E( FINISH ) <= TINY or FINISH = N if no such +* subdiagonal exists. The matrix identified by the elements +* between START and FINISH constitutes an independent +* sub-problem. +* + FINISH = START + 40 CONTINUE + IF( FINISH.LT.N ) THEN + TINY = EPS*SQRT( ABS( D( FINISH ) ) )* + $ SQRT( ABS( D( FINISH+1 ) ) ) + IF( ABS( E( FINISH ) ).GT.TINY ) THEN + FINISH = FINISH + 1 + GO TO 40 + END IF + END IF +* +* (Sub) Problem determined. Compute its size and solve it. +* + M = FINISH - START + 1 + IF( M.GT.SMLSIZ ) THEN +* +* Scale. +* + ORGNRM = DLANST( 'M', M, D( START ), E( START ) ) + CALL DLASCL( 'G', 0, 0, ORGNRM, ONE, M, 1, D( START ), M, + $ INFO ) + CALL DLASCL( 'G', 0, 0, ORGNRM, ONE, M-1, 1, E( START ), + $ M-1, INFO ) +* + CALL ZLAED0( N, M, D( START ), E( START ), Z( 1, START ), + $ LDZ, WORK, N, RWORK, IWORK, INFO ) + IF( INFO.GT.0 ) THEN + INFO = ( INFO / ( M+1 )+START-1 )*( N+1 ) + + $ MOD( INFO, ( M+1 ) ) + START - 1 + GO TO 70 + END IF +* +* Scale back. +* + CALL DLASCL( 'G', 0, 0, ONE, ORGNRM, M, 1, D( START ), M, + $ INFO ) +* + ELSE + CALL DSTEQR( 'I', M, D( START ), E( START ), RWORK, M, + $ RWORK( M*M+1 ), INFO ) + CALL ZLACRM( N, M, Z( 1, START ), LDZ, RWORK, M, WORK, N, + $ RWORK( M*M+1 ) ) + CALL ZLACPY( 'A', N, M, WORK, N, Z( 1, START ), LDZ ) + IF( INFO.GT.0 ) THEN + INFO = START*( N+1 ) + FINISH + GO TO 70 + END IF + END IF +* + START = FINISH + 1 + GO TO 30 + END IF +* +* endwhile +* +* +* Use Selection Sort to minimize swaps of eigenvectors +* + DO 60 II = 2, N + I = II - 1 + K = I + P = D( I ) + DO 50 J = II, N + IF( D( J ).LT.P ) THEN + K = J + P = D( J ) + END IF + 50 CONTINUE + IF( K.NE.I ) THEN + D( K ) = D( I ) + D( I ) = P + CALL ZSWAP( N, Z( 1, I ), 1, Z( 1, K ), 1 ) + END IF + 60 CONTINUE + END IF +* + 70 CONTINUE + WORK( 1 ) = LWMIN + RWORK( 1 ) = LRWMIN + IWORK( 1 ) = LIWMIN +* + RETURN +* +* End of ZSTEDC +* + END diff --git a/lib/linalg/zunm2l.f b/lib/linalg/zunm2l.f new file mode 100644 index 0000000000..48c2dbfc0c --- /dev/null +++ b/lib/linalg/zunm2l.f @@ -0,0 +1,278 @@ +*> \brief \b ZUNM2L multiplies a general matrix by the unitary matrix from a QL factorization determined by cgeqlf (unblocked algorithm). +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download ZUNM2L + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE ZUNM2L( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, +* WORK, INFO ) +* +* .. Scalar Arguments .. +* CHARACTER SIDE, TRANS +* INTEGER INFO, K, LDA, LDC, M, N +* .. +* .. Array Arguments .. +* COMPLEX*16 A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> ZUNM2L overwrites the general complex m-by-n matrix C with +*> +*> Q * C if SIDE = 'L' and TRANS = 'N', or +*> +*> Q**H* C if SIDE = 'L' and TRANS = 'C', or +*> +*> C * Q if SIDE = 'R' and TRANS = 'N', or +*> +*> C * Q**H if SIDE = 'R' and TRANS = 'C', +*> +*> where Q is a complex unitary matrix defined as the product of k +*> elementary reflectors +*> +*> Q = H(k) . . . H(2) H(1) +*> +*> as returned by ZGEQLF. Q is of order m if SIDE = 'L' and of order n +*> if SIDE = 'R'. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] SIDE +*> \verbatim +*> SIDE is CHARACTER*1 +*> = 'L': apply Q or Q**H from the Left +*> = 'R': apply Q or Q**H from the Right +*> \endverbatim +*> +*> \param[in] TRANS +*> \verbatim +*> TRANS is CHARACTER*1 +*> = 'N': apply Q (No transpose) +*> = 'C': apply Q**H (Conjugate transpose) +*> \endverbatim +*> +*> \param[in] M +*> \verbatim +*> M is INTEGER +*> The number of rows of the matrix C. M >= 0. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The number of columns of the matrix C. N >= 0. +*> \endverbatim +*> +*> \param[in] K +*> \verbatim +*> K is INTEGER +*> The number of elementary reflectors whose product defines +*> the matrix Q. +*> If SIDE = 'L', M >= K >= 0; +*> if SIDE = 'R', N >= K >= 0. +*> \endverbatim +*> +*> \param[in] A +*> \verbatim +*> A is COMPLEX*16 array, dimension (LDA,K) +*> The i-th column must contain the vector which defines the +*> elementary reflector H(i), for i = 1,2,...,k, as returned by +*> ZGEQLF in the last k columns of its array argument A. +*> A is modified by the routine but restored on exit. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. +*> If SIDE = 'L', LDA >= max(1,M); +*> if SIDE = 'R', LDA >= max(1,N). +*> \endverbatim +*> +*> \param[in] TAU +*> \verbatim +*> TAU is COMPLEX*16 array, dimension (K) +*> TAU(i) must contain the scalar factor of the elementary +*> reflector H(i), as returned by ZGEQLF. +*> \endverbatim +*> +*> \param[in,out] C +*> \verbatim +*> C is COMPLEX*16 array, dimension (LDC,N) +*> On entry, the m-by-n matrix C. +*> On exit, C is overwritten by Q*C or Q**H*C or C*Q**H or C*Q. +*> \endverbatim +*> +*> \param[in] LDC +*> \verbatim +*> LDC is INTEGER +*> The leading dimension of the array C. LDC >= max(1,M). +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is COMPLEX*16 array, dimension +*> (N) if SIDE = 'L', +*> (M) if SIDE = 'R' +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit +*> < 0: if INFO = -i, the i-th argument had an illegal value +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup complex16OTHERcomputational +* +* ===================================================================== + SUBROUTINE ZUNM2L( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, + $ WORK, INFO ) +* +* -- LAPACK computational routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + CHARACTER SIDE, TRANS + INTEGER INFO, K, LDA, LDC, M, N +* .. +* .. Array Arguments .. + COMPLEX*16 A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + COMPLEX*16 ONE + PARAMETER ( ONE = ( 1.0D+0, 0.0D+0 ) ) +* .. +* .. Local Scalars .. + LOGICAL LEFT, NOTRAN + INTEGER I, I1, I2, I3, MI, NI, NQ + COMPLEX*16 AII, TAUI +* .. +* .. External Functions .. + LOGICAL LSAME + EXTERNAL LSAME +* .. +* .. External Subroutines .. + EXTERNAL XERBLA, ZLARF +* .. +* .. Intrinsic Functions .. + INTRINSIC DCONJG, MAX +* .. +* .. Executable Statements .. +* +* Test the input arguments +* + INFO = 0 + LEFT = LSAME( SIDE, 'L' ) + NOTRAN = LSAME( TRANS, 'N' ) +* +* NQ is the order of Q +* + IF( LEFT ) THEN + NQ = M + ELSE + NQ = N + END IF + IF( .NOT.LEFT .AND. .NOT.LSAME( SIDE, 'R' ) ) THEN + INFO = -1 + ELSE IF( .NOT.NOTRAN .AND. .NOT.LSAME( TRANS, 'C' ) ) THEN + INFO = -2 + ELSE IF( M.LT.0 ) THEN + INFO = -3 + ELSE IF( N.LT.0 ) THEN + INFO = -4 + ELSE IF( K.LT.0 .OR. K.GT.NQ ) THEN + INFO = -5 + ELSE IF( LDA.LT.MAX( 1, NQ ) ) THEN + INFO = -7 + ELSE IF( LDC.LT.MAX( 1, M ) ) THEN + INFO = -10 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'ZUNM2L', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( M.EQ.0 .OR. N.EQ.0 .OR. K.EQ.0 ) + $ RETURN +* + IF( ( LEFT .AND. NOTRAN .OR. .NOT.LEFT .AND. .NOT.NOTRAN ) ) THEN + I1 = 1 + I2 = K + I3 = 1 + ELSE + I1 = K + I2 = 1 + I3 = -1 + END IF +* + IF( LEFT ) THEN + NI = N + ELSE + MI = M + END IF +* + DO 10 I = I1, I2, I3 + IF( LEFT ) THEN +* +* H(i) or H(i)**H is applied to C(1:m-k+i,1:n) +* + MI = M - K + I + ELSE +* +* H(i) or H(i)**H is applied to C(1:m,1:n-k+i) +* + NI = N - K + I + END IF +* +* Apply H(i) or H(i)**H +* + IF( NOTRAN ) THEN + TAUI = TAU( I ) + ELSE + TAUI = DCONJG( TAU( I ) ) + END IF + AII = A( NQ-K+I, I ) + A( NQ-K+I, I ) = ONE + CALL ZLARF( SIDE, MI, NI, A( 1, I ), 1, TAUI, C, LDC, WORK ) + A( NQ-K+I, I ) = AII + 10 CONTINUE + RETURN +* +* End of ZUNM2L +* + END diff --git a/lib/linalg/zunm2r.f b/lib/linalg/zunm2r.f new file mode 100644 index 0000000000..aec5a8bcae --- /dev/null +++ b/lib/linalg/zunm2r.f @@ -0,0 +1,283 @@ +*> \brief \b ZUNM2R multiplies a general matrix by the unitary matrix from a QR factorization determined by cgeqrf (unblocked algorithm). +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download ZUNM2R + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE ZUNM2R( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, +* WORK, INFO ) +* +* .. Scalar Arguments .. +* CHARACTER SIDE, TRANS +* INTEGER INFO, K, LDA, LDC, M, N +* .. +* .. Array Arguments .. +* COMPLEX*16 A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> ZUNM2R overwrites the general complex m-by-n matrix C with +*> +*> Q * C if SIDE = 'L' and TRANS = 'N', or +*> +*> Q**H* C if SIDE = 'L' and TRANS = 'C', or +*> +*> C * Q if SIDE = 'R' and TRANS = 'N', or +*> +*> C * Q**H if SIDE = 'R' and TRANS = 'C', +*> +*> where Q is a complex unitary matrix defined as the product of k +*> elementary reflectors +*> +*> Q = H(1) H(2) . . . H(k) +*> +*> as returned by ZGEQRF. Q is of order m if SIDE = 'L' and of order n +*> if SIDE = 'R'. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] SIDE +*> \verbatim +*> SIDE is CHARACTER*1 +*> = 'L': apply Q or Q**H from the Left +*> = 'R': apply Q or Q**H from the Right +*> \endverbatim +*> +*> \param[in] TRANS +*> \verbatim +*> TRANS is CHARACTER*1 +*> = 'N': apply Q (No transpose) +*> = 'C': apply Q**H (Conjugate transpose) +*> \endverbatim +*> +*> \param[in] M +*> \verbatim +*> M is INTEGER +*> The number of rows of the matrix C. M >= 0. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The number of columns of the matrix C. N >= 0. +*> \endverbatim +*> +*> \param[in] K +*> \verbatim +*> K is INTEGER +*> The number of elementary reflectors whose product defines +*> the matrix Q. +*> If SIDE = 'L', M >= K >= 0; +*> if SIDE = 'R', N >= K >= 0. +*> \endverbatim +*> +*> \param[in] A +*> \verbatim +*> A is COMPLEX*16 array, dimension (LDA,K) +*> The i-th column must contain the vector which defines the +*> elementary reflector H(i), for i = 1,2,...,k, as returned by +*> ZGEQRF in the first k columns of its array argument A. +*> A is modified by the routine but restored on exit. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. +*> If SIDE = 'L', LDA >= max(1,M); +*> if SIDE = 'R', LDA >= max(1,N). +*> \endverbatim +*> +*> \param[in] TAU +*> \verbatim +*> TAU is COMPLEX*16 array, dimension (K) +*> TAU(i) must contain the scalar factor of the elementary +*> reflector H(i), as returned by ZGEQRF. +*> \endverbatim +*> +*> \param[in,out] C +*> \verbatim +*> C is COMPLEX*16 array, dimension (LDC,N) +*> On entry, the m-by-n matrix C. +*> On exit, C is overwritten by Q*C or Q**H*C or C*Q**H or C*Q. +*> \endverbatim +*> +*> \param[in] LDC +*> \verbatim +*> LDC is INTEGER +*> The leading dimension of the array C. LDC >= max(1,M). +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is COMPLEX*16 array, dimension +*> (N) if SIDE = 'L', +*> (M) if SIDE = 'R' +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit +*> < 0: if INFO = -i, the i-th argument had an illegal value +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup complex16OTHERcomputational +* +* ===================================================================== + SUBROUTINE ZUNM2R( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, + $ WORK, INFO ) +* +* -- LAPACK computational routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + CHARACTER SIDE, TRANS + INTEGER INFO, K, LDA, LDC, M, N +* .. +* .. Array Arguments .. + COMPLEX*16 A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + COMPLEX*16 ONE + PARAMETER ( ONE = ( 1.0D+0, 0.0D+0 ) ) +* .. +* .. Local Scalars .. + LOGICAL LEFT, NOTRAN + INTEGER I, I1, I2, I3, IC, JC, MI, NI, NQ + COMPLEX*16 AII, TAUI +* .. +* .. External Functions .. + LOGICAL LSAME + EXTERNAL LSAME +* .. +* .. External Subroutines .. + EXTERNAL XERBLA, ZLARF +* .. +* .. Intrinsic Functions .. + INTRINSIC DCONJG, MAX +* .. +* .. Executable Statements .. +* +* Test the input arguments +* + INFO = 0 + LEFT = LSAME( SIDE, 'L' ) + NOTRAN = LSAME( TRANS, 'N' ) +* +* NQ is the order of Q +* + IF( LEFT ) THEN + NQ = M + ELSE + NQ = N + END IF + IF( .NOT.LEFT .AND. .NOT.LSAME( SIDE, 'R' ) ) THEN + INFO = -1 + ELSE IF( .NOT.NOTRAN .AND. .NOT.LSAME( TRANS, 'C' ) ) THEN + INFO = -2 + ELSE IF( M.LT.0 ) THEN + INFO = -3 + ELSE IF( N.LT.0 ) THEN + INFO = -4 + ELSE IF( K.LT.0 .OR. K.GT.NQ ) THEN + INFO = -5 + ELSE IF( LDA.LT.MAX( 1, NQ ) ) THEN + INFO = -7 + ELSE IF( LDC.LT.MAX( 1, M ) ) THEN + INFO = -10 + END IF + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'ZUNM2R', -INFO ) + RETURN + END IF +* +* Quick return if possible +* + IF( M.EQ.0 .OR. N.EQ.0 .OR. K.EQ.0 ) + $ RETURN +* + IF( ( LEFT .AND. .NOT.NOTRAN .OR. .NOT.LEFT .AND. NOTRAN ) ) THEN + I1 = 1 + I2 = K + I3 = 1 + ELSE + I1 = K + I2 = 1 + I3 = -1 + END IF +* + IF( LEFT ) THEN + NI = N + JC = 1 + ELSE + MI = M + IC = 1 + END IF +* + DO 10 I = I1, I2, I3 + IF( LEFT ) THEN +* +* H(i) or H(i)**H is applied to C(i:m,1:n) +* + MI = M - I + 1 + IC = I + ELSE +* +* H(i) or H(i)**H is applied to C(1:m,i:n) +* + NI = N - I + 1 + JC = I + END IF +* +* Apply H(i) or H(i)**H +* + IF( NOTRAN ) THEN + TAUI = TAU( I ) + ELSE + TAUI = DCONJG( TAU( I ) ) + END IF + AII = A( I, I ) + A( I, I ) = ONE + CALL ZLARF( SIDE, MI, NI, A( I, I ), 1, TAUI, C( IC, JC ), LDC, + $ WORK ) + A( I, I ) = AII + 10 CONTINUE + RETURN +* +* End of ZUNM2R +* + END diff --git a/lib/linalg/zunmql.f b/lib/linalg/zunmql.f new file mode 100644 index 0000000000..06353a0c75 --- /dev/null +++ b/lib/linalg/zunmql.f @@ -0,0 +1,336 @@ +*> \brief \b ZUNMQL +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download ZUNMQL + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE ZUNMQL( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, +* WORK, LWORK, INFO ) +* +* .. Scalar Arguments .. +* CHARACTER SIDE, TRANS +* INTEGER INFO, K, LDA, LDC, LWORK, M, N +* .. +* .. Array Arguments .. +* COMPLEX*16 A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> ZUNMQL overwrites the general complex M-by-N matrix C with +*> +*> SIDE = 'L' SIDE = 'R' +*> TRANS = 'N': Q * C C * Q +*> TRANS = 'C': Q**H * C C * Q**H +*> +*> where Q is a complex unitary matrix defined as the product of k +*> elementary reflectors +*> +*> Q = H(k) . . . H(2) H(1) +*> +*> as returned by ZGEQLF. Q is of order M if SIDE = 'L' and of order N +*> if SIDE = 'R'. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] SIDE +*> \verbatim +*> SIDE is CHARACTER*1 +*> = 'L': apply Q or Q**H from the Left; +*> = 'R': apply Q or Q**H from the Right. +*> \endverbatim +*> +*> \param[in] TRANS +*> \verbatim +*> TRANS is CHARACTER*1 +*> = 'N': No transpose, apply Q; +*> = 'C': Conjugate transpose, apply Q**H. +*> \endverbatim +*> +*> \param[in] M +*> \verbatim +*> M is INTEGER +*> The number of rows of the matrix C. M >= 0. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The number of columns of the matrix C. N >= 0. +*> \endverbatim +*> +*> \param[in] K +*> \verbatim +*> K is INTEGER +*> The number of elementary reflectors whose product defines +*> the matrix Q. +*> If SIDE = 'L', M >= K >= 0; +*> if SIDE = 'R', N >= K >= 0. +*> \endverbatim +*> +*> \param[in] A +*> \verbatim +*> A is COMPLEX*16 array, dimension (LDA,K) +*> The i-th column must contain the vector which defines the +*> elementary reflector H(i), for i = 1,2,...,k, as returned by +*> ZGEQLF in the last k columns of its array argument A. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. +*> If SIDE = 'L', LDA >= max(1,M); +*> if SIDE = 'R', LDA >= max(1,N). +*> \endverbatim +*> +*> \param[in] TAU +*> \verbatim +*> TAU is COMPLEX*16 array, dimension (K) +*> TAU(i) must contain the scalar factor of the elementary +*> reflector H(i), as returned by ZGEQLF. +*> \endverbatim +*> +*> \param[in,out] C +*> \verbatim +*> C is COMPLEX*16 array, dimension (LDC,N) +*> On entry, the M-by-N matrix C. +*> On exit, C is overwritten by Q*C or Q**H*C or C*Q**H or C*Q. +*> \endverbatim +*> +*> \param[in] LDC +*> \verbatim +*> LDC is INTEGER +*> The leading dimension of the array C. LDC >= max(1,M). +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is COMPLEX*16 array, dimension (MAX(1,LWORK)) +*> On exit, if INFO = 0, WORK(1) returns the optimal LWORK. +*> \endverbatim +*> +*> \param[in] LWORK +*> \verbatim +*> LWORK is INTEGER +*> The dimension of the array WORK. +*> If SIDE = 'L', LWORK >= max(1,N); +*> if SIDE = 'R', LWORK >= max(1,M). +*> For good performance, LWORK should generally be larger. +*> +*> If LWORK = -1, then a workspace query is assumed; the routine +*> only calculates the optimal size of the WORK array, returns +*> this value as the first entry of the WORK array, and no error +*> message related to LWORK is issued by XERBLA. +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit +*> < 0: if INFO = -i, the i-th argument had an illegal value +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup complex16OTHERcomputational +* +* ===================================================================== + SUBROUTINE ZUNMQL( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, + $ WORK, LWORK, INFO ) +* +* -- LAPACK computational routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + CHARACTER SIDE, TRANS + INTEGER INFO, K, LDA, LDC, LWORK, M, N +* .. +* .. Array Arguments .. + COMPLEX*16 A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + INTEGER NBMAX, LDT, TSIZE + PARAMETER ( NBMAX = 64, LDT = NBMAX+1, + $ TSIZE = LDT*NBMAX ) +* .. +* .. Local Scalars .. + LOGICAL LEFT, LQUERY, NOTRAN + INTEGER I, I1, I2, I3, IB, IINFO, IWT, LDWORK, LWKOPT, + $ MI, NB, NBMIN, NI, NQ, NW +* .. +* .. External Functions .. + LOGICAL LSAME + INTEGER ILAENV + EXTERNAL LSAME, ILAENV +* .. +* .. External Subroutines .. + EXTERNAL XERBLA, ZLARFB, ZLARFT, ZUNM2L +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX, MIN +* .. +* .. Executable Statements .. +* +* Test the input arguments +* + INFO = 0 + LEFT = LSAME( SIDE, 'L' ) + NOTRAN = LSAME( TRANS, 'N' ) + LQUERY = ( LWORK.EQ.-1 ) +* +* NQ is the order of Q and NW is the minimum dimension of WORK +* + IF( LEFT ) THEN + NQ = M + NW = MAX( 1, N ) + ELSE + NQ = N + NW = MAX( 1, M ) + END IF + IF( .NOT.LEFT .AND. .NOT.LSAME( SIDE, 'R' ) ) THEN + INFO = -1 + ELSE IF( .NOT.NOTRAN .AND. .NOT.LSAME( TRANS, 'C' ) ) THEN + INFO = -2 + ELSE IF( M.LT.0 ) THEN + INFO = -3 + ELSE IF( N.LT.0 ) THEN + INFO = -4 + ELSE IF( K.LT.0 .OR. K.GT.NQ ) THEN + INFO = -5 + ELSE IF( LDA.LT.MAX( 1, NQ ) ) THEN + INFO = -7 + ELSE IF( LDC.LT.MAX( 1, M ) ) THEN + INFO = -10 + ELSE IF( LWORK.LT.NW .AND. .NOT.LQUERY ) THEN + INFO = -12 + END IF +* + IF( INFO.EQ.0 ) THEN +* +* Compute the workspace requirements +* + IF( M.EQ.0 .OR. N.EQ.0 ) THEN + LWKOPT = 1 + ELSE + NB = MIN( NBMAX, ILAENV( 1, 'ZUNMQL', SIDE // TRANS, M, N, + $ K, -1 ) ) + LWKOPT = NW*NB + TSIZE + END IF + WORK( 1 ) = LWKOPT + END IF +* + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'ZUNMQL', -INFO ) + RETURN + ELSE IF( LQUERY ) THEN + RETURN + END IF +* +* Quick return if possible +* + IF( M.EQ.0 .OR. N.EQ.0 ) THEN + RETURN + END IF +* + NBMIN = 2 + LDWORK = NW + IF( NB.GT.1 .AND. NB.LT.K ) THEN + IF( LWORK.LT.LWKOPT ) THEN + NB = (LWORK-TSIZE) / LDWORK + NBMIN = MAX( 2, ILAENV( 2, 'ZUNMQL', SIDE // TRANS, M, N, K, + $ -1 ) ) + END IF + END IF +* + IF( NB.LT.NBMIN .OR. NB.GE.K ) THEN +* +* Use unblocked code +* + CALL ZUNM2L( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, WORK, + $ IINFO ) + ELSE +* +* Use blocked code +* + IWT = 1 + NW*NB + IF( ( LEFT .AND. NOTRAN ) .OR. + $ ( .NOT.LEFT .AND. .NOT.NOTRAN ) ) THEN + I1 = 1 + I2 = K + I3 = NB + ELSE + I1 = ( ( K-1 ) / NB )*NB + 1 + I2 = 1 + I3 = -NB + END IF +* + IF( LEFT ) THEN + NI = N + ELSE + MI = M + END IF +* + DO 10 I = I1, I2, I3 + IB = MIN( NB, K-I+1 ) +* +* Form the triangular factor of the block reflector +* H = H(i+ib-1) . . . H(i+1) H(i) +* + CALL ZLARFT( 'Backward', 'Columnwise', NQ-K+I+IB-1, IB, + $ A( 1, I ), LDA, TAU( I ), WORK( IWT ), LDT ) + IF( LEFT ) THEN +* +* H or H**H is applied to C(1:m-k+i+ib-1,1:n) +* + MI = M - K + I + IB - 1 + ELSE +* +* H or H**H is applied to C(1:m,1:n-k+i+ib-1) +* + NI = N - K + I + IB - 1 + END IF +* +* Apply H or H**H +* + CALL ZLARFB( SIDE, TRANS, 'Backward', 'Columnwise', MI, NI, + $ IB, A( 1, I ), LDA, WORK( IWT ), LDT, C, LDC, + $ WORK, LDWORK ) + 10 CONTINUE + END IF + WORK( 1 ) = LWKOPT + RETURN +* +* End of ZUNMQL +* + END diff --git a/lib/linalg/zunmqr.f b/lib/linalg/zunmqr.f new file mode 100644 index 0000000000..2ae205f4fd --- /dev/null +++ b/lib/linalg/zunmqr.f @@ -0,0 +1,337 @@ +*> \brief \b ZUNMQR +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download ZUNMQR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE ZUNMQR( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, +* WORK, LWORK, INFO ) +* +* .. Scalar Arguments .. +* CHARACTER SIDE, TRANS +* INTEGER INFO, K, LDA, LDC, LWORK, M, N +* .. +* .. Array Arguments .. +* COMPLEX*16 A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> ZUNMQR overwrites the general complex M-by-N matrix C with +*> +*> SIDE = 'L' SIDE = 'R' +*> TRANS = 'N': Q * C C * Q +*> TRANS = 'C': Q**H * C C * Q**H +*> +*> where Q is a complex unitary matrix defined as the product of k +*> elementary reflectors +*> +*> Q = H(1) H(2) . . . H(k) +*> +*> as returned by ZGEQRF. Q is of order M if SIDE = 'L' and of order N +*> if SIDE = 'R'. +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] SIDE +*> \verbatim +*> SIDE is CHARACTER*1 +*> = 'L': apply Q or Q**H from the Left; +*> = 'R': apply Q or Q**H from the Right. +*> \endverbatim +*> +*> \param[in] TRANS +*> \verbatim +*> TRANS is CHARACTER*1 +*> = 'N': No transpose, apply Q; +*> = 'C': Conjugate transpose, apply Q**H. +*> \endverbatim +*> +*> \param[in] M +*> \verbatim +*> M is INTEGER +*> The number of rows of the matrix C. M >= 0. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The number of columns of the matrix C. N >= 0. +*> \endverbatim +*> +*> \param[in] K +*> \verbatim +*> K is INTEGER +*> The number of elementary reflectors whose product defines +*> the matrix Q. +*> If SIDE = 'L', M >= K >= 0; +*> if SIDE = 'R', N >= K >= 0. +*> \endverbatim +*> +*> \param[in] A +*> \verbatim +*> A is COMPLEX*16 array, dimension (LDA,K) +*> The i-th column must contain the vector which defines the +*> elementary reflector H(i), for i = 1,2,...,k, as returned by +*> ZGEQRF in the first k columns of its array argument A. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. +*> If SIDE = 'L', LDA >= max(1,M); +*> if SIDE = 'R', LDA >= max(1,N). +*> \endverbatim +*> +*> \param[in] TAU +*> \verbatim +*> TAU is COMPLEX*16 array, dimension (K) +*> TAU(i) must contain the scalar factor of the elementary +*> reflector H(i), as returned by ZGEQRF. +*> \endverbatim +*> +*> \param[in,out] C +*> \verbatim +*> C is COMPLEX*16 array, dimension (LDC,N) +*> On entry, the M-by-N matrix C. +*> On exit, C is overwritten by Q*C or Q**H*C or C*Q**H or C*Q. +*> \endverbatim +*> +*> \param[in] LDC +*> \verbatim +*> LDC is INTEGER +*> The leading dimension of the array C. LDC >= max(1,M). +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is COMPLEX*16 array, dimension (MAX(1,LWORK)) +*> On exit, if INFO = 0, WORK(1) returns the optimal LWORK. +*> \endverbatim +*> +*> \param[in] LWORK +*> \verbatim +*> LWORK is INTEGER +*> The dimension of the array WORK. +*> If SIDE = 'L', LWORK >= max(1,N); +*> if SIDE = 'R', LWORK >= max(1,M). +*> For good performance, LWORK should generally be larger. +*> +*> If LWORK = -1, then a workspace query is assumed; the routine +*> only calculates the optimal size of the WORK array, returns +*> this value as the first entry of the WORK array, and no error +*> message related to LWORK is issued by XERBLA. +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit +*> < 0: if INFO = -i, the i-th argument had an illegal value +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup complex16OTHERcomputational +* +* ===================================================================== + SUBROUTINE ZUNMQR( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, + $ WORK, LWORK, INFO ) +* +* -- LAPACK computational routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + CHARACTER SIDE, TRANS + INTEGER INFO, K, LDA, LDC, LWORK, M, N +* .. +* .. Array Arguments .. + COMPLEX*16 A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) +* .. +* +* ===================================================================== +* +* .. Parameters .. + INTEGER NBMAX, LDT, TSIZE + PARAMETER ( NBMAX = 64, LDT = NBMAX+1, + $ TSIZE = LDT*NBMAX ) +* .. +* .. Local Scalars .. + LOGICAL LEFT, LQUERY, NOTRAN + INTEGER I, I1, I2, I3, IB, IC, IINFO, IWT, JC, LDWORK, + $ LWKOPT, MI, NB, NBMIN, NI, NQ, NW +* .. +* .. External Functions .. + LOGICAL LSAME + INTEGER ILAENV + EXTERNAL LSAME, ILAENV +* .. +* .. External Subroutines .. + EXTERNAL XERBLA, ZLARFB, ZLARFT, ZUNM2R +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX, MIN +* .. +* .. Executable Statements .. +* +* Test the input arguments +* + INFO = 0 + LEFT = LSAME( SIDE, 'L' ) + NOTRAN = LSAME( TRANS, 'N' ) + LQUERY = ( LWORK.EQ.-1 ) +* +* NQ is the order of Q and NW is the minimum dimension of WORK +* + IF( LEFT ) THEN + NQ = M + NW = MAX( 1, N ) + ELSE + NQ = N + NW = MAX( 1, M ) + END IF + IF( .NOT.LEFT .AND. .NOT.LSAME( SIDE, 'R' ) ) THEN + INFO = -1 + ELSE IF( .NOT.NOTRAN .AND. .NOT.LSAME( TRANS, 'C' ) ) THEN + INFO = -2 + ELSE IF( M.LT.0 ) THEN + INFO = -3 + ELSE IF( N.LT.0 ) THEN + INFO = -4 + ELSE IF( K.LT.0 .OR. K.GT.NQ ) THEN + INFO = -5 + ELSE IF( LDA.LT.MAX( 1, NQ ) ) THEN + INFO = -7 + ELSE IF( LDC.LT.MAX( 1, M ) ) THEN + INFO = -10 + ELSE IF( LWORK.LT.NW .AND. .NOT.LQUERY ) THEN + INFO = -12 + END IF +* + IF( INFO.EQ.0 ) THEN +* +* Compute the workspace requirements +* + NB = MIN( NBMAX, ILAENV( 1, 'ZUNMQR', SIDE // TRANS, M, N, K, + $ -1 ) ) + LWKOPT = NW*NB + TSIZE + WORK( 1 ) = LWKOPT + END IF +* + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'ZUNMQR', -INFO ) + RETURN + ELSE IF( LQUERY ) THEN + RETURN + END IF +* +* Quick return if possible +* + IF( M.EQ.0 .OR. N.EQ.0 .OR. K.EQ.0 ) THEN + WORK( 1 ) = 1 + RETURN + END IF +* + NBMIN = 2 + LDWORK = NW + IF( NB.GT.1 .AND. NB.LT.K ) THEN + IF( LWORK.LT.LWKOPT ) THEN + NB = (LWORK-TSIZE) / LDWORK + NBMIN = MAX( 2, ILAENV( 2, 'ZUNMQR', SIDE // TRANS, M, N, K, + $ -1 ) ) + END IF + END IF +* + IF( NB.LT.NBMIN .OR. NB.GE.K ) THEN +* +* Use unblocked code +* + CALL ZUNM2R( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, WORK, + $ IINFO ) + ELSE +* +* Use blocked code +* + IWT = 1 + NW*NB + IF( ( LEFT .AND. .NOT.NOTRAN ) .OR. + $ ( .NOT.LEFT .AND. NOTRAN ) ) THEN + I1 = 1 + I2 = K + I3 = NB + ELSE + I1 = ( ( K-1 ) / NB )*NB + 1 + I2 = 1 + I3 = -NB + END IF +* + IF( LEFT ) THEN + NI = N + JC = 1 + ELSE + MI = M + IC = 1 + END IF +* + DO 10 I = I1, I2, I3 + IB = MIN( NB, K-I+1 ) +* +* Form the triangular factor of the block reflector +* H = H(i) H(i+1) . . . H(i+ib-1) +* + CALL ZLARFT( 'Forward', 'Columnwise', NQ-I+1, IB, A( I, I ), + $ LDA, TAU( I ), WORK( IWT ), LDT ) + IF( LEFT ) THEN +* +* H or H**H is applied to C(i:m,1:n) +* + MI = M - I + 1 + IC = I + ELSE +* +* H or H**H is applied to C(1:m,i:n) +* + NI = N - I + 1 + JC = I + END IF +* +* Apply H or H**H +* + CALL ZLARFB( SIDE, TRANS, 'Forward', 'Columnwise', MI, NI, + $ IB, A( I, I ), LDA, WORK( IWT ), LDT, + $ C( IC, JC ), LDC, WORK, LDWORK ) + 10 CONTINUE + END IF + WORK( 1 ) = LWKOPT + RETURN +* +* End of ZUNMQR +* + END diff --git a/lib/linalg/zunmtr.f b/lib/linalg/zunmtr.f new file mode 100644 index 0000000000..441a7c2bcc --- /dev/null +++ b/lib/linalg/zunmtr.f @@ -0,0 +1,307 @@ +*> \brief \b ZUNMTR +* +* =========== DOCUMENTATION =========== +* +* Online html documentation available at +* http://www.netlib.org/lapack/explore-html/ +* +*> \htmlonly +*> Download ZUNMTR + dependencies +*> +*> [TGZ] +*> +*> [ZIP] +*> +*> [TXT] +*> \endhtmlonly +* +* Definition: +* =========== +* +* SUBROUTINE ZUNMTR( SIDE, UPLO, TRANS, M, N, A, LDA, TAU, C, LDC, +* WORK, LWORK, INFO ) +* +* .. Scalar Arguments .. +* CHARACTER SIDE, TRANS, UPLO +* INTEGER INFO, LDA, LDC, LWORK, M, N +* .. +* .. Array Arguments .. +* COMPLEX*16 A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) +* .. +* +* +*> \par Purpose: +* ============= +*> +*> \verbatim +*> +*> ZUNMTR overwrites the general complex M-by-N matrix C with +*> +*> SIDE = 'L' SIDE = 'R' +*> TRANS = 'N': Q * C C * Q +*> TRANS = 'C': Q**H * C C * Q**H +*> +*> where Q is a complex unitary matrix of order nq, with nq = m if +*> SIDE = 'L' and nq = n if SIDE = 'R'. Q is defined as the product of +*> nq-1 elementary reflectors, as returned by ZHETRD: +*> +*> if UPLO = 'U', Q = H(nq-1) . . . H(2) H(1); +*> +*> if UPLO = 'L', Q = H(1) H(2) . . . H(nq-1). +*> \endverbatim +* +* Arguments: +* ========== +* +*> \param[in] SIDE +*> \verbatim +*> SIDE is CHARACTER*1 +*> = 'L': apply Q or Q**H from the Left; +*> = 'R': apply Q or Q**H from the Right. +*> \endverbatim +*> +*> \param[in] UPLO +*> \verbatim +*> UPLO is CHARACTER*1 +*> = 'U': Upper triangle of A contains elementary reflectors +*> from ZHETRD; +*> = 'L': Lower triangle of A contains elementary reflectors +*> from ZHETRD. +*> \endverbatim +*> +*> \param[in] TRANS +*> \verbatim +*> TRANS is CHARACTER*1 +*> = 'N': No transpose, apply Q; +*> = 'C': Conjugate transpose, apply Q**H. +*> \endverbatim +*> +*> \param[in] M +*> \verbatim +*> M is INTEGER +*> The number of rows of the matrix C. M >= 0. +*> \endverbatim +*> +*> \param[in] N +*> \verbatim +*> N is INTEGER +*> The number of columns of the matrix C. N >= 0. +*> \endverbatim +*> +*> \param[in] A +*> \verbatim +*> A is COMPLEX*16 array, dimension +*> (LDA,M) if SIDE = 'L' +*> (LDA,N) if SIDE = 'R' +*> The vectors which define the elementary reflectors, as +*> returned by ZHETRD. +*> \endverbatim +*> +*> \param[in] LDA +*> \verbatim +*> LDA is INTEGER +*> The leading dimension of the array A. +*> LDA >= max(1,M) if SIDE = 'L'; LDA >= max(1,N) if SIDE = 'R'. +*> \endverbatim +*> +*> \param[in] TAU +*> \verbatim +*> TAU is COMPLEX*16 array, dimension +*> (M-1) if SIDE = 'L' +*> (N-1) if SIDE = 'R' +*> TAU(i) must contain the scalar factor of the elementary +*> reflector H(i), as returned by ZHETRD. +*> \endverbatim +*> +*> \param[in,out] C +*> \verbatim +*> C is COMPLEX*16 array, dimension (LDC,N) +*> On entry, the M-by-N matrix C. +*> On exit, C is overwritten by Q*C or Q**H*C or C*Q**H or C*Q. +*> \endverbatim +*> +*> \param[in] LDC +*> \verbatim +*> LDC is INTEGER +*> The leading dimension of the array C. LDC >= max(1,M). +*> \endverbatim +*> +*> \param[out] WORK +*> \verbatim +*> WORK is COMPLEX*16 array, dimension (MAX(1,LWORK)) +*> On exit, if INFO = 0, WORK(1) returns the optimal LWORK. +*> \endverbatim +*> +*> \param[in] LWORK +*> \verbatim +*> LWORK is INTEGER +*> The dimension of the array WORK. +*> If SIDE = 'L', LWORK >= max(1,N); +*> if SIDE = 'R', LWORK >= max(1,M). +*> For optimum performance LWORK >= N*NB if SIDE = 'L', and +*> LWORK >=M*NB if SIDE = 'R', where NB is the optimal +*> blocksize. +*> +*> If LWORK = -1, then a workspace query is assumed; the routine +*> only calculates the optimal size of the WORK array, returns +*> this value as the first entry of the WORK array, and no error +*> message related to LWORK is issued by XERBLA. +*> \endverbatim +*> +*> \param[out] INFO +*> \verbatim +*> INFO is INTEGER +*> = 0: successful exit +*> < 0: if INFO = -i, the i-th argument had an illegal value +*> \endverbatim +* +* Authors: +* ======== +* +*> \author Univ. of Tennessee +*> \author Univ. of California Berkeley +*> \author Univ. of Colorado Denver +*> \author NAG Ltd. +* +*> \ingroup complex16OTHERcomputational +* +* ===================================================================== + SUBROUTINE ZUNMTR( SIDE, UPLO, TRANS, M, N, A, LDA, TAU, C, LDC, + $ WORK, LWORK, INFO ) +* +* -- LAPACK computational routine -- +* -- LAPACK is a software package provided by Univ. of Tennessee, -- +* -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- +* +* .. Scalar Arguments .. + CHARACTER SIDE, TRANS, UPLO + INTEGER INFO, LDA, LDC, LWORK, M, N +* .. +* .. Array Arguments .. + COMPLEX*16 A( LDA, * ), C( LDC, * ), TAU( * ), WORK( * ) +* .. +* +* ===================================================================== +* +* .. Local Scalars .. + LOGICAL LEFT, LQUERY, UPPER + INTEGER I1, I2, IINFO, LWKOPT, MI, NB, NI, NQ, NW +* .. +* .. External Functions .. + LOGICAL LSAME + INTEGER ILAENV + EXTERNAL LSAME, ILAENV +* .. +* .. External Subroutines .. + EXTERNAL XERBLA, ZUNMQL, ZUNMQR +* .. +* .. Intrinsic Functions .. + INTRINSIC MAX +* .. +* .. Executable Statements .. +* +* Test the input arguments +* + INFO = 0 + LEFT = LSAME( SIDE, 'L' ) + UPPER = LSAME( UPLO, 'U' ) + LQUERY = ( LWORK.EQ.-1 ) +* +* NQ is the order of Q and NW is the minimum dimension of WORK +* + IF( LEFT ) THEN + NQ = M + NW = MAX( 1, N ) + ELSE + NQ = N + NW = MAX( 1, M ) + END IF + IF( .NOT.LEFT .AND. .NOT.LSAME( SIDE, 'R' ) ) THEN + INFO = -1 + ELSE IF( .NOT.UPPER .AND. .NOT.LSAME( UPLO, 'L' ) ) THEN + INFO = -2 + ELSE IF( .NOT.LSAME( TRANS, 'N' ) .AND. .NOT.LSAME( TRANS, 'C' ) ) + $ THEN + INFO = -3 + ELSE IF( M.LT.0 ) THEN + INFO = -4 + ELSE IF( N.LT.0 ) THEN + INFO = -5 + ELSE IF( LDA.LT.MAX( 1, NQ ) ) THEN + INFO = -7 + ELSE IF( LDC.LT.MAX( 1, M ) ) THEN + INFO = -10 + ELSE IF( LWORK.LT.NW .AND. .NOT.LQUERY ) THEN + INFO = -12 + END IF +* + IF( INFO.EQ.0 ) THEN + IF( UPPER ) THEN + IF( LEFT ) THEN + NB = ILAENV( 1, 'ZUNMQL', SIDE // TRANS, M-1, N, M-1, + $ -1 ) + ELSE + NB = ILAENV( 1, 'ZUNMQL', SIDE // TRANS, M, N-1, N-1, + $ -1 ) + END IF + ELSE + IF( LEFT ) THEN + NB = ILAENV( 1, 'ZUNMQR', SIDE // TRANS, M-1, N, M-1, + $ -1 ) + ELSE + NB = ILAENV( 1, 'ZUNMQR', SIDE // TRANS, M, N-1, N-1, + $ -1 ) + END IF + END IF + LWKOPT = NW*NB + WORK( 1 ) = LWKOPT + END IF +* + IF( INFO.NE.0 ) THEN + CALL XERBLA( 'ZUNMTR', -INFO ) + RETURN + ELSE IF( LQUERY ) THEN + RETURN + END IF +* +* Quick return if possible +* + IF( M.EQ.0 .OR. N.EQ.0 .OR. NQ.EQ.1 ) THEN + WORK( 1 ) = 1 + RETURN + END IF +* + IF( LEFT ) THEN + MI = M - 1 + NI = N + ELSE + MI = M + NI = N - 1 + END IF +* + IF( UPPER ) THEN +* +* Q was determined by a call to ZHETRD with UPLO = 'U' +* + CALL ZUNMQL( SIDE, TRANS, MI, NI, NQ-1, A( 1, 2 ), LDA, TAU, C, + $ LDC, WORK, LWORK, IINFO ) + ELSE +* +* Q was determined by a call to ZHETRD with UPLO = 'L' +* + IF( LEFT ) THEN + I1 = 2 + I2 = 1 + ELSE + I1 = 1 + I2 = 2 + END IF + CALL ZUNMQR( SIDE, TRANS, MI, NI, NQ-1, A( 2, 1 ), LDA, TAU, + $ C( I1, I2 ), LDC, WORK, LWORK, IINFO ) + END IF + WORK( 1 ) = LWKOPT + RETURN +* +* End of ZUNMTR +* + END From 1f4447d1cd4fa1db02f5e21036e37176c79029d4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 21 Jul 2022 05:32:53 -0400 Subject: [PATCH 59/72] add USE_INTERNAL_LINALG to workaround passing BLAS/LAPACK settings to external projects --- cmake/CMakeLists.txt | 8 ++++--- cmake/Modules/Packages/LATTE.cmake | 5 ++-- doc/src/Build_extras.rst | 38 +++++++++++++++++++++++------- 3 files changed, 37 insertions(+), 14 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 669bff1533..d599a500c7 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -404,9 +404,11 @@ endif() if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE) enable_language(C) - find_package(LAPACK) - find_package(BLAS) - if(NOT LAPACK_FOUND OR NOT BLAS_FOUND) + if (NOT USE_INTERNAL_LINALG) + find_package(LAPACK) + find_package(BLAS) + endif() + if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG) include(CheckGeneratorSupport) if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN) status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support") diff --git a/cmake/Modules/Packages/LATTE.cmake b/cmake/Modules/Packages/LATTE.cmake index a96e850f7e..d7793fa257 100644 --- a/cmake/Modules/Packages/LATTE.cmake +++ b/cmake/Modules/Packages/LATTE.cmake @@ -23,8 +23,9 @@ if(DOWNLOAD_LATTE) # CMake cannot pass BLAS or LAPACK library variable to external project if they are a list list(LENGTH BLAS_LIBRARIES} NUM_BLAS) list(LENGTH LAPACK_LIBRARIES NUM_LAPACK) - if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1)) - message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation") + if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1) AND NOT USE_INTERNAL_LINALG) + message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation. " + "Try to configure LAMMPS with '-D USE_INTERNAL_LINALG=on' added as a workaround.") endif() include(ExternalProject) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 14d0e290aa..3dad393a52 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -788,8 +788,10 @@ library. .. code-block:: bash - -D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes - -D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location) + -D DOWNLOAD_LATTE=value # download LATTE for build, value = no (default) or yes + -D LATTE_LIBRARY=path # LATTE library file (only needed if a custom location) + -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK + # value = no (default) or yes If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded and built inside the CMake build directory. If the LATTE library @@ -797,6 +799,13 @@ library. ``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library file, not the directory the library file is in. + The LATTE library requires LAPACK (and BLAS) and CMake can identify + their locations and pass that info to the LATTE build script. But + on some systems this triggers a (current) limitation of CMake and + the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in + those cases to use the bundled linear algebra library and work around + the limitation. + .. tab:: Traditional make You can download and build the LATTE library manually if you @@ -1913,14 +1922,25 @@ within CMake will download the non-commercial use version. .. code-block:: bash - -D DOWNLOAD_QUIP=value # download OpenKIM API v2 for build, value = no (default) or yes - -D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location) + -D DOWNLOAD_QUIP=value # download QUIP library for build, value = no (default) or yes + -D QUIP_LIBRARY=path # path to libquip.a (only needed if a custom location) + -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK + # value = no (default) or yes - CMake will try to download and build the QUIP library from GitHub, if it is not - found on the local machine. This requires to have git installed. It will use the same compilers - and flags as used for compiling LAMMPS. Currently this is only supported for the GNU and the - Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled - and installed QUIP library and CMake cannot find it. + CMake will try to download and build the QUIP library from GitHub, + if it is not found on the local machine. This requires to have git + installed. It will use the same compilers and flags as used for + compiling LAMMPS. Currently this is only supported for the GNU + and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you + want to use a previously compiled and installed QUIP library and + CMake cannot find it. + + The QUIP library requires LAPACK (and BLAS) and CMake can identify + their locations and pass that info to the QUIP build script. But + on some systems this triggers a (current) limitation of CMake and + the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in + those cases to use the bundled linear algebra library and work around + the limitation. .. tab:: Traditional make From 11c46a6e9055a6c6b659b22a242e2ae102c92005 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 21 Jul 2022 08:19:39 -0400 Subject: [PATCH 60/72] correct dangling and inconsistent links to sphinx homepage and rst docs --- doc/src/Build_manual.rst | 24 ++++++++++-------------- doc/src/Modify_style.rst | 15 ++++++++------- 2 files changed, 18 insertions(+), 21 deletions(-) diff --git a/doc/src/Build_manual.rst b/doc/src/Build_manual.rst index 90633d0811..d91ac94be5 100644 --- a/doc/src/Build_manual.rst +++ b/doc/src/Build_manual.rst @@ -48,18 +48,15 @@ Build using GNU make The LAMMPS manual is written in `reStructuredText `_ format which can be translated to different output format using the `Sphinx -`_ document generator tool. It also incorporates programmer -documentation extracted from the LAMMPS C++ sources through the `Doxygen -`_ program. Currently the translation to HTML, PDF -(via LaTeX), ePUB (for many e-book readers) and MOBI (for Amazon Kindle -readers) are supported. For that to work a Python 3 interpreter, the -``doxygen`` tools and internet access to download additional files and -tools are required. This download is usually only required once or -after the documentation folder is returned to a pristine state with -``make clean-all``. - -.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html -.. _sphinx: https://www.sphinx-doc.org +`_ document generator tool. It also +incorporates programmer documentation extracted from the LAMMPS C++ +sources through the `Doxygen `_ program. Currently +the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers) +and MOBI (for Amazon Kindle readers) are supported. For that to work a +Python 3 interpreter, the ``doxygen`` tools and internet access to +download additional files and tools are required. This download is +usually only required once or after the documentation folder is returned +to a pristine state with ``make clean-all``. For the documentation build a python virtual environment is set up in the folder ``doc/docenv`` and various python packages are installed into @@ -252,6 +249,5 @@ manual with ``make spelling``. This requires `a library called enchant positives* (e.g. keywords, names, abbreviations) those can be added to the file ``lammps/doc/utils/sphinx-config/false_positives.txt``. -.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html - .. _lws: https://www.lammps.org +.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html diff --git a/doc/src/Modify_style.rst b/doc/src/Modify_style.rst index 2ed83ed7c6..9b394f23a9 100644 --- a/doc/src/Modify_style.rst +++ b/doc/src/Modify_style.rst @@ -100,13 +100,14 @@ Documentation (strict) Contributions that add new styles or commands or augment existing ones must include the corresponding new or modified documentation in -`ReStructuredText format `_ (.rst files in the ``doc/src/`` folder). The -documentation shall be written in American English and the .rst file -must use only ASCII characters so it can be cleanly translated to PDF -files (via `sphinx `_ and PDFLaTeX). Special characters may be included via -embedded math expression typeset in a LaTeX subset. +`ReStructuredText format `_ (.rst files in the ``doc/src/`` +folder). The documentation shall be written in American English and the +.rst file must use only ASCII characters so it can be cleanly translated +to PDF files (via `sphinx `_ and PDFLaTeX). +Special characters may be included via embedded math expression typeset +in a LaTeX subset. -.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html +.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html When adding new commands, they need to be integrated into the sphinx documentation system, and the corresponding command tables and lists @@ -133,7 +134,7 @@ error free completion of the HTML and PDF build will be performed and also a spell check, a check for correct anchors and labels, and a check for completeness of references all styles in their corresponding tables and lists is run. In case the spell check reports false positives they -can be added to the file doc/utils/sphinx-config/false_positives.txt +can be added to the file ``doc/utils/sphinx-config/false_positives.txt`` Contributions that add or modify the library interface or "public" APIs from the C++ code or the Fortran module must include suitable doxygen From c8cc2b1b24467a18482a07bf90962c3341316622 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 21 Jul 2022 08:41:44 -0400 Subject: [PATCH 61/72] update to LAPACK version 3.10.1 --- lib/linalg/dasum.f | 8 +++--- lib/linalg/daxpy.f | 8 +++--- lib/linalg/dbdsqr.f | 7 ++--- lib/linalg/dcabs1.f | 8 +++--- lib/linalg/dcopy.f | 8 +++--- lib/linalg/ddot.f | 8 +++--- lib/linalg/dgebd2.f | 5 +--- lib/linalg/dgebrd.f | 8 ++---- lib/linalg/dgecon.f | 5 +--- lib/linalg/dgelq2.f | 17 +++++++----- lib/linalg/dgelqf.f | 15 +++++++---- lib/linalg/dgelsd.f | 5 +--- lib/linalg/dgelss.f | 5 +--- lib/linalg/dgemm.f | 15 ++++------- lib/linalg/dgemv.f | 7 ++--- lib/linalg/dgeqr2.f | 18 ++++++++----- lib/linalg/dgeqrf.f | 34 ++++++++++++++++-------- lib/linalg/dger.f | 7 ++--- lib/linalg/dgesv.f | 5 +--- lib/linalg/dgesvd.f | 5 +--- lib/linalg/dgetf2.f | 5 +--- lib/linalg/dgetrf.f | 5 +--- lib/linalg/dgetrf2.f | 5 +--- lib/linalg/dgetri.f | 5 +--- lib/linalg/dgetrs.f | 5 +--- lib/linalg/disnan.f | 5 +--- lib/linalg/dlabad.f | 5 +--- lib/linalg/dlabrd.f | 5 +--- lib/linalg/dlacn2.f | 28 +++++++++++++------- lib/linalg/dlacpy.f | 5 +--- lib/linalg/dladiv.f | 13 +++------- lib/linalg/dlae2.f | 5 +--- lib/linalg/dlaed0.f | 7 ++--- lib/linalg/dlaed1.f | 7 ++--- lib/linalg/dlaed2.f | 7 ++--- lib/linalg/dlaed3.f | 7 ++--- lib/linalg/dlaed4.f | 9 +++---- lib/linalg/dlaed5.f | 9 +++---- lib/linalg/dlaed6.f | 7 ++--- lib/linalg/dlaed7.f | 7 ++--- lib/linalg/dlaed8.f | 7 ++--- lib/linalg/dlaed9.f | 7 ++--- lib/linalg/dlaeda.f | 7 ++--- lib/linalg/dlaev2.f | 5 +--- lib/linalg/dlaisnan.f | 5 +--- lib/linalg/dlals0.f | 5 +--- lib/linalg/dlalsa.f | 7 ++--- lib/linalg/dlalsd.f | 5 +--- lib/linalg/dlamrg.f | 5 +--- lib/linalg/dlange.f | 5 +--- lib/linalg/dlanst.f | 5 +--- lib/linalg/dlansy.f | 5 +--- lib/linalg/dlapy2.f | 15 ++++++----- lib/linalg/dlapy3.f | 15 ++++++----- lib/linalg/dlarf.f | 5 +--- lib/linalg/dlarfb.f | 7 +++-- lib/linalg/dlarfg.f | 7 ++--- lib/linalg/dlarft.f | 5 +--- lib/linalg/dlas2.f | 5 +--- lib/linalg/dlascl.f | 5 +--- lib/linalg/dlasd4.f | 5 +--- lib/linalg/dlasd5.f | 5 +--- lib/linalg/dlasd6.f | 5 +--- lib/linalg/dlasd7.f | 5 +--- lib/linalg/dlasd8.f | 5 +--- lib/linalg/dlasda.f | 5 +--- lib/linalg/dlasdq.f | 5 +--- lib/linalg/dlasdt.f | 5 +--- lib/linalg/dlaset.f | 5 +--- lib/linalg/dlasq1.f | 5 +--- lib/linalg/dlasq2.f | 20 +++++++++------ lib/linalg/dlasq3.f | 5 +--- lib/linalg/dlasq4.f | 5 +--- lib/linalg/dlasq5.f | 5 +--- lib/linalg/dlasq6.f | 5 +--- lib/linalg/dlasr.f | 7 ++--- lib/linalg/dlasrt.f | 5 +--- lib/linalg/dlasv2.f | 5 +--- lib/linalg/dlaswp.f | 5 +--- lib/linalg/dlatrd.f | 5 +--- lib/linalg/dlatrs.f | 5 +--- lib/linalg/dorg2l.f | 5 +--- lib/linalg/dorg2r.f | 5 +--- lib/linalg/dorgbr.f | 13 ++++------ lib/linalg/dorgl2.f | 5 +--- lib/linalg/dorglq.f | 5 +--- lib/linalg/dorgql.f | 5 +--- lib/linalg/dorgqr.f | 5 +--- lib/linalg/dorgtr.f | 5 +--- lib/linalg/dorm2l.f | 5 +--- lib/linalg/dorm2r.f | 5 +--- lib/linalg/dormbr.f | 13 ++++------ lib/linalg/dorml2.f | 5 +--- lib/linalg/dormlq.f | 15 +++++------ lib/linalg/dormql.f | 7 ++--- lib/linalg/dormqr.f | 15 +++++------ lib/linalg/dormtr.f | 13 ++++------ lib/linalg/dpotf2.f | 5 +--- lib/linalg/dpotrf.f | 5 +--- lib/linalg/dpotrf2.f | 5 +--- lib/linalg/drot.f | 8 +++--- lib/linalg/drscl.f | 7 ++--- lib/linalg/dscal.f | 8 +++--- lib/linalg/dstedc.f | 5 +--- lib/linalg/dsteqr.f | 5 +--- lib/linalg/dsterf.f | 5 +--- lib/linalg/dswap.f | 8 +++--- lib/linalg/dsyev.f | 5 +--- lib/linalg/dsyevd.f | 5 +--- lib/linalg/dsygs2.f | 5 +--- lib/linalg/dsygst.f | 5 +--- lib/linalg/dsygv.f | 5 +--- lib/linalg/dsygvd.f | 5 +--- lib/linalg/dsymm.f | 7 ++--- lib/linalg/dsymv.f | 7 ++--- lib/linalg/dsyr2.f | 7 ++--- lib/linalg/dsyr2k.f | 7 ++--- lib/linalg/dsyrk.f | 7 ++--- lib/linalg/dsytd2.f | 5 +--- lib/linalg/dsytrd.f | 5 +--- lib/linalg/dtrmm.f | 7 ++--- lib/linalg/dtrmv.f | 7 ++--- lib/linalg/dtrsm.f | 7 ++--- lib/linalg/dtrsv.f | 7 ++--- lib/linalg/dtrti2.f | 5 +--- lib/linalg/dtrtri.f | 5 +--- lib/linalg/idamax.f | 10 ++++---- lib/linalg/ieeeck.f | 5 +--- lib/linalg/iladlc.f | 5 +--- lib/linalg/iladlr.f | 5 +--- lib/linalg/ilaenv.f | 60 ++++++++++++++++++++++++++----------------- lib/linalg/ilazlc.f | 5 +--- lib/linalg/ilazlr.f | 5 +--- lib/linalg/iparmq.f | 37 ++++++++++++++++---------- lib/linalg/lsame.f | 5 +--- lib/linalg/xerbla.f | 5 +--- lib/linalg/zaxpy.f | 8 +++--- lib/linalg/zcopy.f | 8 +++--- lib/linalg/zdotc.f | 12 ++++----- lib/linalg/zdscal.f | 8 +++--- lib/linalg/zgemm.f | 14 +++------- lib/linalg/zgemv.f | 7 ++--- lib/linalg/zgerc.f | 7 ++--- lib/linalg/zheev.f | 7 ++--- lib/linalg/zheevd.f | 2 +- lib/linalg/zhemv.f | 7 ++--- lib/linalg/zher2.f | 7 ++--- lib/linalg/zher2k.f | 7 ++--- lib/linalg/zhetd2.f | 17 +++++------- lib/linalg/zhetrd.f | 9 +++---- lib/linalg/zhpr.f | 7 ++--- lib/linalg/zlacgv.f | 5 +--- lib/linalg/zladiv.f | 5 +--- lib/linalg/zlanhe.f | 5 +--- lib/linalg/zlarf.f | 5 +--- lib/linalg/zlarfb.f | 7 +++-- lib/linalg/zlarfg.f | 7 ++--- lib/linalg/zlarft.f | 5 +--- lib/linalg/zlascl.f | 5 +--- lib/linalg/zlaset.f | 5 +--- lib/linalg/zlasr.f | 5 +--- lib/linalg/zlatrd.f | 9 +++---- lib/linalg/zpptrf.f | 9 +++---- lib/linalg/zpptri.f | 7 ++--- lib/linalg/zscal.f | 8 +++--- lib/linalg/zsteqr.f | 5 +--- lib/linalg/zswap.f | 8 +++--- lib/linalg/ztpmv.f | 7 ++--- lib/linalg/ztpsv.f | 7 ++--- lib/linalg/ztptri.f | 5 +--- lib/linalg/ztrmm.f | 7 ++--- lib/linalg/ztrmv.f | 7 ++--- lib/linalg/zung2l.f | 5 +--- lib/linalg/zung2r.f | 5 +--- lib/linalg/zungl2.f | 5 +--- lib/linalg/zungql.f | 5 +--- lib/linalg/zungqr.f | 5 +--- lib/linalg/zungtr.f | 5 +--- 178 files changed, 471 insertions(+), 864 deletions(-) diff --git a/lib/linalg/dasum.f b/lib/linalg/dasum.f index cc5977f770..9a360b5acd 100644 --- a/lib/linalg/dasum.f +++ b/lib/linalg/dasum.f @@ -54,8 +54,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level1 * *> \par Further Details: @@ -71,10 +69,9 @@ * ===================================================================== DOUBLE PRECISION FUNCTION DASUM(N,DX,INCX) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX,N @@ -128,4 +125,7 @@ END IF DASUM = DTEMP RETURN +* +* End of DASUM +* END diff --git a/lib/linalg/daxpy.f b/lib/linalg/daxpy.f index cb94fc1e0a..421f7c630b 100644 --- a/lib/linalg/daxpy.f +++ b/lib/linalg/daxpy.f @@ -73,8 +73,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level1 * *> \par Further Details: @@ -89,10 +87,9 @@ * ===================================================================== SUBROUTINE DAXPY(N,DA,DX,INCX,DY,INCY) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION DA @@ -149,4 +146,7 @@ END DO END IF RETURN +* +* End of DAXPY +* END diff --git a/lib/linalg/dbdsqr.f b/lib/linalg/dbdsqr.f index 93db95e7a8..c220a5875d 100644 --- a/lib/linalg/dbdsqr.f +++ b/lib/linalg/dbdsqr.f @@ -166,7 +166,7 @@ *> *> \param[out] WORK *> \verbatim -*> WORK is DOUBLE PRECISION array, dimension (4*N) +*> WORK is DOUBLE PRECISION array, dimension (4*(N-1)) *> \endverbatim *> *> \param[out] INFO @@ -233,18 +233,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup auxOTHERcomputational * * ===================================================================== SUBROUTINE DBDSQR( UPLO, N, NCVT, NRU, NCC, D, E, VT, LDVT, U, $ LDU, C, LDC, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.1) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dcabs1.f b/lib/linalg/dcabs1.f index d6d850ed0f..f6212a8595 100644 --- a/lib/linalg/dcabs1.f +++ b/lib/linalg/dcabs1.f @@ -40,17 +40,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level1 * * ===================================================================== DOUBLE PRECISION FUNCTION DCABS1(Z) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. COMPLEX*16 Z @@ -63,4 +60,7 @@ * DCABS1 = ABS(DBLE(Z)) + ABS(DIMAG(Z)) RETURN +* +* End of DCABS1 +* END diff --git a/lib/linalg/dcopy.f b/lib/linalg/dcopy.f index 27bc08582b..ded46c5ecf 100644 --- a/lib/linalg/dcopy.f +++ b/lib/linalg/dcopy.f @@ -66,8 +66,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level1 * *> \par Further Details: @@ -82,10 +80,9 @@ * ===================================================================== SUBROUTINE DCOPY(N,DX,INCX,DY,INCY) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX,INCY,N @@ -143,4 +140,7 @@ END DO END IF RETURN +* +* End of DCOPY +* END diff --git a/lib/linalg/ddot.f b/lib/linalg/ddot.f index 3d18695aab..683a04bd46 100644 --- a/lib/linalg/ddot.f +++ b/lib/linalg/ddot.f @@ -66,8 +66,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level1 * *> \par Further Details: @@ -82,10 +80,9 @@ * ===================================================================== DOUBLE PRECISION FUNCTION DDOT(N,DX,INCX,DY,INCY) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX,INCY,N @@ -145,4 +142,7 @@ END IF DDOT = DTEMP RETURN +* +* End of DDOT +* END diff --git a/lib/linalg/dgebd2.f b/lib/linalg/dgebd2.f index 2bec4e29c7..daaa187aff 100644 --- a/lib/linalg/dgebd2.f +++ b/lib/linalg/dgebd2.f @@ -132,8 +132,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup doubleGEcomputational * *> \par Further Details: @@ -189,10 +187,9 @@ * ===================================================================== SUBROUTINE DGEBD2( M, N, A, LDA, D, E, TAUQ, TAUP, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.1) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. INTEGER INFO, LDA, M, N diff --git a/lib/linalg/dgebrd.f b/lib/linalg/dgebrd.f index 957cf2e539..0f0d1651a7 100644 --- a/lib/linalg/dgebrd.f +++ b/lib/linalg/dgebrd.f @@ -147,8 +147,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup doubleGEcomputational * *> \par Further Details: @@ -205,10 +203,9 @@ SUBROUTINE DGEBRD( M, N, A, LDA, D, E, TAUQ, TAUP, WORK, LWORK, $ INFO ) * -* -- LAPACK computational routine (version 3.7.1) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. INTEGER INFO, LDA, LWORK, M, N @@ -227,8 +224,7 @@ * .. Local Scalars .. LOGICAL LQUERY INTEGER I, IINFO, J, LDWRKX, LDWRKY, LWKOPT, MINMN, NB, - $ NBMIN, NX - DOUBLE PRECISION WS + $ NBMIN, NX, WS * .. * .. External Subroutines .. EXTERNAL DGEBD2, DGEMM, DLABRD, XERBLA diff --git a/lib/linalg/dgecon.f b/lib/linalg/dgecon.f index be20bbcd2a..aa10dee9a2 100644 --- a/lib/linalg/dgecon.f +++ b/lib/linalg/dgecon.f @@ -116,18 +116,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleGEcomputational * * ===================================================================== SUBROUTINE DGECON( NORM, N, A, LDA, ANORM, RCOND, WORK, IWORK, $ INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER NORM diff --git a/lib/linalg/dgelq2.f b/lib/linalg/dgelq2.f index 04aa57fc19..9915c57d47 100644 --- a/lib/linalg/dgelq2.f +++ b/lib/linalg/dgelq2.f @@ -33,8 +33,16 @@ *> *> \verbatim *> -*> DGELQ2 computes an LQ factorization of a real m by n matrix A: -*> A = L * Q. +*> DGELQ2 computes an LQ factorization of a real m-by-n matrix A: +*> +*> A = ( L 0 ) * Q +*> +*> where: +*> +*> Q is a n-by-n orthogonal matrix; +*> L is a lower-triangular m-by-m matrix; +*> 0 is a m-by-(n-m) zero matrix, if m < n. +*> *> \endverbatim * * Arguments: @@ -96,8 +104,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleGEcomputational * *> \par Further Details: @@ -121,10 +127,9 @@ * ===================================================================== SUBROUTINE DGELQ2( M, N, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, M, N diff --git a/lib/linalg/dgelqf.f b/lib/linalg/dgelqf.f index 834c47168f..ed3372f965 100644 --- a/lib/linalg/dgelqf.f +++ b/lib/linalg/dgelqf.f @@ -34,7 +34,15 @@ *> \verbatim *> *> DGELQF computes an LQ factorization of a real M-by-N matrix A: -*> A = L * Q. +*> +*> A = ( L 0 ) * Q +*> +*> where: +*> +*> Q is a N-by-N orthogonal matrix; +*> L is a lower-triangular M-by-M matrix; +*> 0 is a M-by-(N-M) zero matrix, if M < N. +*> *> \endverbatim * * Arguments: @@ -110,8 +118,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleGEcomputational * *> \par Further Details: @@ -135,10 +141,9 @@ * ===================================================================== SUBROUTINE DGELQF( M, N, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, LWORK, M, N diff --git a/lib/linalg/dgelsd.f b/lib/linalg/dgelsd.f index f2cfd63376..b3b3d8b2d3 100644 --- a/lib/linalg/dgelsd.f +++ b/lib/linalg/dgelsd.f @@ -194,8 +194,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup doubleGEsolve * *> \par Contributors: @@ -209,10 +207,9 @@ SUBROUTINE DGELSD( M, N, NRHS, A, LDA, B, LDB, S, RCOND, RANK, $ WORK, LWORK, IWORK, INFO ) * -* -- LAPACK driver routine (version 3.7.1) -- +* -- LAPACK driver routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. INTEGER INFO, LDA, LDB, LWORK, M, N, NRHS, RANK diff --git a/lib/linalg/dgelss.f b/lib/linalg/dgelss.f index 674a7ba784..8ed703fcf2 100644 --- a/lib/linalg/dgelss.f +++ b/lib/linalg/dgelss.f @@ -164,18 +164,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleGEsolve * * ===================================================================== SUBROUTINE DGELSS( M, N, NRHS, A, LDA, B, LDB, S, RCOND, RANK, $ WORK, LWORK, INFO ) * -* -- LAPACK driver routine (version 3.7.0) -- +* -- LAPACK driver routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, LDB, LWORK, M, N, NRHS, RANK diff --git a/lib/linalg/dgemm.f b/lib/linalg/dgemm.f index 3a60ca4e73..8c1b4f2066 100644 --- a/lib/linalg/dgemm.f +++ b/lib/linalg/dgemm.f @@ -166,8 +166,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level3 * *> \par Further Details: @@ -187,10 +185,9 @@ * ===================================================================== SUBROUTINE DGEMM(TRANSA,TRANSB,M,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC) * -* -- Reference BLAS level3 routine (version 3.7.0) -- +* -- Reference BLAS level3 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA,BETA @@ -215,7 +212,7 @@ * .. * .. Local Scalars .. DOUBLE PRECISION TEMP - INTEGER I,INFO,J,L,NCOLA,NROWA,NROWB + INTEGER I,INFO,J,L,NROWA,NROWB LOGICAL NOTA,NOTB * .. * .. Parameters .. @@ -224,17 +221,15 @@ * .. * * Set NOTA and NOTB as true if A and B respectively are not -* transposed and set NROWA, NCOLA and NROWB as the number of rows -* and columns of A and the number of rows of B respectively. +* transposed and set NROWA and NROWB as the number of rows of A +* and B respectively. * NOTA = LSAME(TRANSA,'N') NOTB = LSAME(TRANSB,'N') IF (NOTA) THEN NROWA = M - NCOLA = K ELSE NROWA = K - NCOLA = M END IF IF (NOTB) THEN NROWB = K @@ -379,6 +374,6 @@ * RETURN * -* End of DGEMM . +* End of DGEMM * END diff --git a/lib/linalg/dgemv.f b/lib/linalg/dgemv.f index 08e395b1cd..6625509b3a 100644 --- a/lib/linalg/dgemv.f +++ b/lib/linalg/dgemv.f @@ -134,8 +134,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level2 * *> \par Further Details: @@ -156,10 +154,9 @@ * ===================================================================== SUBROUTINE DGEMV(TRANS,M,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY) * -* -- Reference BLAS level2 routine (version 3.7.0) -- +* -- Reference BLAS level2 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA,BETA @@ -325,6 +322,6 @@ * RETURN * -* End of DGEMV . +* End of DGEMV * END diff --git a/lib/linalg/dgeqr2.f b/lib/linalg/dgeqr2.f index c1e91e9bde..5791b3a915 100644 --- a/lib/linalg/dgeqr2.f +++ b/lib/linalg/dgeqr2.f @@ -33,8 +33,17 @@ *> *> \verbatim *> -*> DGEQR2 computes a QR factorization of a real m by n matrix A: -*> A = Q * R. +*> DGEQR2 computes a QR factorization of a real m-by-n matrix A: +*> +*> A = Q * ( R ), +*> ( 0 ) +*> +*> where: +*> +*> Q is a m-by-m orthogonal matrix; +*> R is an upper-triangular n-by-n matrix; +*> 0 is a (m-n)-by-n zero matrix, if m > n. +*> *> \endverbatim * * Arguments: @@ -96,8 +105,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleGEcomputational * *> \par Further Details: @@ -121,10 +128,9 @@ * ===================================================================== SUBROUTINE DGEQR2( M, N, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, M, N diff --git a/lib/linalg/dgeqrf.f b/lib/linalg/dgeqrf.f index 83d7d8dd71..705e939286 100644 --- a/lib/linalg/dgeqrf.f +++ b/lib/linalg/dgeqrf.f @@ -34,7 +34,16 @@ *> \verbatim *> *> DGEQRF computes a QR factorization of a real M-by-N matrix A: -*> A = Q * R. +*> +*> A = Q * ( R ), +*> ( 0 ) +*> +*> where: +*> +*> Q is a M-by-M orthogonal matrix; +*> R is an upper-triangular N-by-N matrix; +*> 0 is a (M-N)-by-N zero matrix, if M > N. +*> *> \endverbatim * * Arguments: @@ -86,7 +95,8 @@ *> \param[in] LWORK *> \verbatim *> LWORK is INTEGER -*> The dimension of the array WORK. LWORK >= max(1,N). +*> The dimension of the array WORK. +*> LWORK >= 1, if MIN(M,N) = 0, and LWORK >= N, otherwise. *> For optimum performance LWORK >= N*NB, where NB is *> the optimal blocksize. *> @@ -111,8 +121,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleGEcomputational * *> \par Further Details: @@ -136,10 +144,9 @@ * ===================================================================== SUBROUTINE DGEQRF( M, N, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, LWORK, M, N @@ -169,10 +176,9 @@ * * Test the input arguments * + K = MIN( M, N ) INFO = 0 NB = ILAENV( 1, 'DGEQRF', ' ', M, N, -1, -1 ) - LWKOPT = N*NB - WORK( 1 ) = LWKOPT LQUERY = ( LWORK.EQ.-1 ) IF( M.LT.0 ) THEN INFO = -1 @@ -180,19 +186,25 @@ INFO = -2 ELSE IF( LDA.LT.MAX( 1, M ) ) THEN INFO = -4 - ELSE IF( LWORK.LT.MAX( 1, N ) .AND. .NOT.LQUERY ) THEN - INFO = -7 + ELSE IF( .NOT.LQUERY ) THEN + IF( LWORK.LE.0 .OR. ( M.GT.0 .AND. LWORK.LT.MAX( 1, N ) ) ) + $ INFO = -7 END IF IF( INFO.NE.0 ) THEN CALL XERBLA( 'DGEQRF', -INFO ) RETURN ELSE IF( LQUERY ) THEN + IF( K.EQ.0 ) THEN + LWKOPT = 1 + ELSE + LWKOPT = N*NB + END IF + WORK( 1 ) = LWKOPT RETURN END IF * * Quick return if possible * - K = MIN( M, N ) IF( K.EQ.0 ) THEN WORK( 1 ) = 1 RETURN diff --git a/lib/linalg/dger.f b/lib/linalg/dger.f index bdc8ef4349..8c19cb4e41 100644 --- a/lib/linalg/dger.f +++ b/lib/linalg/dger.f @@ -109,8 +109,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level2 * *> \par Further Details: @@ -130,10 +128,9 @@ * ===================================================================== SUBROUTINE DGER(M,N,ALPHA,X,INCX,Y,INCY,A,LDA) * -* -- Reference BLAS level2 routine (version 3.7.0) -- +* -- Reference BLAS level2 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA @@ -222,6 +219,6 @@ * RETURN * -* End of DGER . +* End of DGER * END diff --git a/lib/linalg/dgesv.f b/lib/linalg/dgesv.f index 23999e167f..3609c52f47 100644 --- a/lib/linalg/dgesv.f +++ b/lib/linalg/dgesv.f @@ -115,17 +115,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleGEsolve * * ===================================================================== SUBROUTINE DGESV( N, NRHS, A, LDA, IPIV, B, LDB, INFO ) * -* -- LAPACK driver routine (version 3.7.0) -- +* -- LAPACK driver routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, LDB, N, NRHS diff --git a/lib/linalg/dgesvd.f b/lib/linalg/dgesvd.f index ddf0bd5c2d..7cc8b35129 100644 --- a/lib/linalg/dgesvd.f +++ b/lib/linalg/dgesvd.f @@ -203,18 +203,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date April 2012 -* *> \ingroup doubleGEsing * * ===================================================================== SUBROUTINE DGESVD( JOBU, JOBVT, M, N, A, LDA, S, U, LDU, $ VT, LDVT, WORK, LWORK, INFO ) * -* -- LAPACK driver routine (version 3.7.0) -- +* -- LAPACK driver routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* April 2012 * * .. Scalar Arguments .. CHARACTER JOBU, JOBVT diff --git a/lib/linalg/dgetf2.f b/lib/linalg/dgetf2.f index 5458a5f3eb..fc1587842e 100644 --- a/lib/linalg/dgetf2.f +++ b/lib/linalg/dgetf2.f @@ -101,17 +101,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleGEcomputational * * ===================================================================== SUBROUTINE DGETF2( M, N, A, LDA, IPIV, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, M, N diff --git a/lib/linalg/dgetrf.f b/lib/linalg/dgetrf.f index 9a340b60f3..73d0f3601a 100644 --- a/lib/linalg/dgetrf.f +++ b/lib/linalg/dgetrf.f @@ -101,17 +101,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleGEcomputational * * ===================================================================== SUBROUTINE DGETRF( M, N, A, LDA, IPIV, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, M, N diff --git a/lib/linalg/dgetrf2.f b/lib/linalg/dgetrf2.f index 77948d2305..40af0793dd 100644 --- a/lib/linalg/dgetrf2.f +++ b/lib/linalg/dgetrf2.f @@ -106,17 +106,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2016 -* *> \ingroup doubleGEcomputational * * ===================================================================== RECURSIVE SUBROUTINE DGETRF2( M, N, A, LDA, IPIV, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, M, N diff --git a/lib/linalg/dgetri.f b/lib/linalg/dgetri.f index 9d8cf2ad3e..92ef90c186 100644 --- a/lib/linalg/dgetri.f +++ b/lib/linalg/dgetri.f @@ -107,17 +107,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleGEcomputational * * ===================================================================== SUBROUTINE DGETRI( N, A, LDA, IPIV, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, LDA, LWORK, N diff --git a/lib/linalg/dgetrs.f b/lib/linalg/dgetrs.f index 7ac727776e..d3464f685a 100644 --- a/lib/linalg/dgetrs.f +++ b/lib/linalg/dgetrs.f @@ -114,17 +114,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleGEcomputational * * ===================================================================== SUBROUTINE DGETRS( TRANS, N, NRHS, A, LDA, IPIV, B, LDB, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER TRANS diff --git a/lib/linalg/disnan.f b/lib/linalg/disnan.f index a565ed36d4..e621b2589c 100644 --- a/lib/linalg/disnan.f +++ b/lib/linalg/disnan.f @@ -52,17 +52,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup OTHERauxiliary * * ===================================================================== LOGICAL FUNCTION DISNAN( DIN ) * -* -- LAPACK auxiliary routine (version 3.7.1) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. DOUBLE PRECISION, INTENT(IN) :: DIN diff --git a/lib/linalg/dlabad.f b/lib/linalg/dlabad.f index 01b8158f66..95b35e53b8 100644 --- a/lib/linalg/dlabad.f +++ b/lib/linalg/dlabad.f @@ -67,17 +67,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE DLABAD( SMALL, LARGE ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION LARGE, SMALL diff --git a/lib/linalg/dlabrd.f b/lib/linalg/dlabrd.f index b5e734dc7c..86dfc10c7c 100644 --- a/lib/linalg/dlabrd.f +++ b/lib/linalg/dlabrd.f @@ -156,8 +156,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup doubleOTHERauxiliary * *> \par Further Details: @@ -210,10 +208,9 @@ SUBROUTINE DLABRD( M, N, NB, A, LDA, D, E, TAUQ, TAUP, X, LDX, Y, $ LDY ) * -* -- LAPACK auxiliary routine (version 3.7.1) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. INTEGER LDA, LDX, LDY, M, N, NB diff --git a/lib/linalg/dlacn2.f b/lib/linalg/dlacn2.f index 952854043a..ee2e7ca266 100644 --- a/lib/linalg/dlacn2.f +++ b/lib/linalg/dlacn2.f @@ -101,8 +101,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERauxiliary * *> \par Further Details: @@ -136,10 +134,9 @@ * ===================================================================== SUBROUTINE DLACN2( N, V, X, ISGN, EST, KASE, ISAVE ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER KASE, N @@ -160,7 +157,7 @@ * .. * .. Local Scalars .. INTEGER I, JLAST - DOUBLE PRECISION ALTSGN, ESTOLD, TEMP + DOUBLE PRECISION ALTSGN, ESTOLD, TEMP, XS * .. * .. External Functions .. INTEGER IDAMAX @@ -171,7 +168,7 @@ EXTERNAL DCOPY * .. * .. Intrinsic Functions .. - INTRINSIC ABS, DBLE, NINT, SIGN + INTRINSIC ABS, DBLE, NINT * .. * .. Executable Statements .. * @@ -199,7 +196,11 @@ EST = DASUM( N, X, 1 ) * DO 30 I = 1, N - X( I ) = SIGN( ONE, X( I ) ) + IF( X(I).GE.ZERO ) THEN + X(I) = ONE + ELSE + X(I) = -ONE + END IF ISGN( I ) = NINT( X( I ) ) 30 CONTINUE KASE = 2 @@ -232,7 +233,12 @@ ESTOLD = EST EST = DASUM( N, V, 1 ) DO 80 I = 1, N - IF( NINT( SIGN( ONE, X( I ) ) ).NE.ISGN( I ) ) + IF( X(I).GE.ZERO ) THEN + XS = ONE + ELSE + XS = -ONE + END IF + IF( NINT( XS ).NE.ISGN( I ) ) $ GO TO 90 80 CONTINUE * REPEATED SIGN VECTOR DETECTED, HENCE ALGORITHM HAS CONVERGED. @@ -244,7 +250,11 @@ $ GO TO 120 * DO 100 I = 1, N - X( I ) = SIGN( ONE, X( I ) ) + IF( X(I).GE.ZERO ) THEN + X(I) = ONE + ELSE + X(I) = -ONE + END IF ISGN( I ) = NINT( X( I ) ) 100 CONTINUE KASE = 2 diff --git a/lib/linalg/dlacpy.f b/lib/linalg/dlacpy.f index d1c396724a..917aa1e2a2 100644 --- a/lib/linalg/dlacpy.f +++ b/lib/linalg/dlacpy.f @@ -96,17 +96,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE DLACPY( UPLO, M, N, A, LDA, B, LDB ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dladiv.f b/lib/linalg/dladiv.f index dd8110adf2..4265618fed 100644 --- a/lib/linalg/dladiv.f +++ b/lib/linalg/dladiv.f @@ -84,17 +84,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date January 2013 -* *> \ingroup doubleOTHERauxiliary * * ===================================================================== SUBROUTINE DLADIV( A, B, C, D, P, Q ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* January 2013 * * .. Scalar Arguments .. DOUBLE PRECISION A, B, C, D, P, Q @@ -178,10 +175,9 @@ SUBROUTINE DLADIV1( A, B, C, D, P, Q ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* January 2013 * * .. Scalar Arguments .. DOUBLE PRECISION A, B, C, D, P, Q @@ -218,10 +214,9 @@ DOUBLE PRECISION FUNCTION DLADIV2( A, B, C, D, R, T ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* January 2013 * * .. Scalar Arguments .. DOUBLE PRECISION A, B, C, D, R, T @@ -251,6 +246,6 @@ * RETURN * -* End of DLADIV12 +* End of DLADIV2 * END diff --git a/lib/linalg/dlae2.f b/lib/linalg/dlae2.f index ed77ff6dfe..a0e3971b41 100644 --- a/lib/linalg/dlae2.f +++ b/lib/linalg/dlae2.f @@ -78,8 +78,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * *> \par Further Details: @@ -102,10 +100,9 @@ * ===================================================================== SUBROUTINE DLAE2( A, B, C, RT1, RT2 ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION A, B, C, RT1, RT2 diff --git a/lib/linalg/dlaed0.f b/lib/linalg/dlaed0.f index 4e92da98ea..fe3b6249e9 100644 --- a/lib/linalg/dlaed0.f +++ b/lib/linalg/dlaed0.f @@ -1,4 +1,4 @@ -*> \brief \b DLAED0 used by sstedc. Computes all eigenvalues and corresponding eigenvectors of an unreduced symmetric tridiagonal matrix using the divide and conquer method. +*> \brief \b DLAED0 used by DSTEDC. Computes all eigenvalues and corresponding eigenvectors of an unreduced symmetric tridiagonal matrix using the divide and conquer method. * * =========== DOCUMENTATION =========== * @@ -158,8 +158,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup auxOTHERcomputational * *> \par Contributors: @@ -172,10 +170,9 @@ SUBROUTINE DLAED0( ICOMPQ, QSIZ, N, D, E, Q, LDQ, QSTORE, LDQS, $ WORK, IWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER ICOMPQ, INFO, LDQ, LDQS, N, QSIZ diff --git a/lib/linalg/dlaed1.f b/lib/linalg/dlaed1.f index 30e71fa241..3718139c14 100644 --- a/lib/linalg/dlaed1.f +++ b/lib/linalg/dlaed1.f @@ -1,4 +1,4 @@ -*> \brief \b DLAED1 used by sstedc. Computes the updated eigensystem of a diagonal matrix after modification by a rank-one symmetric matrix. Used when the original matrix is tridiagonal. +*> \brief \b DLAED1 used by DSTEDC. Computes the updated eigensystem of a diagonal matrix after modification by a rank-one symmetric matrix. Used when the original matrix is tridiagonal. * * =========== DOCUMENTATION =========== * @@ -148,8 +148,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2016 -* *> \ingroup auxOTHERcomputational * *> \par Contributors: @@ -163,10 +161,9 @@ SUBROUTINE DLAED1( N, D, Q, LDQ, INDXQ, RHO, CUTPNT, WORK, IWORK, $ INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2016 * * .. Scalar Arguments .. INTEGER CUTPNT, INFO, LDQ, N diff --git a/lib/linalg/dlaed2.f b/lib/linalg/dlaed2.f index fbcc87a880..9b1f1e0930 100644 --- a/lib/linalg/dlaed2.f +++ b/lib/linalg/dlaed2.f @@ -1,4 +1,4 @@ -*> \brief \b DLAED2 used by sstedc. Merges eigenvalues and deflates secular equation. Used when the original matrix is tridiagonal. +*> \brief \b DLAED2 used by DSTEDC. Merges eigenvalues and deflates secular equation. Used when the original matrix is tridiagonal. * * =========== DOCUMENTATION =========== * @@ -197,8 +197,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup auxOTHERcomputational * *> \par Contributors: @@ -212,10 +210,9 @@ SUBROUTINE DLAED2( K, N, N1, D, Q, LDQ, INDXQ, RHO, Z, DLAMDA, W, $ Q2, INDX, INDXC, INDXP, COLTYP, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDQ, N, N1 diff --git a/lib/linalg/dlaed3.f b/lib/linalg/dlaed3.f index d200fc0a22..c58944e604 100644 --- a/lib/linalg/dlaed3.f +++ b/lib/linalg/dlaed3.f @@ -1,4 +1,4 @@ -*> \brief \b DLAED3 used by sstedc. Finds the roots of the secular equation and updates the eigenvectors. Used when the original matrix is tridiagonal. +*> \brief \b DLAED3 used by DSTEDC. Finds the roots of the secular equation and updates the eigenvectors. Used when the original matrix is tridiagonal. * * =========== DOCUMENTATION =========== * @@ -170,8 +170,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup auxOTHERcomputational * *> \par Contributors: @@ -185,10 +183,9 @@ SUBROUTINE DLAED3( K, N, N1, D, Q, LDQ, RHO, DLAMDA, Q2, INDX, $ CTOT, W, S, INFO ) * -* -- LAPACK computational routine (version 3.7.1) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. INTEGER INFO, K, LDQ, N, N1 diff --git a/lib/linalg/dlaed4.f b/lib/linalg/dlaed4.f index e7dc839df5..3ee3ef920f 100644 --- a/lib/linalg/dlaed4.f +++ b/lib/linalg/dlaed4.f @@ -1,4 +1,4 @@ -*> \brief \b DLAED4 used by sstedc. Finds a single root of the secular equation. +*> \brief \b DLAED4 used by DSTEDC. Finds a single root of the secular equation. * * =========== DOCUMENTATION =========== * @@ -82,7 +82,7 @@ *> \param[out] DELTA *> \verbatim *> DELTA is DOUBLE PRECISION array, dimension (N) -*> If N .GT. 2, DELTA contains (D(j) - lambda_I) in its j-th +*> If N > 2, DELTA contains (D(j) - lambda_I) in its j-th *> component. If N = 1, then DELTA(1) = 1. If N = 2, see DLAED5 *> for detail. The vector DELTA contains the information necessary *> to construct the eigenvectors by DLAED3 and DLAED9. @@ -132,8 +132,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup auxOTHERcomputational * *> \par Contributors: @@ -145,10 +143,9 @@ * ===================================================================== SUBROUTINE DLAED4( N, I, D, Z, DELTA, RHO, DLAM, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER I, INFO, N diff --git a/lib/linalg/dlaed5.f b/lib/linalg/dlaed5.f index 3ea9e401cf..d9e977e6b7 100644 --- a/lib/linalg/dlaed5.f +++ b/lib/linalg/dlaed5.f @@ -1,4 +1,4 @@ -*> \brief \b DLAED5 used by sstedc. Solves the 2-by-2 secular equation. +*> \brief \b DLAED5 used by DSTEDC. Solves the 2-by-2 secular equation. * * =========== DOCUMENTATION =========== * @@ -95,8 +95,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup auxOTHERcomputational * *> \par Contributors: @@ -108,10 +106,9 @@ * ===================================================================== SUBROUTINE DLAED5( I, D, Z, DELTA, RHO, DLAM ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER I @@ -184,6 +181,6 @@ END IF RETURN * -* End OF DLAED5 +* End of DLAED5 * END diff --git a/lib/linalg/dlaed6.f b/lib/linalg/dlaed6.f index daa8db39e4..a0c0364e56 100644 --- a/lib/linalg/dlaed6.f +++ b/lib/linalg/dlaed6.f @@ -1,4 +1,4 @@ -*> \brief \b DLAED6 used by sstedc. Computes one Newton step in solution of the secular equation. +*> \brief \b DLAED6 used by DSTEDC. Computes one Newton step in solution of the secular equation. * * =========== DOCUMENTATION =========== * @@ -115,8 +115,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup auxOTHERcomputational * *> \par Further Details: @@ -140,10 +138,9 @@ * ===================================================================== SUBROUTINE DLAED6( KNITER, ORGATI, RHO, D, Z, FINIT, TAU, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. LOGICAL ORGATI diff --git a/lib/linalg/dlaed7.f b/lib/linalg/dlaed7.f index 9c528added..d968c56752 100644 --- a/lib/linalg/dlaed7.f +++ b/lib/linalg/dlaed7.f @@ -1,4 +1,4 @@ -*> \brief \b DLAED7 used by sstedc. Computes the updated eigensystem of a diagonal matrix after modification by a rank-one symmetric matrix. Used when the original matrix is dense. +*> \brief \b DLAED7 used by DSTEDC. Computes the updated eigensystem of a diagonal matrix after modification by a rank-one symmetric matrix. Used when the original matrix is dense. * * =========== DOCUMENTATION =========== * @@ -244,8 +244,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2016 -* *> \ingroup auxOTHERcomputational * *> \par Contributors: @@ -260,10 +258,9 @@ $ PERM, GIVPTR, GIVCOL, GIVNUM, WORK, IWORK, $ INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2016 * * .. Scalar Arguments .. INTEGER CURLVL, CURPBM, CUTPNT, ICOMPQ, INFO, LDQ, N, diff --git a/lib/linalg/dlaed8.f b/lib/linalg/dlaed8.f index f64679dc05..3631fb4566 100644 --- a/lib/linalg/dlaed8.f +++ b/lib/linalg/dlaed8.f @@ -1,4 +1,4 @@ -*> \brief \b DLAED8 used by sstedc. Merges eigenvalues and deflates secular equation. Used when the original matrix is dense. +*> \brief \b DLAED8 used by DSTEDC. Merges eigenvalues and deflates secular equation. Used when the original matrix is dense. * * =========== DOCUMENTATION =========== * @@ -228,8 +228,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup auxOTHERcomputational * *> \par Contributors: @@ -243,10 +241,9 @@ $ CUTPNT, Z, DLAMDA, Q2, LDQ2, W, PERM, GIVPTR, $ GIVCOL, GIVNUM, INDXP, INDX, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER CUTPNT, GIVPTR, ICOMPQ, INFO, K, LDQ, LDQ2, N, diff --git a/lib/linalg/dlaed9.f b/lib/linalg/dlaed9.f index d3be22502a..b88cdd9077 100644 --- a/lib/linalg/dlaed9.f +++ b/lib/linalg/dlaed9.f @@ -1,4 +1,4 @@ -*> \brief \b DLAED9 used by sstedc. Finds the roots of the secular equation and updates the eigenvectors. Used when the original matrix is dense. +*> \brief \b DLAED9 used by DSTEDC. Finds the roots of the secular equation and updates the eigenvectors. Used when the original matrix is dense. * * =========== DOCUMENTATION =========== * @@ -142,8 +142,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup auxOTHERcomputational * *> \par Contributors: @@ -156,10 +154,9 @@ SUBROUTINE DLAED9( K, KSTART, KSTOP, N, D, Q, LDQ, RHO, DLAMDA, W, $ S, LDS, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, KSTART, KSTOP, LDQ, LDS, N diff --git a/lib/linalg/dlaeda.f b/lib/linalg/dlaeda.f index 4ca08a0879..8864fd7f2a 100644 --- a/lib/linalg/dlaeda.f +++ b/lib/linalg/dlaeda.f @@ -1,4 +1,4 @@ -*> \brief \b DLAEDA used by sstedc. Computes the Z vector determining the rank-one modification of the diagonal matrix. Used when the original matrix is dense. +*> \brief \b DLAEDA used by DSTEDC. Computes the Z vector determining the rank-one modification of the diagonal matrix. Used when the original matrix is dense. * * =========== DOCUMENTATION =========== * @@ -152,8 +152,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup auxOTHERcomputational * *> \par Contributors: @@ -166,10 +164,9 @@ SUBROUTINE DLAEDA( N, TLVLS, CURLVL, CURPBM, PRMPTR, PERM, GIVPTR, $ GIVCOL, GIVNUM, Q, QPTR, Z, ZTEMP, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER CURLVL, CURPBM, INFO, N, TLVLS diff --git a/lib/linalg/dlaev2.f b/lib/linalg/dlaev2.f index 4906f1a20c..9e29991a6d 100644 --- a/lib/linalg/dlaev2.f +++ b/lib/linalg/dlaev2.f @@ -94,8 +94,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * *> \par Further Details: @@ -120,10 +118,9 @@ * ===================================================================== SUBROUTINE DLAEV2( A, B, C, RT1, RT2, CS1, SN1 ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION A, B, C, CS1, RT1, RT2, SN1 diff --git a/lib/linalg/dlaisnan.f b/lib/linalg/dlaisnan.f index c2e87d88a0..2caf5fb1d0 100644 --- a/lib/linalg/dlaisnan.f +++ b/lib/linalg/dlaisnan.f @@ -67,17 +67,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup OTHERauxiliary * * ===================================================================== LOGICAL FUNCTION DLAISNAN( DIN1, DIN2 ) * -* -- LAPACK auxiliary routine (version 3.7.1) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. DOUBLE PRECISION, INTENT(IN) :: DIN1, DIN2 diff --git a/lib/linalg/dlals0.f b/lib/linalg/dlals0.f index d4cff166d6..cfca222806 100644 --- a/lib/linalg/dlals0.f +++ b/lib/linalg/dlals0.f @@ -252,8 +252,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * *> \par Contributors: @@ -268,10 +266,9 @@ $ PERM, GIVPTR, GIVCOL, LDGCOL, GIVNUM, LDGNUM, $ POLES, DIFL, DIFR, Z, K, C, S, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER GIVPTR, ICOMPQ, INFO, K, LDB, LDBX, LDGCOL, diff --git a/lib/linalg/dlalsa.f b/lib/linalg/dlalsa.f index 478ee24b0e..da8e0fa175 100644 --- a/lib/linalg/dlalsa.f +++ b/lib/linalg/dlalsa.f @@ -43,7 +43,7 @@ *> *> \verbatim *> -*> DLALSA is an intermediate step in solving the least squares problem +*> DLALSA is an itermediate step in solving the least squares problem *> by computing the SVD of the coefficient matrix in compact form (The *> singular vectors are computed as products of simple orthorgonal *> matrices.). @@ -250,8 +250,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup doubleOTHERcomputational * *> \par Contributors: @@ -267,10 +265,9 @@ $ GIVCOL, LDGCOL, PERM, GIVNUM, C, S, WORK, $ IWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.1) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. INTEGER ICOMPQ, INFO, LDB, LDBX, LDGCOL, LDU, N, NRHS, diff --git a/lib/linalg/dlalsd.f b/lib/linalg/dlalsd.f index 510e0455a6..d22c45dc6e 100644 --- a/lib/linalg/dlalsd.f +++ b/lib/linalg/dlalsd.f @@ -164,8 +164,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * *> \par Contributors: @@ -179,10 +177,9 @@ SUBROUTINE DLALSD( UPLO, SMLSIZ, N, NRHS, D, E, B, LDB, RCOND, $ RANK, WORK, IWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dlamrg.f b/lib/linalg/dlamrg.f index de19508e45..80bd354b97 100644 --- a/lib/linalg/dlamrg.f +++ b/lib/linalg/dlamrg.f @@ -92,17 +92,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2016 -* *> \ingroup auxOTHERcomputational * * ===================================================================== SUBROUTINE DLAMRG( N1, N2, A, DTRD1, DTRD2, INDEX ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2016 * * .. Scalar Arguments .. INTEGER DTRD1, DTRD2, N1, N2 diff --git a/lib/linalg/dlange.f b/lib/linalg/dlange.f index 9dbf45e818..9d214cb542 100644 --- a/lib/linalg/dlange.f +++ b/lib/linalg/dlange.f @@ -107,17 +107,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleGEauxiliary * * ===================================================================== DOUBLE PRECISION FUNCTION DLANGE( NORM, M, N, A, LDA, WORK ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER NORM diff --git a/lib/linalg/dlanst.f b/lib/linalg/dlanst.f index e952e2dd21..c5bc7ea038 100644 --- a/lib/linalg/dlanst.f +++ b/lib/linalg/dlanst.f @@ -93,17 +93,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * * ===================================================================== DOUBLE PRECISION FUNCTION DLANST( NORM, N, D, E ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER NORM diff --git a/lib/linalg/dlansy.f b/lib/linalg/dlansy.f index 2372fce0a8..949c5535a2 100644 --- a/lib/linalg/dlansy.f +++ b/lib/linalg/dlansy.f @@ -115,17 +115,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleSYauxiliary * * ===================================================================== DOUBLE PRECISION FUNCTION DLANSY( NORM, UPLO, N, A, LDA, WORK ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER NORM, UPLO diff --git a/lib/linalg/dlapy2.f b/lib/linalg/dlapy2.f index bc01829a24..1f63193bb7 100644 --- a/lib/linalg/dlapy2.f +++ b/lib/linalg/dlapy2.f @@ -31,7 +31,7 @@ *> \verbatim *> *> DLAPY2 returns sqrt(x**2+y**2), taking care not to cause unnecessary -*> overflow. +*> overflow and unnecessary underflow. *> \endverbatim * * Arguments: @@ -56,17 +56,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup OTHERauxiliary * * ===================================================================== DOUBLE PRECISION FUNCTION DLAPY2( X, Y ) * -* -- LAPACK auxiliary routine (version 3.7.1) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. DOUBLE PRECISION X, Y @@ -81,13 +78,16 @@ PARAMETER ( ONE = 1.0D0 ) * .. * .. Local Scalars .. - DOUBLE PRECISION W, XABS, YABS, Z + DOUBLE PRECISION W, XABS, YABS, Z, HUGEVAL LOGICAL X_IS_NAN, Y_IS_NAN * .. * .. External Functions .. LOGICAL DISNAN EXTERNAL DISNAN * .. +* .. External Subroutines .. + DOUBLE PRECISION DLAMCH +* .. * .. Intrinsic Functions .. INTRINSIC ABS, MAX, MIN, SQRT * .. @@ -97,13 +97,14 @@ Y_IS_NAN = DISNAN( Y ) IF ( X_IS_NAN ) DLAPY2 = X IF ( Y_IS_NAN ) DLAPY2 = Y + HUGEVAL = DLAMCH( 'Overflow' ) * IF ( .NOT.( X_IS_NAN.OR.Y_IS_NAN ) ) THEN XABS = ABS( X ) YABS = ABS( Y ) W = MAX( XABS, YABS ) Z = MIN( XABS, YABS ) - IF( Z.EQ.ZERO ) THEN + IF( Z.EQ.ZERO .OR. W.GT.HUGEVAL ) THEN DLAPY2 = W ELSE DLAPY2 = W*SQRT( ONE+( Z / W )**2 ) diff --git a/lib/linalg/dlapy3.f b/lib/linalg/dlapy3.f index 3bbba88875..230a65cdb2 100644 --- a/lib/linalg/dlapy3.f +++ b/lib/linalg/dlapy3.f @@ -31,7 +31,7 @@ *> \verbatim *> *> DLAPY3 returns sqrt(x**2+y**2+z**2), taking care not to cause -*> unnecessary overflow. +*> unnecessary overflow and unnecessary underflow. *> \endverbatim * * Arguments: @@ -61,17 +61,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * * ===================================================================== DOUBLE PRECISION FUNCTION DLAPY3( X, Y, Z ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION X, Y, Z @@ -84,18 +81,22 @@ PARAMETER ( ZERO = 0.0D0 ) * .. * .. Local Scalars .. - DOUBLE PRECISION W, XABS, YABS, ZABS + DOUBLE PRECISION W, XABS, YABS, ZABS, HUGEVAL +* .. +* .. External Subroutines .. + DOUBLE PRECISION DLAMCH * .. * .. Intrinsic Functions .. INTRINSIC ABS, MAX, SQRT * .. * .. Executable Statements .. * + HUGEVAL = DLAMCH( 'Overflow' ) XABS = ABS( X ) YABS = ABS( Y ) ZABS = ABS( Z ) W = MAX( XABS, YABS, ZABS ) - IF( W.EQ.ZERO ) THEN + IF( W.EQ.ZERO .OR. W.GT.HUGEVAL ) THEN * W can be zero for max(0,nan,0) * adding all three entries together will make sure * NaN will not disappear. diff --git a/lib/linalg/dlarf.f b/lib/linalg/dlarf.f index e99d0bb2a9..ed21638645 100644 --- a/lib/linalg/dlarf.f +++ b/lib/linalg/dlarf.f @@ -117,17 +117,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERauxiliary * * ===================================================================== SUBROUTINE DLARF( SIDE, M, N, V, INCV, TAU, C, LDC, WORK ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE diff --git a/lib/linalg/dlarfb.f b/lib/linalg/dlarfb.f index 5b2cc2ba80..a3fa083b43 100644 --- a/lib/linalg/dlarfb.f +++ b/lib/linalg/dlarfb.f @@ -92,6 +92,8 @@ *> K is INTEGER *> The order of the matrix T (= the number of elementary *> reflectors whose product defines the block reflector). +*> If SIDE = 'L', M >= K >= 0; +*> if SIDE = 'R', N >= K >= 0. *> \endverbatim *> *> \param[in] V @@ -159,8 +161,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2013 -* *> \ingroup doubleOTHERauxiliary * *> \par Further Details: @@ -195,10 +195,9 @@ SUBROUTINE DLARFB( SIDE, TRANS, DIRECT, STOREV, M, N, K, V, LDV, $ T, LDT, C, LDC, WORK, LDWORK ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2013 * * .. Scalar Arguments .. CHARACTER DIRECT, SIDE, STOREV, TRANS diff --git a/lib/linalg/dlarfg.f b/lib/linalg/dlarfg.f index cb177a5703..9bfb45a6b0 100644 --- a/lib/linalg/dlarfg.f +++ b/lib/linalg/dlarfg.f @@ -99,17 +99,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERauxiliary * * ===================================================================== SUBROUTINE DLARFG( N, ALPHA, X, INCX, TAU ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX, N @@ -170,7 +167,7 @@ CALL DSCAL( N-1, RSAFMN, X, INCX ) BETA = BETA*RSAFMN ALPHA = ALPHA*RSAFMN - IF( ABS( BETA ).LT.SAFMIN ) + IF( (ABS( BETA ).LT.SAFMIN) .AND. (KNT .LT. 20) ) $ GO TO 10 * * New BETA is at most 1, at least SAFMIN diff --git a/lib/linalg/dlarft.f b/lib/linalg/dlarft.f index e69a6b792e..a8d9de61f1 100644 --- a/lib/linalg/dlarft.f +++ b/lib/linalg/dlarft.f @@ -130,8 +130,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERauxiliary * *> \par Further Details: @@ -163,10 +161,9 @@ * ===================================================================== SUBROUTINE DLARFT( DIRECT, STOREV, N, K, V, LDV, TAU, T, LDT ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER DIRECT, STOREV diff --git a/lib/linalg/dlas2.f b/lib/linalg/dlas2.f index 83873bc612..ea929e86f7 100644 --- a/lib/linalg/dlas2.f +++ b/lib/linalg/dlas2.f @@ -78,8 +78,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * *> \par Further Details: @@ -107,10 +105,9 @@ * ===================================================================== SUBROUTINE DLAS2( F, G, H, SSMIN, SSMAX ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION F, G, H, SSMAX, SSMIN diff --git a/lib/linalg/dlascl.f b/lib/linalg/dlascl.f index 03e1000a87..05ad1c4f3c 100644 --- a/lib/linalg/dlascl.f +++ b/lib/linalg/dlascl.f @@ -136,17 +136,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2016 -* *> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE DLASCL( TYPE, KL, KU, CFROM, CTO, M, N, A, LDA, INFO ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2016 * * .. Scalar Arguments .. CHARACTER TYPE diff --git a/lib/linalg/dlasd4.f b/lib/linalg/dlasd4.f index 8b4a8762c8..acfd896b3b 100644 --- a/lib/linalg/dlasd4.f +++ b/lib/linalg/dlasd4.f @@ -140,8 +140,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * *> \par Contributors: @@ -153,10 +151,9 @@ * ===================================================================== SUBROUTINE DLASD4( N, I, D, Z, DELTA, RHO, SIGMA, WORK, INFO ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER I, INFO, N diff --git a/lib/linalg/dlasd5.f b/lib/linalg/dlasd5.f index 4896ba6b97..645c2fdc3e 100644 --- a/lib/linalg/dlasd5.f +++ b/lib/linalg/dlasd5.f @@ -103,8 +103,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * *> \par Contributors: @@ -116,10 +114,9 @@ * ===================================================================== SUBROUTINE DLASD5( I, D, Z, DELTA, RHO, DSIGMA, WORK ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER I diff --git a/lib/linalg/dlasd6.f b/lib/linalg/dlasd6.f index 5cab78a070..51e67588dd 100644 --- a/lib/linalg/dlasd6.f +++ b/lib/linalg/dlasd6.f @@ -297,8 +297,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2016 -* *> \ingroup OTHERauxiliary * *> \par Contributors: @@ -313,10 +311,9 @@ $ LDGNUM, POLES, DIFL, DIFR, Z, K, C, S, WORK, $ IWORK, INFO ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2016 * * .. Scalar Arguments .. INTEGER GIVPTR, ICOMPQ, INFO, K, LDGCOL, LDGNUM, NL, diff --git a/lib/linalg/dlasd7.f b/lib/linalg/dlasd7.f index 66f665cf88..ff9ba4c36a 100644 --- a/lib/linalg/dlasd7.f +++ b/lib/linalg/dlasd7.f @@ -264,8 +264,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * *> \par Contributors: @@ -280,10 +278,9 @@ $ PERM, GIVPTR, GIVCOL, LDGCOL, GIVNUM, LDGNUM, $ C, S, INFO ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER GIVPTR, ICOMPQ, INFO, K, LDGCOL, LDGNUM, NL, diff --git a/lib/linalg/dlasd8.f b/lib/linalg/dlasd8.f index fc5c48c528..a769bdb22e 100644 --- a/lib/linalg/dlasd8.f +++ b/lib/linalg/dlasd8.f @@ -152,8 +152,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup OTHERauxiliary * *> \par Contributors: @@ -166,10 +164,9 @@ SUBROUTINE DLASD8( ICOMPQ, K, D, Z, VF, VL, DIFL, DIFR, LDDIFR, $ DSIGMA, WORK, INFO ) * -* -- LAPACK auxiliary routine (version 3.7.1) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. INTEGER ICOMPQ, INFO, K, LDDIFR diff --git a/lib/linalg/dlasda.f b/lib/linalg/dlasda.f index f41a108b80..3e169a4edb 100644 --- a/lib/linalg/dlasda.f +++ b/lib/linalg/dlasda.f @@ -258,8 +258,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup OTHERauxiliary * *> \par Contributors: @@ -273,10 +271,9 @@ $ DIFL, DIFR, Z, POLES, GIVPTR, GIVCOL, LDGCOL, $ PERM, GIVNUM, C, S, WORK, IWORK, INFO ) * -* -- LAPACK auxiliary routine (version 3.7.1) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. INTEGER ICOMPQ, INFO, LDGCOL, LDU, N, SMLSIZ, SQRE diff --git a/lib/linalg/dlasdq.f b/lib/linalg/dlasdq.f index e7d3575a98..0c39b24f0d 100644 --- a/lib/linalg/dlasdq.f +++ b/lib/linalg/dlasdq.f @@ -197,8 +197,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2016 -* *> \ingroup OTHERauxiliary * *> \par Contributors: @@ -211,10 +209,9 @@ SUBROUTINE DLASDQ( UPLO, SQRE, N, NCVT, NRU, NCC, D, E, VT, LDVT, $ U, LDU, C, LDC, WORK, INFO ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dlasdt.f b/lib/linalg/dlasdt.f index 37da2d035e..0d9999ea62 100644 --- a/lib/linalg/dlasdt.f +++ b/lib/linalg/dlasdt.f @@ -92,8 +92,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * *> \par Contributors: @@ -105,10 +103,9 @@ * ===================================================================== SUBROUTINE DLASDT( N, LVL, ND, INODE, NDIML, NDIMR, MSUB ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER LVL, MSUB, N, ND diff --git a/lib/linalg/dlaset.f b/lib/linalg/dlaset.f index 3a0c469a3c..625c757b6b 100644 --- a/lib/linalg/dlaset.f +++ b/lib/linalg/dlaset.f @@ -103,17 +103,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE DLASET( UPLO, M, N, ALPHA, BETA, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dlasq1.f b/lib/linalg/dlasq1.f index 468676eebd..27fa30736e 100644 --- a/lib/linalg/dlasq1.f +++ b/lib/linalg/dlasq1.f @@ -101,17 +101,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup auxOTHERcomputational * * ===================================================================== SUBROUTINE DLASQ1( N, D, E, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, N diff --git a/lib/linalg/dlasq2.f b/lib/linalg/dlasq2.f index 68d9228704..608ca7a619 100644 --- a/lib/linalg/dlasq2.f +++ b/lib/linalg/dlasq2.f @@ -95,8 +95,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup auxOTHERcomputational * *> \par Further Details: @@ -112,10 +110,9 @@ * ===================================================================== SUBROUTINE DLASQ2( N, Z, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, N @@ -184,10 +181,18 @@ * * 2-by-2 case. * - IF( Z( 2 ).LT.ZERO .OR. Z( 3 ).LT.ZERO ) THEN - INFO = -2 + IF( Z( 1 ).LT.ZERO ) THEN + INFO = -201 CALL XERBLA( 'DLASQ2', 2 ) RETURN + ELSE IF( Z( 2 ).LT.ZERO ) THEN + INFO = -202 + CALL XERBLA( 'DLASQ2', 2 ) + RETURN + ELSE IF( Z( 3 ).LT.ZERO ) THEN + INFO = -203 + CALL XERBLA( 'DLASQ2', 2 ) + RETURN ELSE IF( Z( 3 ).GT.Z( 1 ) ) THEN D = Z( 3 ) Z( 3 ) = Z( 1 ) @@ -267,8 +272,7 @@ * * Check whether the machine is IEEE conformable. * - IEEE = ILAENV( 10, 'DLASQ2', 'N', 1, 2, 3, 4 ).EQ.1 .AND. - $ ILAENV( 11, 'DLASQ2', 'N', 1, 2, 3, 4 ).EQ.1 + IEEE = ( ILAENV( 10, 'DLASQ2', 'N', 1, 2, 3, 4 ).EQ.1 ) * * Rearrange data for locality: Z=(q1,qq1,e1,ee1,q2,qq2,e2,ee2,...). * diff --git a/lib/linalg/dlasq3.f b/lib/linalg/dlasq3.f index c095bdbbb5..e4bdafe06e 100644 --- a/lib/linalg/dlasq3.f +++ b/lib/linalg/dlasq3.f @@ -173,8 +173,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2016 -* *> \ingroup auxOTHERcomputational * * ===================================================================== @@ -182,10 +180,9 @@ $ ITER, NDIV, IEEE, TTYPE, DMIN1, DMIN2, DN, DN1, $ DN2, G, TAU ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2016 * * .. Scalar Arguments .. LOGICAL IEEE diff --git a/lib/linalg/dlasq4.f b/lib/linalg/dlasq4.f index d4ddbbc7b2..2652ddb2ba 100644 --- a/lib/linalg/dlasq4.f +++ b/lib/linalg/dlasq4.f @@ -135,8 +135,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2016 -* *> \ingroup auxOTHERcomputational * *> \par Further Details: @@ -151,10 +149,9 @@ SUBROUTINE DLASQ4( I0, N0, Z, PP, N0IN, DMIN, DMIN1, DMIN2, DN, $ DN1, DN2, TAU, TTYPE, G ) * -* -- LAPACK computational routine (version 3.7.1) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2016 * * .. Scalar Arguments .. INTEGER I0, N0, N0IN, PP, TTYPE diff --git a/lib/linalg/dlasq5.f b/lib/linalg/dlasq5.f index 3812c879fa..5679ab60a5 100644 --- a/lib/linalg/dlasq5.f +++ b/lib/linalg/dlasq5.f @@ -136,18 +136,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup auxOTHERcomputational * * ===================================================================== SUBROUTINE DLASQ5( I0, N0, Z, PP, TAU, SIGMA, DMIN, DMIN1, DMIN2, $ DN, DNM1, DNM2, IEEE, EPS ) * -* -- LAPACK computational routine (version 3.7.1) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. LOGICAL IEEE diff --git a/lib/linalg/dlasq6.f b/lib/linalg/dlasq6.f index d871386bdb..9218b5060e 100644 --- a/lib/linalg/dlasq6.f +++ b/lib/linalg/dlasq6.f @@ -111,18 +111,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup auxOTHERcomputational * * ===================================================================== SUBROUTINE DLASQ6( I0, N0, Z, PP, DMIN, DMIN1, DMIN2, DN, $ DNM1, DNM2 ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER I0, N0, PP diff --git a/lib/linalg/dlasr.f b/lib/linalg/dlasr.f index 6059c6293a..dd0cedd85e 100644 --- a/lib/linalg/dlasr.f +++ b/lib/linalg/dlasr.f @@ -175,7 +175,7 @@ *> \verbatim *> A is DOUBLE PRECISION array, dimension (LDA,N) *> The M-by-N matrix A. On exit, A is overwritten by P*A if -*> SIDE = 'R' or by A*P**T if SIDE = 'L'. +*> SIDE = 'L' or by A*P**T if SIDE = 'R'. *> \endverbatim *> *> \param[in] LDA @@ -192,17 +192,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE DLASR( SIDE, PIVOT, DIRECT, M, N, C, S, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER DIRECT, PIVOT, SIDE diff --git a/lib/linalg/dlasrt.f b/lib/linalg/dlasrt.f index 4705311d78..d789239e3d 100644 --- a/lib/linalg/dlasrt.f +++ b/lib/linalg/dlasrt.f @@ -81,17 +81,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2016 -* *> \ingroup auxOTHERcomputational * * ===================================================================== SUBROUTINE DLASRT( ID, N, D, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2016 * * .. Scalar Arguments .. CHARACTER ID diff --git a/lib/linalg/dlasv2.f b/lib/linalg/dlasv2.f index 9371d6d3b2..64a06dee1a 100644 --- a/lib/linalg/dlasv2.f +++ b/lib/linalg/dlasv2.f @@ -107,8 +107,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * *> \par Further Details: @@ -138,10 +136,9 @@ * ===================================================================== SUBROUTINE DLASV2( F, G, H, SSMIN, SSMAX, SNR, CSR, SNL, CSL ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION CSL, CSR, F, G, H, SNL, SNR, SSMAX, SSMIN diff --git a/lib/linalg/dlaswp.f b/lib/linalg/dlaswp.f index 202fd8df1b..b35729a205 100644 --- a/lib/linalg/dlaswp.f +++ b/lib/linalg/dlaswp.f @@ -99,8 +99,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup doubleOTHERauxiliary * *> \par Further Details: @@ -115,10 +113,9 @@ * ===================================================================== SUBROUTINE DLASWP( N, A, LDA, K1, K2, IPIV, INCX ) * -* -- LAPACK auxiliary routine (version 3.7.1) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. INTEGER INCX, K1, K2, LDA, N diff --git a/lib/linalg/dlatrd.f b/lib/linalg/dlatrd.f index a1df43e48a..010a85a212 100644 --- a/lib/linalg/dlatrd.f +++ b/lib/linalg/dlatrd.f @@ -139,8 +139,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERauxiliary * *> \par Further Details: @@ -198,10 +196,9 @@ * ===================================================================== SUBROUTINE DLATRD( UPLO, N, NB, A, LDA, E, TAU, W, LDW ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dlatrs.f b/lib/linalg/dlatrs.f index 5ad5f66c55..43f92911d7 100644 --- a/lib/linalg/dlatrs.f +++ b/lib/linalg/dlatrs.f @@ -158,8 +158,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERauxiliary * *> \par Further Details: @@ -238,10 +236,9 @@ SUBROUTINE DLATRS( UPLO, TRANS, DIAG, NORMIN, N, A, LDA, X, SCALE, $ CNORM, INFO ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER DIAG, NORMIN, TRANS, UPLO diff --git a/lib/linalg/dorg2l.f b/lib/linalg/dorg2l.f index 36ff4e5d4b..0a42d4cf5a 100644 --- a/lib/linalg/dorg2l.f +++ b/lib/linalg/dorg2l.f @@ -107,17 +107,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORG2L( M, N, K, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, M, N diff --git a/lib/linalg/dorg2r.f b/lib/linalg/dorg2r.f index 4b71011a9f..c64ad4b0ac 100644 --- a/lib/linalg/dorg2r.f +++ b/lib/linalg/dorg2r.f @@ -107,17 +107,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORG2R( M, N, K, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, M, N diff --git a/lib/linalg/dorgbr.f b/lib/linalg/dorgbr.f index cfebda5abd..1b242ff97f 100644 --- a/lib/linalg/dorgbr.f +++ b/lib/linalg/dorgbr.f @@ -150,17 +150,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date April 2012 -* *> \ingroup doubleGBcomputational * * ===================================================================== SUBROUTINE DORGBR( VECT, M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* April 2012 * * .. Scalar Arguments .. CHARACTER VECT @@ -221,8 +218,8 @@ CALL DORGQR( M, N, K, A, LDA, TAU, WORK, -1, IINFO ) ELSE IF( M.GT.1 ) THEN - CALL DORGQR( M-1, M-1, M-1, A( 2, 2 ), LDA, TAU, WORK, - $ -1, IINFO ) + CALL DORGQR( M-1, M-1, M-1, A, LDA, TAU, WORK, -1, + $ IINFO ) END IF END IF ELSE @@ -230,8 +227,8 @@ CALL DORGLQ( M, N, K, A, LDA, TAU, WORK, -1, IINFO ) ELSE IF( N.GT.1 ) THEN - CALL DORGLQ( N-1, N-1, N-1, A( 2, 2 ), LDA, TAU, WORK, - $ -1, IINFO ) + CALL DORGLQ( N-1, N-1, N-1, A, LDA, TAU, WORK, -1, + $ IINFO ) END IF END IF END IF diff --git a/lib/linalg/dorgl2.f b/lib/linalg/dorgl2.f index 5d8985d758..ce1d2c6750 100644 --- a/lib/linalg/dorgl2.f +++ b/lib/linalg/dorgl2.f @@ -106,17 +106,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORGL2( M, N, K, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, M, N diff --git a/lib/linalg/dorglq.f b/lib/linalg/dorglq.f index 912b5de84e..8c37c18b75 100644 --- a/lib/linalg/dorglq.f +++ b/lib/linalg/dorglq.f @@ -120,17 +120,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORGLQ( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, LWORK, M, N diff --git a/lib/linalg/dorgql.f b/lib/linalg/dorgql.f index ea12be91b1..45e5bf19f1 100644 --- a/lib/linalg/dorgql.f +++ b/lib/linalg/dorgql.f @@ -121,17 +121,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORGQL( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, LWORK, M, N diff --git a/lib/linalg/dorgqr.f b/lib/linalg/dorgqr.f index 628eeacba7..a41ce7ed56 100644 --- a/lib/linalg/dorgqr.f +++ b/lib/linalg/dorgqr.f @@ -121,17 +121,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORGQR( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, LWORK, M, N diff --git a/lib/linalg/dorgtr.f b/lib/linalg/dorgtr.f index 72623eac06..0a0ab15a78 100644 --- a/lib/linalg/dorgtr.f +++ b/lib/linalg/dorgtr.f @@ -116,17 +116,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORGTR( UPLO, N, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dorm2l.f b/lib/linalg/dorm2l.f index 1014cb2378..c99039c541 100644 --- a/lib/linalg/dorm2l.f +++ b/lib/linalg/dorm2l.f @@ -151,18 +151,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORM2L( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, $ WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS diff --git a/lib/linalg/dorm2r.f b/lib/linalg/dorm2r.f index 632b70e740..ac88eec8dc 100644 --- a/lib/linalg/dorm2r.f +++ b/lib/linalg/dorm2r.f @@ -151,18 +151,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORM2R( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, $ WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS diff --git a/lib/linalg/dormbr.f b/lib/linalg/dormbr.f index f035d0ae66..86abb10072 100644 --- a/lib/linalg/dormbr.f +++ b/lib/linalg/dormbr.f @@ -187,18 +187,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORMBR( VECT, SIDE, TRANS, M, N, K, A, LDA, TAU, C, $ LDC, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS, VECT @@ -240,10 +237,10 @@ * IF( LEFT ) THEN NQ = M - NW = N + NW = MAX( 1, N ) ELSE NQ = N - NW = M + NW = MAX( 1, M ) END IF IF( .NOT.APPLYQ .AND. .NOT.LSAME( VECT, 'P' ) ) THEN INFO = -1 @@ -263,7 +260,7 @@ INFO = -8 ELSE IF( LDC.LT.MAX( 1, M ) ) THEN INFO = -11 - ELSE IF( LWORK.LT.MAX( 1, NW ) .AND. .NOT.LQUERY ) THEN + ELSE IF( LWORK.LT.NW .AND. .NOT.LQUERY ) THEN INFO = -13 END IF * @@ -285,7 +282,7 @@ $ -1 ) END IF END IF - LWKOPT = MAX( 1, NW )*NB + LWKOPT = NW*NB WORK( 1 ) = LWKOPT END IF * diff --git a/lib/linalg/dorml2.f b/lib/linalg/dorml2.f index 2c55c7f1fd..a9ddd460d8 100644 --- a/lib/linalg/dorml2.f +++ b/lib/linalg/dorml2.f @@ -151,18 +151,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORML2( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, $ WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS diff --git a/lib/linalg/dormlq.f b/lib/linalg/dormlq.f index bb5469d273..ef039285ab 100644 --- a/lib/linalg/dormlq.f +++ b/lib/linalg/dormlq.f @@ -159,18 +159,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORMLQ( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, $ WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS @@ -217,10 +214,10 @@ * IF( LEFT ) THEN NQ = M - NW = N + NW = MAX( 1, N ) ELSE NQ = N - NW = M + NW = MAX( 1, M ) END IF IF( .NOT.LEFT .AND. .NOT.LSAME( SIDE, 'R' ) ) THEN INFO = -1 @@ -236,7 +233,7 @@ INFO = -7 ELSE IF( LDC.LT.MAX( 1, M ) ) THEN INFO = -10 - ELSE IF( LWORK.LT.MAX( 1, NW ) .AND. .NOT.LQUERY ) THEN + ELSE IF( LWORK.LT.NW .AND. .NOT.LQUERY ) THEN INFO = -12 END IF * @@ -246,7 +243,7 @@ * NB = MIN( NBMAX, ILAENV( 1, 'DORMLQ', SIDE // TRANS, M, N, K, $ -1 ) ) - LWKOPT = MAX( 1, NW )*NB + TSIZE + LWKOPT = NW*NB + TSIZE WORK( 1 ) = LWKOPT END IF * @@ -267,7 +264,7 @@ NBMIN = 2 LDWORK = NW IF( NB.GT.1 .AND. NB.LT.K ) THEN - IF( LWORK.LT.NW*NB+TSIZE ) THEN + IF( LWORK.LT.LWKOPT ) THEN NB = (LWORK-TSIZE) / LDWORK NBMIN = MAX( 2, ILAENV( 2, 'DORMLQ', SIDE // TRANS, M, N, K, $ -1 ) ) diff --git a/lib/linalg/dormql.f b/lib/linalg/dormql.f index 7d2b5d6c32..7c9f189e0d 100644 --- a/lib/linalg/dormql.f +++ b/lib/linalg/dormql.f @@ -159,18 +159,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORMQL( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, $ WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS @@ -269,7 +266,7 @@ NBMIN = 2 LDWORK = NW IF( NB.GT.1 .AND. NB.LT.K ) THEN - IF( LWORK.LT.NW*NB+TSIZE ) THEN + IF( LWORK.LT.LWKOPT ) THEN NB = (LWORK-TSIZE) / LDWORK NBMIN = MAX( 2, ILAENV( 2, 'DORMQL', SIDE // TRANS, M, N, K, $ -1 ) ) diff --git a/lib/linalg/dormqr.f b/lib/linalg/dormqr.f index 7f2ebb9ace..4d0bae3a5f 100644 --- a/lib/linalg/dormqr.f +++ b/lib/linalg/dormqr.f @@ -159,18 +159,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORMQR( SIDE, TRANS, M, N, K, A, LDA, TAU, C, LDC, $ WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS @@ -216,10 +213,10 @@ * IF( LEFT ) THEN NQ = M - NW = N + NW = MAX( 1, N ) ELSE NQ = N - NW = M + NW = MAX( 1, M ) END IF IF( .NOT.LEFT .AND. .NOT.LSAME( SIDE, 'R' ) ) THEN INFO = -1 @@ -235,7 +232,7 @@ INFO = -7 ELSE IF( LDC.LT.MAX( 1, M ) ) THEN INFO = -10 - ELSE IF( LWORK.LT.MAX( 1, NW ) .AND. .NOT.LQUERY ) THEN + ELSE IF( LWORK.LT.NW .AND. .NOT.LQUERY ) THEN INFO = -12 END IF * @@ -245,7 +242,7 @@ * NB = MIN( NBMAX, ILAENV( 1, 'DORMQR', SIDE // TRANS, M, N, K, $ -1 ) ) - LWKOPT = MAX( 1, NW )*NB + TSIZE + LWKOPT = NW*NB + TSIZE WORK( 1 ) = LWKOPT END IF * @@ -266,7 +263,7 @@ NBMIN = 2 LDWORK = NW IF( NB.GT.1 .AND. NB.LT.K ) THEN - IF( LWORK.LT.NW*NB+TSIZE ) THEN + IF( LWORK.LT.LWKOPT ) THEN NB = (LWORK-TSIZE) / LDWORK NBMIN = MAX( 2, ILAENV( 2, 'DORMQR', SIDE // TRANS, M, N, K, $ -1 ) ) diff --git a/lib/linalg/dormtr.f b/lib/linalg/dormtr.f index d2443c1dac..1f664d63cc 100644 --- a/lib/linalg/dormtr.f +++ b/lib/linalg/dormtr.f @@ -163,18 +163,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DORMTR( SIDE, UPLO, TRANS, M, N, A, LDA, TAU, C, LDC, $ WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE, TRANS, UPLO @@ -214,10 +211,10 @@ * IF( LEFT ) THEN NQ = M - NW = N + NW = MAX( 1, N ) ELSE NQ = N - NW = M + NW = MAX( 1, M ) END IF IF( .NOT.LEFT .AND. .NOT.LSAME( SIDE, 'R' ) ) THEN INFO = -1 @@ -234,7 +231,7 @@ INFO = -7 ELSE IF( LDC.LT.MAX( 1, M ) ) THEN INFO = -10 - ELSE IF( LWORK.LT.MAX( 1, NW ) .AND. .NOT.LQUERY ) THEN + ELSE IF( LWORK.LT.NW .AND. .NOT.LQUERY ) THEN INFO = -12 END IF * @@ -256,7 +253,7 @@ $ -1 ) END IF END IF - LWKOPT = MAX( 1, NW )*NB + LWKOPT = NW*NB WORK( 1 ) = LWKOPT END IF * diff --git a/lib/linalg/dpotf2.f b/lib/linalg/dpotf2.f index 1fb60a903b..08fa4957fd 100644 --- a/lib/linalg/dpotf2.f +++ b/lib/linalg/dpotf2.f @@ -102,17 +102,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doublePOcomputational * * ===================================================================== SUBROUTINE DPOTF2( UPLO, N, A, LDA, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dpotrf.f b/lib/linalg/dpotrf.f index 1fa75a4654..1679fc3cd8 100644 --- a/lib/linalg/dpotrf.f +++ b/lib/linalg/dpotrf.f @@ -100,17 +100,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doublePOcomputational * * ===================================================================== SUBROUTINE DPOTRF( UPLO, N, A, LDA, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dpotrf2.f b/lib/linalg/dpotrf2.f index 0d419c4f00..6c28ce6d67 100644 --- a/lib/linalg/dpotrf2.f +++ b/lib/linalg/dpotrf2.f @@ -99,17 +99,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doublePOcomputational * * ===================================================================== RECURSIVE SUBROUTINE DPOTRF2( UPLO, N, A, LDA, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/drot.f b/lib/linalg/drot.f index 0d33ea76c8..0386626c8f 100644 --- a/lib/linalg/drot.f +++ b/lib/linalg/drot.f @@ -76,8 +76,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level1 * *> \par Further Details: @@ -92,10 +90,9 @@ * ===================================================================== SUBROUTINE DROT(N,DX,INCX,DY,INCY,C,S) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION C,S @@ -139,4 +136,7 @@ END DO END IF RETURN +* +* End of DROT +* END diff --git a/lib/linalg/drscl.f b/lib/linalg/drscl.f index 9251143680..fcd8569650 100644 --- a/lib/linalg/drscl.f +++ b/lib/linalg/drscl.f @@ -77,17 +77,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERauxiliary * * ===================================================================== SUBROUTINE DRSCL( N, SA, SX, INCX ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX, N @@ -112,7 +109,7 @@ EXTERNAL DLAMCH * .. * .. External Subroutines .. - EXTERNAL DSCAL + EXTERNAL DSCAL, DLABAD * .. * .. Intrinsic Functions .. INTRINSIC ABS diff --git a/lib/linalg/dscal.f b/lib/linalg/dscal.f index e0a92de6ba..3713427334 100644 --- a/lib/linalg/dscal.f +++ b/lib/linalg/dscal.f @@ -62,8 +62,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level1 * *> \par Further Details: @@ -79,10 +77,9 @@ * ===================================================================== SUBROUTINE DSCAL(N,DA,DX,INCX) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION DA @@ -133,4 +130,7 @@ END DO END IF RETURN +* +* End of DSCAL +* END diff --git a/lib/linalg/dstedc.f b/lib/linalg/dstedc.f index 61b44bc06b..2ed84afaac 100644 --- a/lib/linalg/dstedc.f +++ b/lib/linalg/dstedc.f @@ -173,8 +173,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup auxOTHERcomputational * *> \par Contributors: @@ -188,10 +186,9 @@ SUBROUTINE DSTEDC( COMPZ, N, D, E, Z, LDZ, WORK, LWORK, IWORK, $ LIWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.1) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. CHARACTER COMPZ diff --git a/lib/linalg/dsteqr.f b/lib/linalg/dsteqr.f index c34a548984..50a9188c7c 100644 --- a/lib/linalg/dsteqr.f +++ b/lib/linalg/dsteqr.f @@ -124,17 +124,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup auxOTHERcomputational * * ===================================================================== SUBROUTINE DSTEQR( COMPZ, N, D, E, Z, LDZ, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER COMPZ diff --git a/lib/linalg/dsterf.f b/lib/linalg/dsterf.f index 3401894819..b0f8d36084 100644 --- a/lib/linalg/dsterf.f +++ b/lib/linalg/dsterf.f @@ -79,17 +79,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup auxOTHERcomputational * * ===================================================================== SUBROUTINE DSTERF( N, D, E, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, N diff --git a/lib/linalg/dswap.f b/lib/linalg/dswap.f index 94dfea3bb9..b7600aa2d4 100644 --- a/lib/linalg/dswap.f +++ b/lib/linalg/dswap.f @@ -66,8 +66,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level1 * *> \par Further Details: @@ -82,10 +80,9 @@ * ===================================================================== SUBROUTINE DSWAP(N,DX,INCX,DY,INCY) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX,INCY,N @@ -150,4 +147,7 @@ END DO END IF RETURN +* +* End of DSWAP +* END diff --git a/lib/linalg/dsyev.f b/lib/linalg/dsyev.f index ee8c479abe..da7557ee02 100644 --- a/lib/linalg/dsyev.f +++ b/lib/linalg/dsyev.f @@ -125,17 +125,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleSYeigen * * ===================================================================== SUBROUTINE DSYEV( JOBZ, UPLO, N, A, LDA, W, WORK, LWORK, INFO ) * -* -- LAPACK driver routine (version 3.7.0) -- +* -- LAPACK driver routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER JOBZ, UPLO diff --git a/lib/linalg/dsyevd.f b/lib/linalg/dsyevd.f index 2db67846dc..edbe896fe8 100644 --- a/lib/linalg/dsyevd.f +++ b/lib/linalg/dsyevd.f @@ -167,8 +167,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleSYeigen * *> \par Contributors: @@ -185,10 +183,9 @@ SUBROUTINE DSYEVD( JOBZ, UPLO, N, A, LDA, W, WORK, LWORK, IWORK, $ LIWORK, INFO ) * -* -- LAPACK driver routine (version 3.7.0) -- +* -- LAPACK driver routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER JOBZ, UPLO diff --git a/lib/linalg/dsygs2.f b/lib/linalg/dsygs2.f index a54955c01e..8a39bea77e 100644 --- a/lib/linalg/dsygs2.f +++ b/lib/linalg/dsygs2.f @@ -120,17 +120,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleSYcomputational * * ===================================================================== SUBROUTINE DSYGS2( ITYPE, UPLO, N, A, LDA, B, LDB, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dsygst.f b/lib/linalg/dsygst.f index 5055acdf1d..05b90372ab 100644 --- a/lib/linalg/dsygst.f +++ b/lib/linalg/dsygst.f @@ -120,17 +120,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleSYcomputational * * ===================================================================== SUBROUTINE DSYGST( ITYPE, UPLO, N, A, LDA, B, LDB, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dsygv.f b/lib/linalg/dsygv.f index 651abc5c7b..5208dbb1f1 100644 --- a/lib/linalg/dsygv.f +++ b/lib/linalg/dsygv.f @@ -167,18 +167,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleSYeigen * * ===================================================================== SUBROUTINE DSYGV( ITYPE, JOBZ, UPLO, N, A, LDA, B, LDB, W, WORK, $ LWORK, INFO ) * -* -- LAPACK driver routine (version 3.7.0) -- +* -- LAPACK driver routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER JOBZ, UPLO diff --git a/lib/linalg/dsygvd.f b/lib/linalg/dsygvd.f index 29c78283a7..61134bedce 100644 --- a/lib/linalg/dsygvd.f +++ b/lib/linalg/dsygvd.f @@ -203,8 +203,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleSYeigen * *> \par Further Details: @@ -227,10 +225,9 @@ SUBROUTINE DSYGVD( ITYPE, JOBZ, UPLO, N, A, LDA, B, LDB, W, WORK, $ LWORK, IWORK, LIWORK, INFO ) * -* -- LAPACK driver routine (version 3.7.0) -- +* -- LAPACK driver routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER JOBZ, UPLO diff --git a/lib/linalg/dsymm.f b/lib/linalg/dsymm.f index 622d2469f1..683e79f6ad 100644 --- a/lib/linalg/dsymm.f +++ b/lib/linalg/dsymm.f @@ -168,8 +168,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level3 * *> \par Further Details: @@ -189,10 +187,9 @@ * ===================================================================== SUBROUTINE DSYMM(SIDE,UPLO,M,N,ALPHA,A,LDA,B,LDB,BETA,C,LDC) * -* -- Reference BLAS level3 routine (version 3.7.0) -- +* -- Reference BLAS level3 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA,BETA @@ -362,6 +359,6 @@ * RETURN * -* End of DSYMM . +* End of DSYMM * END diff --git a/lib/linalg/dsymv.f b/lib/linalg/dsymv.f index 4bf973f10a..17310d7c62 100644 --- a/lib/linalg/dsymv.f +++ b/lib/linalg/dsymv.f @@ -130,8 +130,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level2 * *> \par Further Details: @@ -152,10 +150,9 @@ * ===================================================================== SUBROUTINE DSYMV(UPLO,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY) * -* -- Reference BLAS level2 routine (version 3.7.0) -- +* -- Reference BLAS level2 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA,BETA @@ -328,6 +325,6 @@ * RETURN * -* End of DSYMV . +* End of DSYMV * END diff --git a/lib/linalg/dsyr2.f b/lib/linalg/dsyr2.f index 8970c4dcfd..4bad19b96b 100644 --- a/lib/linalg/dsyr2.f +++ b/lib/linalg/dsyr2.f @@ -126,8 +126,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level2 * *> \par Further Details: @@ -147,10 +145,9 @@ * ===================================================================== SUBROUTINE DSYR2(UPLO,N,ALPHA,X,INCX,Y,INCY,A,LDA) * -* -- Reference BLAS level2 routine (version 3.7.0) -- +* -- Reference BLAS level2 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA @@ -293,6 +290,6 @@ * RETURN * -* End of DSYR2 . +* End of DSYR2 * END diff --git a/lib/linalg/dsyr2k.f b/lib/linalg/dsyr2k.f index f3a5940c7f..f5d16e0854 100644 --- a/lib/linalg/dsyr2k.f +++ b/lib/linalg/dsyr2k.f @@ -170,8 +170,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level3 * *> \par Further Details: @@ -192,10 +190,9 @@ * ===================================================================== SUBROUTINE DSYR2K(UPLO,TRANS,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC) * -* -- Reference BLAS level3 routine (version 3.7.0) -- +* -- Reference BLAS level3 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA,BETA @@ -394,6 +391,6 @@ * RETURN * -* End of DSYR2K. +* End of DSYR2K * END diff --git a/lib/linalg/dsyrk.f b/lib/linalg/dsyrk.f index 4be4d8d3c4..0548c0ce2f 100644 --- a/lib/linalg/dsyrk.f +++ b/lib/linalg/dsyrk.f @@ -148,8 +148,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level3 * *> \par Further Details: @@ -169,10 +167,9 @@ * ===================================================================== SUBROUTINE DSYRK(UPLO,TRANS,N,K,ALPHA,A,LDA,BETA,C,LDC) * -* -- Reference BLAS level3 routine (version 3.7.0) -- +* -- Reference BLAS level3 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA,BETA @@ -359,6 +356,6 @@ * RETURN * -* End of DSYRK . +* End of DSYRK * END diff --git a/lib/linalg/dsytd2.f b/lib/linalg/dsytd2.f index 6fb4d5507e..977b6daa41 100644 --- a/lib/linalg/dsytd2.f +++ b/lib/linalg/dsytd2.f @@ -120,8 +120,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleSYcomputational * *> \par Further Details: @@ -173,10 +171,9 @@ * ===================================================================== SUBROUTINE DSYTD2( UPLO, N, A, LDA, D, E, TAU, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dsytrd.f b/lib/linalg/dsytrd.f index d330b241fa..3dcfc3db2b 100644 --- a/lib/linalg/dsytrd.f +++ b/lib/linalg/dsytrd.f @@ -139,8 +139,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleSYcomputational * *> \par Further Details: @@ -192,10 +190,9 @@ * ===================================================================== SUBROUTINE DSYTRD( UPLO, N, A, LDA, D, E, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/dtrmm.f b/lib/linalg/dtrmm.f index 0241c4d146..b2cc0a1fa8 100644 --- a/lib/linalg/dtrmm.f +++ b/lib/linalg/dtrmm.f @@ -156,8 +156,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level3 * *> \par Further Details: @@ -177,10 +175,9 @@ * ===================================================================== SUBROUTINE DTRMM(SIDE,UPLO,TRANSA,DIAG,M,N,ALPHA,A,LDA,B,LDB) * -* -- Reference BLAS level3 routine (version 3.7.0) -- +* -- Reference BLAS level3 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA @@ -410,6 +407,6 @@ * RETURN * -* End of DTRMM . +* End of DTRMM * END diff --git a/lib/linalg/dtrmv.f b/lib/linalg/dtrmv.f index 11c12ac724..e8af8e6136 100644 --- a/lib/linalg/dtrmv.f +++ b/lib/linalg/dtrmv.f @@ -125,8 +125,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level2 * *> \par Further Details: @@ -147,10 +145,9 @@ * ===================================================================== SUBROUTINE DTRMV(UPLO,TRANS,DIAG,N,A,LDA,X,INCX) * -* -- Reference BLAS level2 routine (version 3.7.0) -- +* -- Reference BLAS level2 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX,LDA,N @@ -337,6 +334,6 @@ * RETURN * -* End of DTRMV . +* End of DTRMV * END diff --git a/lib/linalg/dtrsm.f b/lib/linalg/dtrsm.f index 5a92bcafd0..fa8080bc92 100644 --- a/lib/linalg/dtrsm.f +++ b/lib/linalg/dtrsm.f @@ -159,8 +159,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level3 * *> \par Further Details: @@ -181,10 +179,9 @@ * ===================================================================== SUBROUTINE DTRSM(SIDE,UPLO,TRANSA,DIAG,M,N,ALPHA,A,LDA,B,LDB) * -* -- Reference BLAS level3 routine (version 3.7.0) -- +* -- Reference BLAS level3 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA @@ -438,6 +435,6 @@ * RETURN * -* End of DTRSM . +* End of DTRSM * END diff --git a/lib/linalg/dtrsv.f b/lib/linalg/dtrsv.f index 331f1d4311..d8ea9fa898 100644 --- a/lib/linalg/dtrsv.f +++ b/lib/linalg/dtrsv.f @@ -136,17 +136,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup double_blas_level1 * * ===================================================================== SUBROUTINE DTRSV(UPLO,TRANS,DIAG,N,A,LDA,X,INCX) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX,LDA,N @@ -333,6 +330,6 @@ * RETURN * -* End of DTRSV . +* End of DTRSV * END diff --git a/lib/linalg/dtrti2.f b/lib/linalg/dtrti2.f index 0a9d5b696c..0d9115554c 100644 --- a/lib/linalg/dtrti2.f +++ b/lib/linalg/dtrti2.f @@ -103,17 +103,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DTRTI2( UPLO, DIAG, N, A, LDA, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER DIAG, UPLO diff --git a/lib/linalg/dtrtri.f b/lib/linalg/dtrtri.f index d34b40bcc0..1cf9a9aafb 100644 --- a/lib/linalg/dtrtri.f +++ b/lib/linalg/dtrtri.f @@ -102,17 +102,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup doubleOTHERcomputational * * ===================================================================== SUBROUTINE DTRTRI( UPLO, DIAG, N, A, LDA, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER DIAG, UPLO diff --git a/lib/linalg/idamax.f b/lib/linalg/idamax.f index 17041680a4..1be301ea3e 100644 --- a/lib/linalg/idamax.f +++ b/lib/linalg/idamax.f @@ -43,7 +43,7 @@ *> \param[in] INCX *> \verbatim *> INCX is INTEGER -*> storage spacing between elements of SX +*> storage spacing between elements of DX *> \endverbatim * * Authors: @@ -54,8 +54,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup aux_blas * *> \par Further Details: @@ -71,10 +69,9 @@ * ===================================================================== INTEGER FUNCTION IDAMAX(N,DX,INCX) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX,N @@ -123,4 +120,7 @@ END DO END IF RETURN +* +* End of IDAMAX +* END diff --git a/lib/linalg/ieeeck.f b/lib/linalg/ieeeck.f index 2655958b4a..74065c3b4e 100644 --- a/lib/linalg/ieeeck.f +++ b/lib/linalg/ieeeck.f @@ -75,17 +75,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * * ===================================================================== INTEGER FUNCTION IEEECK( ISPEC, ZERO, ONE ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER ISPEC diff --git a/lib/linalg/iladlc.f b/lib/linalg/iladlc.f index c6476113d1..a98e7218bf 100644 --- a/lib/linalg/iladlc.f +++ b/lib/linalg/iladlc.f @@ -71,17 +71,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * * ===================================================================== INTEGER FUNCTION ILADLC( M, N, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER M, N, LDA diff --git a/lib/linalg/iladlr.f b/lib/linalg/iladlr.f index e8951d86cc..b1abded84b 100644 --- a/lib/linalg/iladlr.f +++ b/lib/linalg/iladlr.f @@ -71,17 +71,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * * ===================================================================== INTEGER FUNCTION ILADLR( M, N, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER M, N, LDA diff --git a/lib/linalg/ilaenv.f b/lib/linalg/ilaenv.f index 2be0581517..af28503986 100644 --- a/lib/linalg/ilaenv.f +++ b/lib/linalg/ilaenv.f @@ -79,9 +79,9 @@ *> = 9: maximum size of the subproblems at the bottom of the *> computation tree in the divide-and-conquer algorithm *> (used by xGELSD and xGESDD) -*> =10: ieee NaN arithmetic can be trusted not to trap +*> =10: ieee infinity and NaN arithmetic can be trusted not to trap *> =11: infinity arithmetic can be trusted not to trap -*> 12 <= ISPEC <= 16: +*> 12 <= ISPEC <= 17: *> xHSEQR or related subroutines, *> see IPARMQ for detailed explanation *> \endverbatim @@ -132,8 +132,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * *> \par Further Details: @@ -162,10 +160,9 @@ * ===================================================================== INTEGER FUNCTION ILAENV( ISPEC, NAME, OPTS, N1, N2, N3, N4 ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER*( * ) NAME, OPTS @@ -176,8 +173,8 @@ * * .. Local Scalars .. INTEGER I, IC, IZ, NB, NBMIN, NX - LOGICAL CNAME, SNAME - CHARACTER C1*1, C2*2, C4*2, C3*3, SUBNAM*6 + LOGICAL CNAME, SNAME, TWOSTAGE + CHARACTER C1*1, C2*2, C4*2, C3*3, SUBNAM*16 * .. * .. Intrinsic Functions .. INTRINSIC CHAR, ICHAR, INT, MIN, REAL @@ -189,8 +186,7 @@ * .. Executable Statements .. * GO TO ( 10, 10, 10, 80, 90, 100, 110, 120, - $ 130, 140, 150, 160, 160, 160, 160, 160, - $ 170, 170, 170, 170, 170 )ISPEC + $ 130, 140, 150, 160, 160, 160, 160, 160, 160)ISPEC * * Invalid value for ISPEC * @@ -257,6 +253,8 @@ C2 = SUBNAM( 2: 3 ) C3 = SUBNAM( 4: 6 ) C4 = C3( 2: 3 ) + TWOSTAGE = LEN( SUBNAM ).GE.11 + $ .AND. SUBNAM( 11: 11 ).EQ.'2' * GO TO ( 50, 60, 70 )ISPEC * @@ -270,7 +268,16 @@ * NB = 1 * - IF( C2.EQ.'GE' ) THEN + IF( SUBNAM(2:6).EQ.'LAORH' ) THEN +* +* This is for *LAORHR_GETRFNP routine +* + IF( SNAME ) THEN + NB = 32 + ELSE + NB = 32 + END IF + ELSE IF( C2.EQ.'GE' ) THEN IF( C3.EQ.'TRF' ) THEN IF( SNAME ) THEN NB = 64 @@ -360,9 +367,17 @@ ELSE IF( C2.EQ.'SY' ) THEN IF( C3.EQ.'TRF' ) THEN IF( SNAME ) THEN - NB = 64 + IF( TWOSTAGE ) THEN + NB = 192 + ELSE + NB = 64 + END IF ELSE - NB = 64 + IF( TWOSTAGE ) THEN + NB = 192 + ELSE + NB = 64 + END IF END IF ELSE IF( SNAME .AND. C3.EQ.'TRD' ) THEN NB = 32 @@ -371,7 +386,11 @@ END IF ELSE IF( CNAME .AND. C2.EQ.'HE' ) THEN IF( C3.EQ.'TRF' ) THEN - NB = 64 + IF( TWOSTAGE ) THEN + NB = 192 + ELSE + NB = 64 + END IF ELSE IF( C3.EQ.'TRD' ) THEN NB = 32 ELSE IF( C3.EQ.'GST' ) THEN @@ -664,7 +683,7 @@ * 140 CONTINUE * -* ISPEC = 10: ieee NaN arithmetic can be trusted not to trap +* ISPEC = 10: ieee and infinity NaN arithmetic can be trusted not to trap * * ILAENV = 0 ILAENV = 1 @@ -675,7 +694,7 @@ * 150 CONTINUE * -* ISPEC = 11: infinity arithmetic can be trusted not to trap +* ISPEC = 11: ieee infinity arithmetic can be trusted not to trap * * ILAENV = 0 ILAENV = 1 @@ -686,17 +705,10 @@ * 160 CONTINUE * -* 12 <= ISPEC <= 16: xHSEQR or related subroutines. +* 12 <= ISPEC <= 17: xHSEQR or related subroutines. * ILAENV = IPARMQ( ISPEC, NAME, OPTS, N1, N2, N3, N4 ) RETURN -* - 170 CONTINUE -* -* 17 <= ISPEC <= 21: 2stage eigenvalues and SVD or related subroutines. -* - ILAENV = IPARAM2STAGE( ISPEC, NAME, OPTS, N1, N2, N3, N4 ) - RETURN * * End of ILAENV * diff --git a/lib/linalg/ilazlc.f b/lib/linalg/ilazlc.f index 07dfc93e31..8af3430e61 100644 --- a/lib/linalg/ilazlc.f +++ b/lib/linalg/ilazlc.f @@ -71,17 +71,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERauxiliary * * ===================================================================== INTEGER FUNCTION ILAZLC( M, N, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER M, N, LDA diff --git a/lib/linalg/ilazlr.f b/lib/linalg/ilazlr.f index 4ca4ed1a44..e0134a6a35 100644 --- a/lib/linalg/ilazlr.f +++ b/lib/linalg/ilazlr.f @@ -71,17 +71,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERauxiliary * * ===================================================================== INTEGER FUNCTION ILAZLR( M, N, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER M, N, LDA diff --git a/lib/linalg/iparmq.f b/lib/linalg/iparmq.f index e576e0db01..54c05471ca 100644 --- a/lib/linalg/iparmq.f +++ b/lib/linalg/iparmq.f @@ -60,7 +60,7 @@ *> invest in an (expensive) multi-shift QR sweep. *> If the aggressive early deflation subroutine *> finds LD converged eigenvalues from an order -*> NW deflation window and LD.GT.(NW*NIBBLE)/100, +*> NW deflation window and LD > (NW*NIBBLE)/100, *> then the next QR sweep is skipped and early *> deflation is applied immediately to the *> remaining active diagonal block. Setting @@ -100,17 +100,21 @@ *> IPARMQ(ISPEC=16)=1 may be more efficient than *> IPARMQ(ISPEC=16)=2 despite the greater level of *> arithmetic work implied by the latter choice.) +*> +*> ISPEC=17: (ICOST) An estimate of the relative cost of flops +*> within the near-the-diagonal shift chase compared +*> to flops within the BLAS calls of a QZ sweep. *> \endverbatim *> *> \param[in] NAME *> \verbatim -*> NAME is character string +*> NAME is CHARACTER string *> Name of the calling subroutine *> \endverbatim *> *> \param[in] OPTS *> \verbatim -*> OPTS is character string +*> OPTS is CHARACTER string *> This is a concatenation of the string arguments to *> TTQRE. *> \endverbatim @@ -147,8 +151,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2017 -* *> \ingroup OTHERauxiliary * *> \par Further Details: @@ -184,8 +186,8 @@ *> This depends on ILO, IHI and NS, the *> number of simultaneous shifts returned *> by IPARMQ(ISPEC=15). The default for -*> (IHI-ILO+1).LE.500 is NS. The default -*> for (IHI-ILO+1).GT.500 is 3*NS/2. +*> (IHI-ILO+1) <= 500 is NS. The default +*> for (IHI-ILO+1) > 500 is 3*NS/2. *> *> IPARMQ(ISPEC=14) Nibble crossover point. Default: 14. *> @@ -217,15 +219,18 @@ *> IPARMQ(ISPEC=16) Select structured matrix multiply. *> (See ISPEC=16 above for details.) *> Default: 3. +*> +*> IPARMQ(ISPEC=17) Relative cost heuristic for blocksize selection. +*> Expressed as a percentage. +*> Default: 10. *> \endverbatim *> * ===================================================================== INTEGER FUNCTION IPARMQ( ISPEC, NAME, OPTS, N, ILO, IHI, LWORK ) * -* -- LAPACK auxiliary routine (version 3.7.1) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2017 * * .. Scalar Arguments .. INTEGER IHI, ILO, ISPEC, LWORK, N @@ -233,12 +238,12 @@ * * ================================================================ * .. Parameters .. - INTEGER INMIN, INWIN, INIBL, ISHFTS, IACC22 + INTEGER INMIN, INWIN, INIBL, ISHFTS, IACC22, ICOST PARAMETER ( INMIN = 12, INWIN = 13, INIBL = 14, - $ ISHFTS = 15, IACC22 = 16 ) - INTEGER NMIN, K22MIN, KACMIN, NIBBLE, KNWSWP + $ ISHFTS = 15, IACC22 = 16, ICOST = 17 ) + INTEGER NMIN, K22MIN, KACMIN, NIBBLE, KNWSWP, RCOST PARAMETER ( NMIN = 75, K22MIN = 14, KACMIN = 14, - $ NIBBLE = 14, KNWSWP = 500 ) + $ NIBBLE = 14, KNWSWP = 500, RCOST = 10 ) REAL TWO PARAMETER ( TWO = 2.0 ) * .. @@ -384,6 +389,12 @@ $ IPARMQ = 2 END IF * + ELSE IF( ISPEC.EQ.ICOST ) THEN +* +* === Relative cost of near-the-diagonal chase vs +* BLAS updates === +* + IPARMQ = RCOST ELSE * ===== invalid value of ispec ===== IPARMQ = -1 diff --git a/lib/linalg/lsame.f b/lib/linalg/lsame.f index d819478696..6aa4007065 100644 --- a/lib/linalg/lsame.f +++ b/lib/linalg/lsame.f @@ -46,17 +46,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup aux_blas * * ===================================================================== LOGICAL FUNCTION LSAME(CA,CB) * -* -- Reference BLAS level1 routine (version 3.1) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER CA,CB diff --git a/lib/linalg/xerbla.f b/lib/linalg/xerbla.f index 4a0350988c..6b141499ee 100644 --- a/lib/linalg/xerbla.f +++ b/lib/linalg/xerbla.f @@ -63,17 +63,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup OTHERauxiliary * * ===================================================================== SUBROUTINE XERBLA( SRNAME, INFO ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER*(*) SRNAME diff --git a/lib/linalg/zaxpy.f b/lib/linalg/zaxpy.f index b7b9ee69e4..35c0e4b892 100644 --- a/lib/linalg/zaxpy.f +++ b/lib/linalg/zaxpy.f @@ -72,8 +72,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level1 * *> \par Further Details: @@ -88,10 +86,9 @@ * ===================================================================== SUBROUTINE ZAXPY(N,ZA,ZX,INCX,ZY,INCY) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ZA @@ -136,4 +133,7 @@ END IF * RETURN +* +* End of ZAXPY +* END diff --git a/lib/linalg/zcopy.f b/lib/linalg/zcopy.f index 3777079730..1efcdb6b0f 100644 --- a/lib/linalg/zcopy.f +++ b/lib/linalg/zcopy.f @@ -65,8 +65,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level1 * *> \par Further Details: @@ -81,10 +79,9 @@ * ===================================================================== SUBROUTINE ZCOPY(N,ZX,INCX,ZY,INCY) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX,INCY,N @@ -122,4 +119,7 @@ END DO END IF RETURN +* +* End of ZCOPY +* END diff --git a/lib/linalg/zdotc.f b/lib/linalg/zdotc.f index e6cd11b21d..bcc29e2dad 100644 --- a/lib/linalg/zdotc.f +++ b/lib/linalg/zdotc.f @@ -39,7 +39,7 @@ *> *> \param[in] ZX *> \verbatim -*> ZX is REAL array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) +*> ZX is COMPLEX*16 array, dimension ( 1 + ( N - 1 )*abs( INCX ) ) *> \endverbatim *> *> \param[in] INCX @@ -50,7 +50,7 @@ *> *> \param[in] ZY *> \verbatim -*> ZY is REAL array, dimension ( 1 + ( N - 1 )*abs( INCY ) ) +*> ZY is COMPLEX*16 array, dimension ( 1 + ( N - 1 )*abs( INCY ) ) *> \endverbatim *> *> \param[in] INCY @@ -67,8 +67,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level1 * *> \par Further Details: @@ -83,10 +81,9 @@ * ===================================================================== COMPLEX*16 FUNCTION ZDOTC(N,ZX,INCX,ZY,INCY) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX,INCY,N @@ -131,4 +128,7 @@ END IF ZDOTC = ZTEMP RETURN +* +* End of ZDOTC +* END diff --git a/lib/linalg/zdscal.f b/lib/linalg/zdscal.f index 71d4da55be..b3546ba206 100644 --- a/lib/linalg/zdscal.f +++ b/lib/linalg/zdscal.f @@ -61,8 +61,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level1 * *> \par Further Details: @@ -78,10 +76,9 @@ * ===================================================================== SUBROUTINE ZDSCAL(N,DA,ZX,INCX) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION DA @@ -117,4 +114,7 @@ END DO END IF RETURN +* +* End of ZDSCAL +* END diff --git a/lib/linalg/zgemm.f b/lib/linalg/zgemm.f index c3ac7551d1..0b712f1b73 100644 --- a/lib/linalg/zgemm.f +++ b/lib/linalg/zgemm.f @@ -166,8 +166,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level3 * *> \par Further Details: @@ -187,10 +185,9 @@ * ===================================================================== SUBROUTINE ZGEMM(TRANSA,TRANSB,M,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC) * -* -- Reference BLAS level3 routine (version 3.7.0) -- +* -- Reference BLAS level3 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA,BETA @@ -215,7 +212,7 @@ * .. * .. Local Scalars .. COMPLEX*16 TEMP - INTEGER I,INFO,J,L,NCOLA,NROWA,NROWB + INTEGER I,INFO,J,L,NROWA,NROWB LOGICAL CONJA,CONJB,NOTA,NOTB * .. * .. Parameters .. @@ -228,8 +225,7 @@ * Set NOTA and NOTB as true if A and B respectively are not * conjugated or transposed, set CONJA and CONJB as true if A and * B respectively are to be transposed but not conjugated and set -* NROWA, NCOLA and NROWB as the number of rows and columns of A -* and the number of rows of B respectively. +* NROWA and NROWB as the number of rows of A and B respectively. * NOTA = LSAME(TRANSA,'N') NOTB = LSAME(TRANSB,'N') @@ -237,10 +233,8 @@ CONJB = LSAME(TRANSB,'C') IF (NOTA) THEN NROWA = M - NCOLA = K ELSE NROWA = K - NCOLA = M END IF IF (NOTB) THEN NROWB = K @@ -478,6 +472,6 @@ * RETURN * -* End of ZGEMM . +* End of ZGEMM * END diff --git a/lib/linalg/zgemv.f b/lib/linalg/zgemv.f index 7088d383f4..2664454b94 100644 --- a/lib/linalg/zgemv.f +++ b/lib/linalg/zgemv.f @@ -136,8 +136,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level2 * *> \par Further Details: @@ -158,10 +156,9 @@ * ===================================================================== SUBROUTINE ZGEMV(TRANS,M,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY) * -* -- Reference BLAS level2 routine (version 3.7.0) -- +* -- Reference BLAS level2 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA,BETA @@ -345,6 +342,6 @@ * RETURN * -* End of ZGEMV . +* End of ZGEMV * END diff --git a/lib/linalg/zgerc.f b/lib/linalg/zgerc.f index 058dccfc1c..2eb4349367 100644 --- a/lib/linalg/zgerc.f +++ b/lib/linalg/zgerc.f @@ -109,8 +109,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level2 * *> \par Further Details: @@ -130,10 +128,9 @@ * ===================================================================== SUBROUTINE ZGERC(M,N,ALPHA,X,INCX,Y,INCY,A,LDA) * -* -- Reference BLAS level2 routine (version 3.7.0) -- +* -- Reference BLAS level2 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA @@ -222,6 +219,6 @@ * RETURN * -* End of ZGERC . +* End of ZGERC * END diff --git a/lib/linalg/zheev.f b/lib/linalg/zheev.f index 3e87778740..59af34a742 100644 --- a/lib/linalg/zheev.f +++ b/lib/linalg/zheev.f @@ -132,18 +132,15 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16HEeigen * * ===================================================================== SUBROUTINE ZHEEV( JOBZ, UPLO, N, A, LDA, W, WORK, LWORK, RWORK, $ INFO ) * -* -- LAPACK driver routine (version 3.7.0) -- +* -- LAPACK driver routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER JOBZ, UPLO @@ -224,7 +221,7 @@ END IF * IF( N.EQ.1 ) THEN - W( 1 ) = A( 1, 1 ) + W( 1 ) = DBLE( A( 1, 1 ) ) WORK( 1 ) = 1 IF( WANTZ ) $ A( 1, 1 ) = CONE diff --git a/lib/linalg/zheevd.f b/lib/linalg/zheevd.f index 7f58c7f726..a6484eb032 100644 --- a/lib/linalg/zheevd.f +++ b/lib/linalg/zheevd.f @@ -284,7 +284,7 @@ LIWMIN = 1 END IF LOPT = MAX( LWMIN, N + - $ N*ILAENV( 1, 'ZHETRD', UPLO, N, -1, -1, -1 ) ) + $ ILAENV( 1, 'ZHETRD', UPLO, N, -1, -1, -1 ) ) LROPT = LRWMIN LIOPT = LIWMIN END IF diff --git a/lib/linalg/zhemv.f b/lib/linalg/zhemv.f index 3ea0753f40..dad68bf25b 100644 --- a/lib/linalg/zhemv.f +++ b/lib/linalg/zhemv.f @@ -132,8 +132,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level2 * *> \par Further Details: @@ -154,10 +152,9 @@ * ===================================================================== SUBROUTINE ZHEMV(UPLO,N,ALPHA,A,LDA,X,INCX,BETA,Y,INCY) * -* -- Reference BLAS level2 routine (version 3.7.0) -- +* -- Reference BLAS level2 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA,BETA @@ -332,6 +329,6 @@ * RETURN * -* End of ZHEMV . +* End of ZHEMV * END diff --git a/lib/linalg/zher2.f b/lib/linalg/zher2.f index e3a383189d..d1f2b57ec4 100644 --- a/lib/linalg/zher2.f +++ b/lib/linalg/zher2.f @@ -129,8 +129,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level2 * *> \par Further Details: @@ -150,10 +148,9 @@ * ===================================================================== SUBROUTINE ZHER2(UPLO,N,ALPHA,X,INCX,Y,INCY,A,LDA) * -* -- Reference BLAS level2 routine (version 3.7.0) -- +* -- Reference BLAS level2 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA @@ -312,6 +309,6 @@ * RETURN * -* End of ZHER2 . +* End of ZHER2 * END diff --git a/lib/linalg/zher2k.f b/lib/linalg/zher2k.f index 474c65e575..5c75083cd5 100644 --- a/lib/linalg/zher2k.f +++ b/lib/linalg/zher2k.f @@ -174,8 +174,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level3 * *> \par Further Details: @@ -198,10 +196,9 @@ * ===================================================================== SUBROUTINE ZHER2K(UPLO,TRANS,N,K,ALPHA,A,LDA,B,LDB,BETA,C,LDC) * -* -- Reference BLAS level3 routine (version 3.7.0) -- +* -- Reference BLAS level3 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA @@ -438,6 +435,6 @@ * RETURN * -* End of ZHER2K. +* End of ZHER2K * END diff --git a/lib/linalg/zhetd2.f b/lib/linalg/zhetd2.f index 6c5b8aae3d..a6d900b7c7 100644 --- a/lib/linalg/zhetd2.f +++ b/lib/linalg/zhetd2.f @@ -122,8 +122,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16HEcomputational * *> \par Further Details: @@ -175,10 +173,9 @@ * ===================================================================== SUBROUTINE ZHETD2( UPLO, N, A, LDA, D, E, TAU, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO @@ -248,7 +245,7 @@ * ALPHA = A( I, I+1 ) CALL ZLARFG( I, ALPHA, A( 1, I+1 ), 1, TAUI ) - E( I ) = ALPHA + E( I ) = DBLE( ALPHA ) * IF( TAUI.NE.ZERO ) THEN * @@ -276,10 +273,10 @@ A( I, I ) = DBLE( A( I, I ) ) END IF A( I, I+1 ) = E( I ) - D( I+1 ) = A( I+1, I+1 ) + D( I+1 ) = DBLE( A( I+1, I+1 ) ) TAU( I ) = TAUI 10 CONTINUE - D( 1 ) = A( 1, 1 ) + D( 1 ) = DBLE( A( 1, 1 ) ) ELSE * * Reduce the lower triangle of A @@ -292,7 +289,7 @@ * ALPHA = A( I+1, I ) CALL ZLARFG( N-I, ALPHA, A( MIN( I+2, N ), I ), 1, TAUI ) - E( I ) = ALPHA + E( I ) = DBLE( ALPHA ) * IF( TAUI.NE.ZERO ) THEN * @@ -321,10 +318,10 @@ A( I+1, I+1 ) = DBLE( A( I+1, I+1 ) ) END IF A( I+1, I ) = E( I ) - D( I ) = A( I, I ) + D( I ) = DBLE( A( I, I ) ) TAU( I ) = TAUI 20 CONTINUE - D( N ) = A( N, N ) + D( N ) = DBLE( A( N, N ) ) END IF * RETURN diff --git a/lib/linalg/zhetrd.f b/lib/linalg/zhetrd.f index 51c9fc2ec9..5b7d6546cc 100644 --- a/lib/linalg/zhetrd.f +++ b/lib/linalg/zhetrd.f @@ -139,8 +139,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16HEcomputational * *> \par Further Details: @@ -192,10 +190,9 @@ * ===================================================================== SUBROUTINE ZHETRD( UPLO, N, A, LDA, D, E, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO @@ -328,7 +325,7 @@ * DO 10 J = I, I + NB - 1 A( J-1, J ) = E( J-1 ) - D( J ) = A( J, J ) + D( J ) = DBLE( A( J, J ) ) 10 CONTINUE 20 CONTINUE * @@ -360,7 +357,7 @@ * DO 30 J = I, I + NB - 1 A( J+1, J ) = E( J ) - D( J ) = A( J, J ) + D( J ) = DBLE( A( J, J ) ) 30 CONTINUE 40 CONTINUE * diff --git a/lib/linalg/zhpr.f b/lib/linalg/zhpr.f index af82dfbd8c..2ba5774a21 100644 --- a/lib/linalg/zhpr.f +++ b/lib/linalg/zhpr.f @@ -109,8 +109,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level2 * *> \par Further Details: @@ -130,10 +128,9 @@ * ===================================================================== SUBROUTINE ZHPR(UPLO,N,ALPHA,X,INCX,AP) * -* -- Reference BLAS level2 routine (version 3.7.0) -- +* -- Reference BLAS level2 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. DOUBLE PRECISION ALPHA @@ -274,6 +271,6 @@ * RETURN * -* End of ZHPR . +* End of ZHPR * END diff --git a/lib/linalg/zlacgv.f b/lib/linalg/zlacgv.f index 1e3ca6e73f..dc935e08f4 100644 --- a/lib/linalg/zlacgv.f +++ b/lib/linalg/zlacgv.f @@ -67,17 +67,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERauxiliary * * ===================================================================== SUBROUTINE ZLACGV( N, X, INCX ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX, N diff --git a/lib/linalg/zladiv.f b/lib/linalg/zladiv.f index 0bf6ea87d5..ae111d73d6 100644 --- a/lib/linalg/zladiv.f +++ b/lib/linalg/zladiv.f @@ -57,17 +57,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERauxiliary * * ===================================================================== COMPLEX*16 FUNCTION ZLADIV( X, Y ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. COMPLEX*16 X, Y diff --git a/lib/linalg/zlanhe.f b/lib/linalg/zlanhe.f index 7c7f7f3be4..bbb4843ffd 100644 --- a/lib/linalg/zlanhe.f +++ b/lib/linalg/zlanhe.f @@ -117,17 +117,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16HEauxiliary * * ===================================================================== DOUBLE PRECISION FUNCTION ZLANHE( NORM, UPLO, N, A, LDA, WORK ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER NORM, UPLO diff --git a/lib/linalg/zlarf.f b/lib/linalg/zlarf.f index f1be80d37b..e555d18ecd 100644 --- a/lib/linalg/zlarf.f +++ b/lib/linalg/zlarf.f @@ -121,17 +121,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERauxiliary * * ===================================================================== SUBROUTINE ZLARF( SIDE, M, N, V, INCV, TAU, C, LDC, WORK ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER SIDE diff --git a/lib/linalg/zlarfb.f b/lib/linalg/zlarfb.f index b4a2b4d1a0..c5f424db31 100644 --- a/lib/linalg/zlarfb.f +++ b/lib/linalg/zlarfb.f @@ -92,6 +92,8 @@ *> K is INTEGER *> The order of the matrix T (= the number of elementary *> reflectors whose product defines the block reflector). +*> If SIDE = 'L', M >= K >= 0; +*> if SIDE = 'R', N >= K >= 0. *> \endverbatim *> *> \param[in] V @@ -159,8 +161,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2013 -* *> \ingroup complex16OTHERauxiliary * *> \par Further Details: @@ -195,10 +195,9 @@ SUBROUTINE ZLARFB( SIDE, TRANS, DIRECT, STOREV, M, N, K, V, LDV, $ T, LDT, C, LDC, WORK, LDWORK ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2013 * * .. Scalar Arguments .. CHARACTER DIRECT, SIDE, STOREV, TRANS diff --git a/lib/linalg/zlarfg.f b/lib/linalg/zlarfg.f index f8a795d547..d69796cadc 100644 --- a/lib/linalg/zlarfg.f +++ b/lib/linalg/zlarfg.f @@ -99,17 +99,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERauxiliary * * ===================================================================== SUBROUTINE ZLARFG( N, ALPHA, X, INCX, TAU ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX, N @@ -175,7 +172,7 @@ BETA = BETA*RSAFMN ALPHI = ALPHI*RSAFMN ALPHR = ALPHR*RSAFMN - IF( ABS( BETA ).LT.SAFMIN ) + IF( (ABS( BETA ).LT.SAFMIN) .AND. (KNT .LT. 20) ) $ GO TO 10 * * New BETA is at most 1, at least SAFMIN diff --git a/lib/linalg/zlarft.f b/lib/linalg/zlarft.f index 78ad2f1481..5ad0996fab 100644 --- a/lib/linalg/zlarft.f +++ b/lib/linalg/zlarft.f @@ -130,8 +130,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2016 -* *> \ingroup complex16OTHERauxiliary * *> \par Further Details: @@ -163,10 +161,9 @@ * ===================================================================== SUBROUTINE ZLARFT( DIRECT, STOREV, N, K, V, LDV, TAU, T, LDT ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2016 * * .. Scalar Arguments .. CHARACTER DIRECT, STOREV diff --git a/lib/linalg/zlascl.f b/lib/linalg/zlascl.f index c53c6f5ad7..3d53f5ae60 100644 --- a/lib/linalg/zlascl.f +++ b/lib/linalg/zlascl.f @@ -136,17 +136,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date June 2016 -* *> \ingroup complex16OTHERauxiliary * * ===================================================================== SUBROUTINE ZLASCL( TYPE, KL, KU, CFROM, CTO, M, N, A, LDA, INFO ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* June 2016 * * .. Scalar Arguments .. CHARACTER TYPE diff --git a/lib/linalg/zlaset.f b/lib/linalg/zlaset.f index 796678217b..00f5f595fc 100644 --- a/lib/linalg/zlaset.f +++ b/lib/linalg/zlaset.f @@ -99,17 +99,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERauxiliary * * ===================================================================== SUBROUTINE ZLASET( UPLO, M, N, ALPHA, BETA, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO diff --git a/lib/linalg/zlasr.f b/lib/linalg/zlasr.f index 69891ba522..07c91329c4 100644 --- a/lib/linalg/zlasr.f +++ b/lib/linalg/zlasr.f @@ -193,17 +193,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERauxiliary * * ===================================================================== SUBROUTINE ZLASR( SIDE, PIVOT, DIRECT, M, N, C, S, A, LDA ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER DIRECT, PIVOT, SIDE diff --git a/lib/linalg/zlatrd.f b/lib/linalg/zlatrd.f index ccc040993f..ee2a484723 100644 --- a/lib/linalg/zlatrd.f +++ b/lib/linalg/zlatrd.f @@ -140,8 +140,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERauxiliary * *> \par Further Details: @@ -199,10 +197,9 @@ * ===================================================================== SUBROUTINE ZLATRD( UPLO, N, NB, A, LDA, E, TAU, W, LDW ) * -* -- LAPACK auxiliary routine (version 3.7.0) -- +* -- LAPACK auxiliary routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO @@ -271,7 +268,7 @@ * ALPHA = A( I-1, I ) CALL ZLARFG( I-1, ALPHA, A( 1, I ), 1, TAU( I-1 ) ) - E( I-1 ) = ALPHA + E( I-1 ) = DBLE( ALPHA ) A( I-1, I ) = ONE * * Compute W(1:i-1,i) @@ -325,7 +322,7 @@ ALPHA = A( I+1, I ) CALL ZLARFG( N-I, ALPHA, A( MIN( I+2, N ), I ), 1, $ TAU( I ) ) - E( I ) = ALPHA + E( I ) = DBLE( ALPHA ) A( I+1, I ) = ONE * * Compute W(i+1:n,i) diff --git a/lib/linalg/zpptrf.f b/lib/linalg/zpptrf.f index 6e50b46828..a34d639131 100644 --- a/lib/linalg/zpptrf.f +++ b/lib/linalg/zpptrf.f @@ -92,8 +92,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERcomputational * *> \par Further Details: @@ -119,10 +117,9 @@ * ===================================================================== SUBROUTINE ZPPTRF( UPLO, N, AP, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO @@ -192,8 +189,8 @@ * * Compute U(J,J) and test for non-positive-definiteness. * - AJJ = DBLE( AP( JJ ) ) - ZDOTC( J-1, AP( JC ), 1, AP( JC ), - $ 1 ) + AJJ = DBLE( AP( JJ ) ) - DBLE( ZDOTC( J-1, + $ AP( JC ), 1, AP( JC ), 1 ) ) IF( AJJ.LE.ZERO ) THEN AP( JJ ) = AJJ GO TO 30 diff --git a/lib/linalg/zpptri.f b/lib/linalg/zpptri.f index cde2f6dc72..a74466eb80 100644 --- a/lib/linalg/zpptri.f +++ b/lib/linalg/zpptri.f @@ -86,17 +86,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZPPTRI( UPLO, N, AP, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO @@ -164,7 +161,7 @@ JJ = JJ + J IF( J.GT.1 ) $ CALL ZHPR( 'Upper', J-1, ONE, AP( JC ), 1, AP ) - AJJ = AP( JJ ) + AJJ = DBLE( AP( JJ ) ) CALL ZDSCAL( J, AJJ, AP( JC ), 1 ) 10 CONTINUE * diff --git a/lib/linalg/zscal.f b/lib/linalg/zscal.f index 9f6d4b1d39..8085f5a399 100644 --- a/lib/linalg/zscal.f +++ b/lib/linalg/zscal.f @@ -61,8 +61,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level1 * *> \par Further Details: @@ -78,10 +76,9 @@ * ===================================================================== SUBROUTINE ZSCAL(N,ZA,ZX,INCX) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ZA @@ -114,4 +111,7 @@ END DO END IF RETURN +* +* End of ZSCAL +* END diff --git a/lib/linalg/zsteqr.f b/lib/linalg/zsteqr.f index ac47890685..47f4004e8d 100644 --- a/lib/linalg/zsteqr.f +++ b/lib/linalg/zsteqr.f @@ -125,17 +125,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZSTEQR( COMPZ, N, D, E, Z, LDZ, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER COMPZ diff --git a/lib/linalg/zswap.f b/lib/linalg/zswap.f index 6768d5e6e0..93f8fc52d0 100644 --- a/lib/linalg/zswap.f +++ b/lib/linalg/zswap.f @@ -65,8 +65,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level1 * *> \par Further Details: @@ -81,10 +79,9 @@ * ===================================================================== SUBROUTINE ZSWAP(N,ZX,INCX,ZY,INCY) * -* -- Reference BLAS level1 routine (version 3.7.0) -- +* -- Reference BLAS level1 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX,INCY,N @@ -126,4 +123,7 @@ END DO END IF RETURN +* +* End of ZSWAP +* END diff --git a/lib/linalg/ztpmv.f b/lib/linalg/ztpmv.f index 65aa2a0abc..363fd5a2ac 100644 --- a/lib/linalg/ztpmv.f +++ b/lib/linalg/ztpmv.f @@ -120,8 +120,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level2 * *> \par Further Details: @@ -142,10 +140,9 @@ * ===================================================================== SUBROUTINE ZTPMV(UPLO,TRANS,DIAG,N,AP,X,INCX) * -* -- Reference BLAS level2 routine (version 3.7.0) -- +* -- Reference BLAS level2 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX,N @@ -383,6 +380,6 @@ * RETURN * -* End of ZTPMV . +* End of ZTPMV * END diff --git a/lib/linalg/ztpsv.f b/lib/linalg/ztpsv.f index 538888424a..c6f24d0b27 100644 --- a/lib/linalg/ztpsv.f +++ b/lib/linalg/ztpsv.f @@ -123,8 +123,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level2 * *> \par Further Details: @@ -144,10 +142,9 @@ * ===================================================================== SUBROUTINE ZTPSV(UPLO,TRANS,DIAG,N,AP,X,INCX) * -* -- Reference BLAS level2 routine (version 3.7.0) -- +* -- Reference BLAS level2 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX,N @@ -385,6 +382,6 @@ * RETURN * -* End of ZTPSV . +* End of ZTPSV * END diff --git a/lib/linalg/ztptri.f b/lib/linalg/ztptri.f index 35388194c3..31284ad637 100644 --- a/lib/linalg/ztptri.f +++ b/lib/linalg/ztptri.f @@ -91,8 +91,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERcomputational * *> \par Further Details: @@ -117,10 +115,9 @@ * ===================================================================== SUBROUTINE ZTPTRI( UPLO, DIAG, N, AP, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER DIAG, UPLO diff --git a/lib/linalg/ztrmm.f b/lib/linalg/ztrmm.f index 0f445f52a7..c59c367cee 100644 --- a/lib/linalg/ztrmm.f +++ b/lib/linalg/ztrmm.f @@ -156,8 +156,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level3 * *> \par Further Details: @@ -177,10 +175,9 @@ * ===================================================================== SUBROUTINE ZTRMM(SIDE,UPLO,TRANSA,DIAG,M,N,ALPHA,A,LDA,B,LDB) * -* -- Reference BLAS level3 routine (version 3.7.0) -- +* -- Reference BLAS level3 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. COMPLEX*16 ALPHA @@ -447,6 +444,6 @@ * RETURN * -* End of ZTRMM . +* End of ZTRMM * END diff --git a/lib/linalg/ztrmv.f b/lib/linalg/ztrmv.f index 52d1ae6799..e8314facb7 100644 --- a/lib/linalg/ztrmv.f +++ b/lib/linalg/ztrmv.f @@ -125,8 +125,6 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16_blas_level2 * *> \par Further Details: @@ -147,10 +145,9 @@ * ===================================================================== SUBROUTINE ZTRMV(UPLO,TRANS,DIAG,N,A,LDA,X,INCX) * -* -- Reference BLAS level2 routine (version 3.7.0) -- +* -- Reference BLAS level2 routine -- * -- Reference BLAS is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INCX,LDA,N @@ -368,6 +365,6 @@ * RETURN * -* End of ZTRMV . +* End of ZTRMV * END diff --git a/lib/linalg/zung2l.f b/lib/linalg/zung2l.f index 1a48c4d6bc..add5cb946b 100644 --- a/lib/linalg/zung2l.f +++ b/lib/linalg/zung2l.f @@ -107,17 +107,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZUNG2L( M, N, K, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, M, N diff --git a/lib/linalg/zung2r.f b/lib/linalg/zung2r.f index 4a3fed0f0d..2823b7ebdd 100644 --- a/lib/linalg/zung2r.f +++ b/lib/linalg/zung2r.f @@ -107,17 +107,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZUNG2R( M, N, K, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, M, N diff --git a/lib/linalg/zungl2.f b/lib/linalg/zungl2.f index 0774cc4405..e7a0b59603 100644 --- a/lib/linalg/zungl2.f +++ b/lib/linalg/zungl2.f @@ -106,17 +106,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZUNGL2( M, N, K, A, LDA, TAU, WORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, M, N diff --git a/lib/linalg/zungql.f b/lib/linalg/zungql.f index c63a47db56..1804ca65ff 100644 --- a/lib/linalg/zungql.f +++ b/lib/linalg/zungql.f @@ -121,17 +121,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZUNGQL( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, LWORK, M, N diff --git a/lib/linalg/zungqr.f b/lib/linalg/zungqr.f index 5f95b64e88..b3f2c4507f 100644 --- a/lib/linalg/zungqr.f +++ b/lib/linalg/zungqr.f @@ -121,17 +121,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZUNGQR( M, N, K, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. INTEGER INFO, K, LDA, LWORK, M, N diff --git a/lib/linalg/zungtr.f b/lib/linalg/zungtr.f index 728854332f..01e100a8cd 100644 --- a/lib/linalg/zungtr.f +++ b/lib/linalg/zungtr.f @@ -116,17 +116,14 @@ *> \author Univ. of Colorado Denver *> \author NAG Ltd. * -*> \date December 2016 -* *> \ingroup complex16OTHERcomputational * * ===================================================================== SUBROUTINE ZUNGTR( UPLO, N, A, LDA, TAU, WORK, LWORK, INFO ) * -* -- LAPACK computational routine (version 3.7.0) -- +* -- LAPACK computational routine -- * -- LAPACK is a software package provided by Univ. of Tennessee, -- * -- Univ. of California Berkeley, Univ. of Colorado Denver and NAG Ltd..-- -* December 2016 * * .. Scalar Arguments .. CHARACTER UPLO From 7901a317c0d6f90bd8f3130c53789bd6f5c6b0ee Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 20 Jul 2022 16:01:53 -0400 Subject: [PATCH 62/72] Initial version of an LAMMPS older version code update guide --- doc/src/Developer.rst | 1 + doc/src/Developer_updating.rst | 304 ++++++++++++++++++++ doc/utils/sphinx-config/false_positives.txt | 4 + 3 files changed, 309 insertions(+) create mode 100644 doc/src/Developer_updating.rst diff --git a/doc/src/Developer.rst b/doc/src/Developer.rst index bb10fcffd7..dc3fac94ce 100644 --- a/doc/src/Developer.rst +++ b/doc/src/Developer.rst @@ -17,6 +17,7 @@ of time and requests from the LAMMPS user community. Developer_flow Developer_write Developer_notes + Developer_updating Developer_plugins Developer_unittest Classes diff --git a/doc/src/Developer_updating.rst b/doc/src/Developer_updating.rst new file mode 100644 index 0000000000..13e1772589 --- /dev/null +++ b/doc/src/Developer_updating.rst @@ -0,0 +1,304 @@ +Notes for updating code written for older LAMMPS versions +--------------------------------------------------------- + +This section documents how C++ source files that were written for an +older version of LAMMPS need to be updated to be compatible with the +current and future version(s). Due to the active development of LAMMPS +it is likely to always be incomplete. Please contact developer@lammps.org +in case you run across an issue that is not (yet) listed here. Please +also review the latest information about the LAMMPS :doc:`programming style +conventions `. + +Available topics in chronological order are: + +- `Rename of pack/unpack_comm() to pack/unpack_forward_comm()`_ +- `Use ev_init() to initialize variables derived from eflag and vflag`_ +- `Use utils::numeric() functions instead of force->numeric()`_ +- `Use utils::open_potential() function to open potential files`_ +- `Simplify customized error messages`_ +- `Use of "override" instead of "virtual"`_ +- `Simplified and more compact neighbor list requests`_ + +---- + +Rename of pack/unpack_comm() to pack/unpack_forward_comm() +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. versionchanged:: 8Aug2014 + +In this change set the functions to pack data into communication buffers +and to unpack data from communication buffers for :doc:`forward +communications ` were renamed from ``pack_comm()`` +and ``unpack_comm()`` to ``pack_forward_comm()`` and +``unpack_forward_comm()``, respectively. Also the meaning of the return +value of these functions was changed: rather than returning the number +of items per atom stored in the buffer, now the total number of items +added (or unpacked) needs to be returned. Here is an example from the +`PairEAM` class. Of course the member function declaration in corresponding +header file needs to be updated accordingly. + +Old: + +.. code-block:: C++ + + int PairEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) + { + int m = 0; + for (int i = 0; i < n; i++) { + int j = list[i]; + buf[m++] = fp[j]; + } + return 1; + } + +New: + +.. code-block:: C++ + + int PairEAM::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc) + { + int m = 0; + for (int i = 0; i < n; i++) { + int j = list[i]; + buf[m++] = fp[j]; + } + return m; + } + +.. note:: + + Because the various "pack" and "unpack" functions are defined in the + respective base classes as dummy functions doing nothing, and because + of the the name mismatch the custom versions in the derived class + will no longer be called, there will be no compilation error when + this change is not applied. Only calculations will suddenly produce + incorrect results because the required forward communication calls + will cease to function correctly. + +Use ev_init() to initialize variables derived from eflag and vflag +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. versionchanged:: 29Mar2019 + +There are several variables that need to be initialized based on +the values of the "eflag" and "vflag" variables and since sometimes +there are new bits added and new variables need to be set to 1 or 0. +To make this consistent, across all styles, there is now an inline +function ``ev_init(eflag, vflag)`` that makes those settings +consistently and calls either ``ev_setup()`` or ``ev_unset()``. +Example from a pair style: + +Old: + +.. code-block:: C++ + + if (eflag || vflag) ev_setup(eflag, vflag); + else evflag = vflag_fdotr = eflag_global = eflag_atom = 0; + +New: + +.. code-block:: C++ + + ev_init(eflag, vflag); + +Not applying this change will not cause a compilation error, but +can lead to inconsistent behavior and incorrect tallying of +energy or virial. + +Use utils::numeric() functions instead of force->numeric() +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. versionchanged:: 18Sep2020 + +The "numeric()" conversion functions (including "inumeric()", +"bnumeric()", and "tnumeric()") have been moved from the Force class to +the utils namespace. Also they take an additional argument that selects +whether the ``Error::all()`` or ``Error::one()`` function should be +called in case of an error. The former should be used when *all* MPI +processes call the conversion function and the latter *must* be used +when they are called from only one or a subset of the MPI processes. + +Old: + +.. code-block:: C++ + + val = force->numeric(FLERR, arg[1]); + num = force->inumeric(FLERR, arg[2]); + +New: + +.. code-block:: C++ + + val = utils::numeric(FLERR, true, arg[1], lmp); + num = utils::inumeric(FLERR, false, arg[2], lmp); + +.. seealso:: + + :cpp:func:`utils::numeric() `, + :cpp:func:`utils::inumeric() `, + :cpp:func:`utils::bnumeric() `, + :cpp:func:`utils::tnumeric() ` + +Use utils::open_potential() function to open potential files +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. versionchanged:: 18Sep2020 + +The :cpp:func:`utils::open_potential() +` function must be used to replace +calls to ``force->open_potential()`` and should be used to replace +``fopen()`` for opening potential files for reading. The custom +function does three additional steps compared to ``fopen()``: 1) it will +try to parse the ``UNITS:`` and ``DATE:`` metadata will stop with an +error on a units mismatch and will print the date info, if present, in +the log file; 2) for pair styles that support it, it will set up +possible automatic unit conversions based on the embedded unit +information and LAMMPS' current units setting; 3) it will not only try +to open a potential file at the given path, but will also search in the +folders listed in the ``LAMMPS_POTENTIALS`` environment variable. This +allows to keep potential files in a common location instead of having to +copy them around for simulations. + +Old: + +.. code-block:: C++ + + fp = force->open_potential(filename); + fp = fopen(filename, "r"); + +New: + +.. code-block:: C++ + + fp = utils::open_potential(filename, lmp); + +Simplify customized error messages +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. versionchanged:: 14May2021 + +Aided by features of the bundled {fmt} library, error messages now +can have a variable number of arguments and the string will be interpreted +as a {fmt} style format string so that custom error messages can be +easily customized without having to use temporary buffers and ``sprintf()``. +Example: + +Old: + +.. code-block:: C++ + + if (fptr == NULL) { + char str[128]; + sprintf(str,"Cannot open AEAM potential file %s",filename); + error->one(FLERR,str); + } + +New: + +.. code-block:: C++ + + if (fptr == nullptr) + error->one(FLERR, "Cannot open AEAM potential file {}: {}", filename, utils::getsyserror()); + +Use of "override" instead of "virtual" +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. versionchanged:: 17Feb2022 + +Since LAMMPS requires C++11 we switched to use the "override" keyword +instead of "virtual" to indicate polymorphism in derived classes. This +allows the C++ compiler to better detect inconsistencies when an +override is intended or not. Please note that "override" has to be +added to **all** polymorph functions in derived classes and "virtual" +*only* to the function in the base class (or the destructor). Here is +an example from the ``FixWallReflect`` class: + +Old: + +.. code-block:: C++ + + FixWallReflect(class LAMMPS *, int, char **); + virtual ~FixWallReflect(); + int setmask(); + void init(); + void post_integrate(); + +New: + +.. code-block:: C++ + + FixWallReflect(class LAMMPS *, int, char **); + ~FixWallReflect() override; + int setmask() override; + void init() override; + void post_integrate() override; + +This change set will neither cause a compilation failure, nor will it +change functionality, but if you plan to submit the updated code for +inclusion into the LAMMPS distribution, it will be requested for achieve +a consistent :doc:`programming style `. + +Simplified function names for forward and reverse communication +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. versionchanged:: 24Mar2022 + +Rather then using the function name to distinguish between the different +forward and reverse communication functions for styles, LAMMPS now uses +the type of the "this" pointer argument. + +Old: + +.. code-block:: C++ + + comm->forward_comm_pair(this); + comm->forward_comm_fix(this); + comm->forward_comm_compute(this); + comm->forward_comm_dump(this); + comm->reverse_comm_pair(this); + comm->reverse_comm_fix(this); + comm->reverse_comm_compute(this); + comm->reverse_comm_dump(this); + +New: + +.. code-block:: C++ + + comm->forward_comm(this); + comm->reverse_comm(this); + +This change is required or else the code will not compile. + +Simplified and more compact neighbor list requests +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +.. versionchanged:: 24Mar2022 + +This change set reduces the amount of code required to request a +neighbor list. It enforces consistency and no longer requires to change +internal data of the request. More information on neighbor list +requests can be :doc:`found here `. Example from the +``ComputeRDF`` class: + +Old: + +.. code-block:: C++ + + int irequest = neighbor->request(this,instance_me); + neighbor->requests[irequest]->pair = 0; + neighbor->requests[irequest]->compute = 1; + neighbor->requests[irequest]->occasional = 1; + if (cutflag) { + neighbor->requests[irequest]->cut = 1; + neighbor->requests[irequest]->cutoff = mycutneigh; + } + +New: + +.. code-block:: C++ + + auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL); + if (cutflag) req->set_cutoff(mycutneigh); + +Public access to the ``NeighRequest`` class data members has been +removed so this update is *required* to avoid compilation failure. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 9f6edbec4c..9006f99e50 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -291,6 +291,7 @@ blocksize blueviolet bn bni +bnumeric bo Bochkarev Bochum @@ -1482,6 +1483,7 @@ intra intralayer intramolecular ints +inumeric inv invariants inversed @@ -2706,6 +2708,7 @@ polydispersity polyelectrolyte polyhedra Polym +polymorph polymorphism Ponder popen @@ -3463,6 +3466,7 @@ tmin Tmin tmp tN +tnumeric Tobias Toennies Tohoku From cdf600b8cd81354d859b38e91165bf1c5401c795 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 22 Jul 2022 14:34:09 -0400 Subject: [PATCH 63/72] update description --- doc/src/Developer_updating.rst | 36 ++++++++++++++++++++++++++-------- 1 file changed, 28 insertions(+), 8 deletions(-) diff --git a/doc/src/Developer_updating.rst b/doc/src/Developer_updating.rst index 13e1772589..f33632d91a 100644 --- a/doc/src/Developer_updating.rst +++ b/doc/src/Developer_updating.rst @@ -1,16 +1,21 @@ Notes for updating code written for older LAMMPS versions --------------------------------------------------------- -This section documents how C++ source files that were written for an -older version of LAMMPS need to be updated to be compatible with the -current and future version(s). Due to the active development of LAMMPS -it is likely to always be incomplete. Please contact developer@lammps.org -in case you run across an issue that is not (yet) listed here. Please -also review the latest information about the LAMMPS :doc:`programming style -conventions `. +This section documents how C++ source files that are available *outside +of the LAMMPS source distribution* (e.g. in external USER packages or as +source files provided as a supplement to a publication) that are written +for an older version of LAMMPS and thus need to be updated to be +compatible with the current version of LAMMPS. Due to the active +development of LAMMPS it is likely to always be incomplete. Please +contact developer@lammps.org in case you run across an issue that is not +(yet) listed here. Please also review the latest information about the +LAMMPS :doc:`programming style conventions `, especially +if you are considering to submit the updated version for inclusion into +the LAMMPS distribution. -Available topics in chronological order are: +Available topics in mostly chronological order are: +- `Setting flags in the constructor`_ - `Rename of pack/unpack_comm() to pack/unpack_forward_comm()`_ - `Use ev_init() to initialize variables derived from eflag and vflag`_ - `Use utils::numeric() functions instead of force->numeric()`_ @@ -21,6 +26,21 @@ Available topics in chronological order are: ---- +Setting flags in the constructor +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ + +As LAMMPS gains additional functionality, new flags may need to be set +in the constructor or a class to signal compatibility with such features. +Most of the time the defaults are chosen conservatively, but sometimes +the conservative choice is the uncommon choice, and then those settings +need to be made when updating code. + +Pair styles: + + - ``manybody_flag``: set to 1 if your pair style is not pair-wise additive + - ``restartinfo``: set to 0 if your pair style does not store data in restart files + + Rename of pack/unpack_comm() to pack/unpack_forward_comm() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From b2cdc4091908478a3054b55d48d3e2516ccdf6ef Mon Sep 17 00:00:00 2001 From: Paulius Velesko Date: Tue, 26 Jul 2022 16:00:43 +0000 Subject: [PATCH 64/72] Enable CHIP-SPV support --- cmake/Modules/Packages/GPU.cmake | 14 ++++++++++++-- lib/gpu/lal_pre_cuda_hip.h | 12 ++++++------ 2 files changed, 18 insertions(+), 8 deletions(-) diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index 75569aa55d..36409378be 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -233,7 +233,7 @@ elseif(GPU_API STREQUAL "OPENCL") elseif(GPU_API STREQUAL "HIP") if(NOT DEFINED HIP_PATH) if(NOT DEFINED ENV{HIP_PATH}) - set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to HIP installation") + message(FATAL_ERROR "GPU_API=HIP requires HIP_PATH to be defined") else() set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation") endif() @@ -261,6 +261,8 @@ elseif(GPU_API STREQUAL "HIP") if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd") set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture") + elseif(HIP_PLATFORM STREQUAL "spirv") + set(HIP_ARCH "spirv" CACHE STRING "HIP target architecture") elseif(HIP_PLATFORM STREQUAL "nvcc") find_package(CUDA REQUIRED) set(HIP_ARCH "sm_50" CACHE STRING "HIP primary CUDA architecture (e.g. sm_60)") @@ -321,7 +323,15 @@ elseif(GPU_API STREQUAL "HIP") set(CUBIN_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin") set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h") - if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd") + if(HIP_PLATFORM STREQUAL "spirv") + configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY) + + add_custom_command(OUTPUT ${CUBIN_FILE} + VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} -c -O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE} + DEPENDS ${CU_CPP_FILE} + COMMENT "Gerating ${CU_NAME}.cubin") + + elseif(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd") configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY) if(HIP_COMPILER STREQUAL "clang") diff --git a/lib/gpu/lal_pre_cuda_hip.h b/lib/gpu/lal_pre_cuda_hip.h index 47a005b998..f6ab1b5b6b 100644 --- a/lib/gpu/lal_pre_cuda_hip.h +++ b/lib/gpu/lal_pre_cuda_hip.h @@ -30,7 +30,7 @@ // ------------------------------------------------------------------------- -#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) +#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) || defined(__HIP_PLATFORM_SPIRV__) #define CONFIG_ID 303 #define SIMD_SIZE 64 #else @@ -112,7 +112,7 @@ // KERNEL MACROS - TEXTURES // ------------------------------------------------------------------------- -#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) +#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) || defined(__HIP_PLATFORM_SPIRV__) #define _texture(name, type) __device__ type* name #define _texture_2d(name, type) __device__ type* name #else @@ -135,8 +135,8 @@ ans=__hiloint2double(qt.y, qt.x); \ } #else - #define fetch4(ans,i,pos_tex) ans=tex1Dfetch(pos_tex, i); - #define fetch(ans,i,q_tex) ans=tex1Dfetch(q_tex,i); + #define fetch4(ans,i,pos_tex) tex1Dfetch(&ans, pos_tex, i); + #define fetch(ans,i,q_tex) tex1Dfetch(&ans, q_tex,i); #endif #else #define fetch4(ans,i,x) ans=x[i] @@ -152,7 +152,7 @@ #define mu_tex mu_ #endif -#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) +#if defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) || defined(__HIP_PLATFORM_SPIRV__) #undef fetch4 #undef fetch @@ -209,7 +209,7 @@ #endif #endif -#if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) +#if defined(CUDA_PRE_NINE) || defined(__HIP_PLATFORM_HCC__) || defined(__HIP_PLATFORM_AMD__) || defined(__HIP_PLATFORM_SPIRV__) #ifdef _SINGLE_SINGLE #define shfl_down __shfl_down From e973a4b31c74f3fab26010e324a863d8b02a6bd1 Mon Sep 17 00:00:00 2001 From: Paulius Velesko Date: Tue, 26 Jul 2022 16:14:43 +0000 Subject: [PATCH 65/72] workaround for CHIP-SPV different textrure func --- .gitignore | 1 - lib/gpu/lal_pre_cuda_hip.h | 7 +++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.gitignore b/.gitignore index 0cc211ab09..bd2d0ea705 100644 --- a/.gitignore +++ b/.gitignore @@ -55,4 +55,3 @@ out/RelWithDebInfo out/Release out/x86 out/x64 -benchmark/* diff --git a/lib/gpu/lal_pre_cuda_hip.h b/lib/gpu/lal_pre_cuda_hip.h index f6ab1b5b6b..ec666a2863 100644 --- a/lib/gpu/lal_pre_cuda_hip.h +++ b/lib/gpu/lal_pre_cuda_hip.h @@ -134,9 +134,12 @@ int2 qt = tex1Dfetch(q_tex,i); \ ans=__hiloint2double(qt.y, qt.x); \ } + #elseif defined(__HIP_PLATFORM_SPIRV__) + #define fetch4(ans,i,pos_tex) tex1Dfetch(&ans, pos_tex, i); + #define fetch(ans,i,q_tex) tex1Dfetch(&ans, q_tex,i); #else - #define fetch4(ans,i,pos_tex) tex1Dfetch(&ans, pos_tex, i); - #define fetch(ans,i,q_tex) tex1Dfetch(&ans, q_tex,i); + #define fetch4(ans,i,pos_tex) ans=tex1Dfetch(pos_tex, i); + #define fetch(ans,i,q_tex) ans=tex1Dfetch(q_tex,i); #endif #else #define fetch4(ans,i,x) ans=x[i] From 8d5149fade70fdc4c487deb80a233c115308452a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 25 Jul 2022 20:20:28 -0600 Subject: [PATCH 66/72] Add citation information to GitHub --- .gitattributes | 1 + CITATION.cff | 84 ++++++++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 CITATION.cff diff --git a/.gitattributes b/.gitattributes index f81d32a235..77eb7f93f3 100644 --- a/.gitattributes +++ b/.gitattributes @@ -3,6 +3,7 @@ .github export-ignore .lgtm.yml export-ignore SECURITY.md export-ignore +CITATION.cff export-ignore * text=auto *.jpg -text *.pdf -text diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000000..4f5d1d5402 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,84 @@ +cff-version: 1.2.0 +title: "LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator" +type: software +authors: + - family-names: "Plimpton" + given-names: "Steven J." + - family-names: "Kohlmeyer" + given-names: "Axel" + orcid: "https://orcid.org/0000-0001-6204-6475" + - family-names: "Thompson" + given-names: "Aidan P." + orcid: "https://orcid.org/0000-0002-0324-9114" + - family-names: "Moore" + given-names: "Stan G." + - family-names: "Berger" + given-names: "Richard" + orcid: "https://orcid.org/0000-0002-3044-8266" +doi: 10.5281/zenodo.3726416 +license: GPL-2.0-only +message: "If you are referencing LAMMPS in a publication, please cite the paper below." +preferred-citation: + type: article + doi: "10.1016/j.cpc.2021.108171" + url: "https://www.sciencedirect.com/science/article/pii/S0010465521002836" + authors: + - family-names: "Thompson" + given-names: "Aidan P." + orcid: "https://orcid.org/0000-0002-0324-9114" + - family-names: "Aktulga" + given-names: "H. Metin" + - family-names: "Berger" + given-names: "Richard" + orcid: "https://orcid.org/0000-0002-3044-8266" + - family-names: "Bolintineanu" + given-names: "Dan S." + - family-names: "Brown" + given-names: "W. Michael" + - family-names: "Crozier" + given-names: "Paul S." + - family-names: "in 't Veld" + given-names: "Pieter J." + - family-names: "Kohlmeyer" + given-names: "Axel" + orcid: "https://orcid.org/0000-0001-6204-6475" + - family-names: "Moore" + given-names: "Stan G." + - family-names: "Nguyen" + given-names: "Trung Dac" + - family-names: "Shan" + given-names: "Ray" + - family-names: "Stevens" + given-names: "Mark J." + - family-names: "Tranchida" + given-names: "Julien" + - family-names: "Trott" + given-names: "Christian" + - family-names: "Plimpton" + given-names: "Steven J." + title: "LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales" + journal: "Computer Physics Communications" + keywords: + - Molecular dynamics + - Materials modeling + - Parallel algorithms + - LAMMPS + month: 2 + volume: 271 + issn: 0010-4655 + pages: 108171 + year: 2022 +references: + - title: "Fast Parallel Algorithms for Short-Range Molecular Dynamics" + type: article + journal: Journal of Computational Physics + volume: 117 + number: 1 + pages: "1-19" + year: 1995 + issn: 0021-9991 + doi: 10.1006/jcph.1995.1039 + url: https://www.sciencedirect.com/science/article/pii/S002199918571039X + authors: + - family-names: "Plimpton" + given-names: "Steve" From 6a5d56994a56fbfc97b448dce23aca3207e826fa Mon Sep 17 00:00:00 2001 From: Paulius Velesko Date: Wed, 27 Jul 2022 06:25:36 +0000 Subject: [PATCH 67/72] PR comments --- cmake/Modules/Packages/GPU.cmake | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index 36409378be..243b5111de 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -233,7 +233,8 @@ elseif(GPU_API STREQUAL "OPENCL") elseif(GPU_API STREQUAL "HIP") if(NOT DEFINED HIP_PATH) if(NOT DEFINED ENV{HIP_PATH}) - message(FATAL_ERROR "GPU_API=HIP requires HIP_PATH to be defined") + message(FATAL_ERROR "GPU_API=HIP requires HIP_PATH to be defined.\n" + "Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.") else() set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation") endif() @@ -323,15 +324,7 @@ elseif(GPU_API STREQUAL "HIP") set(CUBIN_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin") set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h") - if(HIP_PLATFORM STREQUAL "spirv") - configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY) - - add_custom_command(OUTPUT ${CUBIN_FILE} - VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} -c -O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE} - DEPENDS ${CU_CPP_FILE} - COMMENT "Gerating ${CU_NAME}.cubin") - - elseif(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd") + if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd") configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY) if(HIP_COMPILER STREQUAL "clang") @@ -350,7 +343,14 @@ elseif(GPU_API STREQUAL "HIP") VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE} DEPENDS ${CU_FILE} COMMENT "Generating ${CU_NAME}.cubin") - endif() + elseif(HIP_PLATFORM STREQUAL "spirv") + configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY) + + add_custom_command(OUTPUT ${CUBIN_FILE} + VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} -c -O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE} + DEPENDS ${CU_CPP_FILE} + COMMENT "Gerating ${CU_NAME}.cubin") + endif() add_custom_command(OUTPUT ${CUBIN_H_FILE} COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR} -D VARNAME=${CU_NAME} -D HEADER_FILE=${CUBIN_H_FILE} -D SOURCE_FILE=${CUBIN_FILE} -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateBinaryHeader.cmake From 24b3de87277bd0b74241b224d310ecc86eb4fe10 Mon Sep 17 00:00:00 2001 From: Paulius Velesko Date: Wed, 27 Jul 2022 06:41:19 +0000 Subject: [PATCH 68/72] update documentation for CMake --- doc/src/Build_extras.rst | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 14d0e290aa..094abc15e5 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -123,6 +123,7 @@ CMake build -D GPU_API=value # value = opencl (default) or cuda or hip -D GPU_PREC=value # precision setting # value = double or mixed (default) or single + -D HIP_PATH # path to HIP installation. Must be set if GPU_API=HIP -D GPU_ARCH=value # primary GPU hardware choice for GPU_API=cuda # value = sm_XX, see below # default is sm_50 @@ -179,10 +180,17 @@ set appropriate environment variables. Some variables such as :code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc` and the linker to work correctly. +Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP +code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must +set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not +yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you +should only use this option in preparations to run on Aurora system at ANL. + .. code:: bash # AMDGPU target (ROCm <= 4.0) export HIP_PLATFORM=hcc + export HIP_PATH=/path/to/HIP/install export HCC_AMDGPU_TARGET=gfx906 cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc .. make -j 4 @@ -191,6 +199,7 @@ and the linker to work correctly. # AMDGPU target (ROCm >= 4.1) export HIP_PLATFORM=amd + export HIP_PATH=/path/to/HIP/install cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc .. make -j 4 @@ -199,10 +208,20 @@ and the linker to work correctly. # CUDA target (not recommended, use GPU_ARCH=cuda) # !!! DO NOT set CMAKE_CXX_COMPILER !!! export HIP_PLATFORM=nvcc + export HIP_PATH=/path/to/HIP/install export CUDA_PATH=/usr/local/cuda cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=sm_70 .. make -j 4 +.. code:: bash + + # SPIR-V target (Intel GPUs) + export HIP_PLATFORM=spirv + export HIP_PATH=/path/to/HIP/install + export CMAKE_CXX_COMPILER= + cmake -D PKG_GPU=on -D GPU_API=HIP .. + make -j 4 + Traditional make ^^^^^^^^^^^^^^^^ From e7ffa7fae3b79f094c7cf2d0dddebf10c06292f4 Mon Sep 17 00:00:00 2001 From: Paulius Velesko Date: Wed, 27 Jul 2022 08:34:35 +0000 Subject: [PATCH 69/72] Add Makefile support for CHIP-SPV --- lib/gpu/Makefile.hip | 35 ++++++++++++++++++++++++++++------- 1 file changed, 28 insertions(+), 7 deletions(-) diff --git a/lib/gpu/Makefile.hip b/lib/gpu/Makefile.hip index 9b6087bcc3..a9f077b843 100644 --- a/lib/gpu/Makefile.hip +++ b/lib/gpu/Makefile.hip @@ -1,6 +1,9 @@ # /* ---------------------------------------------------------------------- # Generic Linux Makefile for HIP -# - export HIP_PLATFORM=amd (or nvcc) before execution +# - export HIP_PATH=/path/to/HIP/install path to the HIP implementation +# such as hipamd or CHIP-SPV. +# - export HIP_PLATFORM= specify the HIP platform to use. +# Optional. If not set, will be determined by ${HIP_PATH}/bin/hipconfig. # - change HIP_ARCH for your GPU # ------------------------------------------------------------------------- */ @@ -20,9 +23,21 @@ HIP_OPTS = -O3 HIP_HOST_OPTS = -Wno-deprecated-declarations -fopenmp HIP_HOST_INCLUDE = +ifndef HIP_PATH +$(error HIP_PATH is not set) +endif + +ifndef HIP_PLATFORM + HIP_PLATFORM=$(shell $(HIP_PATH)/bin/hipconfig --platform) +endif +HIP_COMPILER=$(shell $(HIP_PATH)/bin/hipconfig --compiler) + # use device sort # requires linking with hipcc and hipCUB + (rocPRIM or CUB for AMD or Nvidia respectively) -HIP_HOST_OPTS += -DUSE_HIP_DEVICE_SORT +ifneq (spirv,$(HIP_PLATFORM)) + # hipCUB not aviable for CHIP-SPV + HIP_HOST_OPTS += -DUSE_HIP_DEVICE_SORT +endif # path to cub HIP_HOST_INCLUDE += -I./ # path to hipcub @@ -39,10 +54,6 @@ HIP_HOST_OPTS += -DMPI_GERYON -DUCL_NO_EXIT MPI_COMP_OPTS = $(shell mpicxx --showme:compile) MPI_LINK_OPTS = $(shell mpicxx --showme:link) -HIP_PATH ?= $(wildcard /opt/rocm/hip) -HIP_PLATFORM=$(shell $(HIP_PATH)/bin/hipconfig --platform) -HIP_COMPILER=$(shell $(HIP_PATH)/bin/hipconfig --compiler) - ifeq (hcc,$(HIP_PLATFORM)) # possible values: gfx803,gfx900,gfx906 HIP_ARCH = gfx906 @@ -55,6 +66,8 @@ else ifeq (nvcc,$(HIP_PLATFORM)) -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] -gencode arch=compute_53,code=[sm_53,compute_53]\ -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] -gencode arch=compute_62,code=[sm_62,compute_62]\ -gencode arch=compute_70,code=[sm_70,compute_70] -gencode arch=compute_72,code=[sm_72,compute_72] -gencode arch=compute_75,code=[sm_75,compute_75] +else ifeq (spirv,$(HIP_PLATFORM)) + HIP_ARCH = spirv endif BIN_DIR = . @@ -71,7 +84,15 @@ BSH = /bin/sh HIP_OPTS += -DUSE_HIP $(HIP_PRECISION) HIP_GPU_OPTS += $(HIP_OPTS) -I./ -ifeq (clang,$(HIP_COMPILER)) +ifeq (spirv,$(HIP_PLATFORM)) + HIP_HOST_OPTS += -fPIC + HIP_GPU_CC = $(HIP_PATH)/bin/hipcc -c + HIP_GPU_OPTS_S = + HIP_GPU_OPTS_E = + HIP_KERNEL_SUFFIX = .cpp + HIP_LIBS_TARGET = + export HCC_AMDGPU_TARGET := $(HIP_ARCH) +else ifeq (clang,$(HIP_COMPILER)) HIP_HOST_OPTS += -fPIC HIP_GPU_CC = $(HIP_PATH)/bin/hipcc --genco HIP_GPU_OPTS_S = --offload-arch=$(HIP_ARCH) From 56642ae184e4d89a516432b1f761428fd90a4fbc Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 27 Jul 2022 05:36:05 -0400 Subject: [PATCH 70/72] add a few more keywords --- CITATION.cff | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 4f5d1d5402..a8712ddcf2 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,3 +1,5 @@ +# YAML 1.2 +--- cff-version: 1.2.0 title: "LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator" type: software @@ -17,6 +19,11 @@ authors: orcid: "https://orcid.org/0000-0002-3044-8266" doi: 10.5281/zenodo.3726416 license: GPL-2.0-only +url: https://www.lammps.org +repository-code: https://github.com/lammps/lammps/ +keywords: + - "Molecular Dynamics" + - "Materials Modeling" message: "If you are referencing LAMMPS in a publication, please cite the paper below." preferred-citation: type: article From 5fee276348114d53ccac27cad3f8386f694ad0f2 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 28 Jul 2022 07:03:58 -0400 Subject: [PATCH 71/72] add some GNU Make magic(tm) to Makefile.hip to adapt itself to OpenMPI and MPICH --- lib/gpu/Makefile.hip | 35 +++++++++++++++++++++++------------ 1 file changed, 23 insertions(+), 12 deletions(-) diff --git a/lib/gpu/Makefile.hip b/lib/gpu/Makefile.hip index a9f077b843..f5a0d03608 100644 --- a/lib/gpu/Makefile.hip +++ b/lib/gpu/Makefile.hip @@ -35,8 +35,8 @@ HIP_COMPILER=$(shell $(HIP_PATH)/bin/hipconfig --compiler) # use device sort # requires linking with hipcc and hipCUB + (rocPRIM or CUB for AMD or Nvidia respectively) ifneq (spirv,$(HIP_PLATFORM)) - # hipCUB not aviable for CHIP-SPV - HIP_HOST_OPTS += -DUSE_HIP_DEVICE_SORT +# hipCUB not aviable for CHIP-SPV +HIP_HOST_OPTS += -DUSE_HIP_DEVICE_SORT endif # path to cub HIP_HOST_INCLUDE += -I./ @@ -44,30 +44,41 @@ HIP_HOST_INCLUDE += -I./ HIP_HOST_INCLUDE += -I$(HIP_PATH)/../include ifeq (amd,$(HIP_PLATFORM)) - # newer version of ROCm (5.1+) require c++14 for rocprim - HIP_OPTS += -std=c++14 +# newer version of ROCm (5.1+) require c++14 for rocprim +HIP_OPTS += -std=c++14 endif # use mpi HIP_HOST_OPTS += -DMPI_GERYON -DUCL_NO_EXIT # this settings should match LAMMPS Makefile -MPI_COMP_OPTS = $(shell mpicxx --showme:compile) +# automatic flag detection for OpenMPI +ifeq ($(shell mpicxx --showme:compile >/dev/null 2>&1; echo $$?), 0) +MPI_COMP_OPTS = $(shell mpicxx --showme:compile) -DOMPI_SKIP_MPICXX=1 MPI_LINK_OPTS = $(shell mpicxx --showme:link) +# automatic flag detection for MPICH +else ifeq ($(shell mpicxx -compile_info >/dev/null 2>&1; echo $$?),0) +MPI_COMP_OPTS = $(filter -I%,$(shell mpicxx -compile_info)) -DMPICH_IGNORE_CXX_SEEK +MPI_LINK_OPTS = $(filter -Wl%,$(shell mpicxx -link_info)) $(filter -L%,$(shell mpicxx -link_info)) $(filter -l%,$(shell mpicxx -link_info)) +# for other MPI libs: must set flags manually, if needed +else +MPI_COMP_OPTS = +MPI_LINK_OPTS = +endif ifeq (hcc,$(HIP_PLATFORM)) - # possible values: gfx803,gfx900,gfx906 - HIP_ARCH = gfx906 +# possible values: gfx803,gfx900,gfx906 +HIP_ARCH = gfx906 else ifeq (amd,$(HIP_PLATFORM)) - # possible values: gfx803,gfx900,gfx906 - HIP_ARCH = gfx906 +# possible values: gfx803,gfx900,gfx906 +HIP_ARCH = gfx906 else ifeq (nvcc,$(HIP_PLATFORM)) - HIP_OPTS += --use_fast_math - HIP_ARCH = -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_32,code=[sm_32,compute_32] -gencode arch=compute_35,code=[sm_35,compute_35] \ +HIP_OPTS += --use_fast_math +HIP_ARCH = -gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_32,code=[sm_32,compute_32] -gencode arch=compute_35,code=[sm_35,compute_35] \ -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] -gencode arch=compute_53,code=[sm_53,compute_53]\ -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] -gencode arch=compute_62,code=[sm_62,compute_62]\ -gencode arch=compute_70,code=[sm_70,compute_70] -gencode arch=compute_72,code=[sm_72,compute_72] -gencode arch=compute_75,code=[sm_75,compute_75] else ifeq (spirv,$(HIP_PLATFORM)) - HIP_ARCH = spirv +HIP_ARCH = spirv endif BIN_DIR = . From 3f293e1c136ae8b0afe9854f3da9b42a98dd94f8 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 29 Jul 2022 17:56:01 -0600 Subject: [PATCH 72/72] Use pip install -e util/converters in doc build --- doc/Makefile | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/doc/Makefile b/doc/Makefile index 8841ae4825..45cd5767b1 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -242,7 +242,6 @@ $(MATHJAX): $(ANCHORCHECK): $(VENV) @( \ . $(VENV)/bin/activate; \ - (cd utils/converters;\ - python setup.py develop);\ + pip install -e utils/converters;\ deactivate;\ )