#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
-typedef struct {
+typedef struct
+{
int ai, aj;
} gmx_conection_t;
-typedef struct gmx_conect_t {
+typedef struct gmx_conect_t
+{
int nconect;
gmx_bool bSorted;
- gmx_conection_t *conect;
+ gmx_conection_t* conect;
} gmx_conect_t;
-static const char *pdbtp[epdbNR] = {
- "ATOM ", "HETATM", "ANISOU", "CRYST1",
- "COMPND", "MODEL", "ENDMDL", "TER", "HEADER", "TITLE", "REMARK",
- "CONECT"
-};
-
+static const char* pdbtp[epdbNR] = { "ATOM ", "HETATM", "ANISOU", "CRYST1", "COMPND", "MODEL",
+ "ENDMDL", "TER", "HEADER", "TITLE", "REMARK", "CONECT" };
#define REMARK_SIM_BOX "REMARK THIS IS A SIMULATION BOX"
-static void xlate_atomname_pdb2gmx(char *name)
+static void xlate_atomname_pdb2gmx(char* name)
{
int i, length;
char temp;
temp = name[0];
for (i = 1; i < length; i++)
{
- name[i-1] = name[i];
+ name[i - 1] = name[i];
}
- name[length-1] = temp;
+ name[length - 1] = temp;
}
}
static std::string xlate_atomname_gmx2pdb(std::string name)
{
size_t length = name.size();
- if (length > 3 && std::isdigit(name[length-1]))
+ if (length > 3 && std::isdigit(name[length - 1]))
{
- char temp = name[length-1];
- for (size_t i = length-1; i > 0; --i)
+ char temp = name[length - 1];
+ for (size_t i = length - 1; i > 0; --i)
{
- name[i] = name[i-1];
+ name[i] = name[i - 1];
}
name[0] = temp;
}
}
-void gmx_write_pdb_box(FILE *out, int ePBC, const matrix box)
+void gmx_write_pdb_box(FILE* out, int ePBC, const matrix box)
{
real alpha, beta, gamma;
return;
}
- if (norm2(box[YY])*norm2(box[ZZ]) != 0)
+ if (norm2(box[YY]) * norm2(box[ZZ]) != 0)
{
- alpha = RAD2DEG*gmx_angle(box[YY], box[ZZ]);
+ alpha = RAD2DEG * gmx_angle(box[YY], box[ZZ]);
}
else
{
alpha = 90;
}
- if (norm2(box[XX])*norm2(box[ZZ]) != 0)
+ if (norm2(box[XX]) * norm2(box[ZZ]) != 0)
{
- beta = RAD2DEG*gmx_angle(box[XX], box[ZZ]);
+ beta = RAD2DEG * gmx_angle(box[XX], box[ZZ]);
}
else
{
- beta = 90;
+ beta = 90;
}
- if (norm2(box[XX])*norm2(box[YY]) != 0)
+ if (norm2(box[XX]) * norm2(box[YY]) != 0)
{
- gamma = RAD2DEG*gmx_angle(box[XX], box[YY]);
+ gamma = RAD2DEG * gmx_angle(box[XX], box[YY]);
}
else
{
fprintf(out, "REMARK THIS IS A SIMULATION BOX\n");
if (ePBC != epbcSCREW)
{
- fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
- 10*norm(box[XX]), 10*norm(box[YY]), 10*norm(box[ZZ]),
- alpha, beta, gamma, "P 1", 1);
+ fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n", 10 * norm(box[XX]),
+ 10 * norm(box[YY]), 10 * norm(box[ZZ]), alpha, beta, gamma, "P 1", 1);
}
else
{
/* Double the a-vector length and write the correct space group */
- fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n",
- 20*norm(box[XX]), 10*norm(box[YY]), 10*norm(box[ZZ]),
- alpha, beta, gamma, "P 21 1 1", 1);
-
+ fprintf(out, "CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f %-11s%4d\n", 20 * norm(box[XX]),
+ 10 * norm(box[YY]), 10 * norm(box[ZZ]), alpha, beta, gamma, "P 21 1 1", 1);
}
}
-static void read_cryst1(char *line, int *ePBC, matrix box)
+static void read_cryst1(char* line, int* ePBC, matrix box)
{
#define SG_SIZE 11
- char sa[12], sb[12], sc[12], sg[SG_SIZE+1], ident;
+ char sa[12], sb[12], sc[12], sg[SG_SIZE + 1], ident;
double fa, fb, fc, alpha, beta, gamma, cosa, cosb, cosg, sing;
int syma, symb, symc;
int ePBC_file;
ePBC_file = -1;
if (strlen(line) >= 55)
{
- strncpy(sg, line+55, SG_SIZE);
+ strncpy(sg, line + 55, SG_SIZE);
sg[SG_SIZE] = '\0';
ident = ' ';
syma = 0;
symb = 0;
symc = 0;
sscanf(sg, "%c %d %d %d", &ident, &syma, &symb, &symc);
- if (ident == 'P' && syma == 1 && symb <= 1 && symc <= 1)
+ if (ident == 'P' && syma == 1 && symb <= 1 && symc <= 1)
{
- fc = strtod(sc, nullptr)*0.1;
+ fc = strtod(sc, nullptr) * 0.1;
ePBC_file = (fc > 0 ? epbcXYZ : epbcXY);
}
if (ident == 'P' && syma == 21 && symb == 1 && symc == 1)
if (box)
{
- fa = strtod(sa, nullptr)*0.1;
- fb = strtod(sb, nullptr)*0.1;
- fc = strtod(sc, nullptr)*0.1;
+ fa = strtod(sa, nullptr) * 0.1;
+ fb = strtod(sb, nullptr) * 0.1;
+ fc = strtod(sc, nullptr) * 0.1;
if (ePBC_file == epbcSCREW)
{
fa *= 0.5;
{
if (alpha != 90.0)
{
- cosa = std::cos(alpha*DEG2RAD);
+ cosa = std::cos(alpha * DEG2RAD);
}
else
{
}
if (beta != 90.0)
{
- cosb = std::cos(beta*DEG2RAD);
+ cosb = std::cos(beta * DEG2RAD);
}
else
{
}
if (gamma != 90.0)
{
- cosg = std::cos(gamma*DEG2RAD);
- sing = std::sin(gamma*DEG2RAD);
+ cosg = std::cos(gamma * DEG2RAD);
+ sing = std::sin(gamma * DEG2RAD);
}
else
{
cosg = 0;
sing = 1;
}
- box[YY][XX] = fb*cosg;
- box[YY][YY] = fb*sing;
- box[ZZ][XX] = fc*cosb;
- box[ZZ][YY] = fc*(cosa - cosb*cosg)/sing;
- box[ZZ][ZZ] = std::sqrt(fc*fc
- - box[ZZ][XX]*box[ZZ][XX] - box[ZZ][YY]*box[ZZ][YY]);
+ box[YY][XX] = fb * cosg;
+ box[YY][YY] = fb * sing;
+ box[ZZ][XX] = fc * cosb;
+ box[ZZ][YY] = fc * (cosa - cosb * cosg) / sing;
+ box[ZZ][ZZ] = std::sqrt(fc * fc - box[ZZ][XX] * box[ZZ][XX] - box[ZZ][YY] * box[ZZ][YY]);
}
else
{
}
}
-static int
-gmx_fprintf_pqr_atomline(FILE * fp,
- enum PDB_record record,
- int atom_seq_number,
- const char * atom_name,
- const char * res_name,
- char chain_id,
- int res_seq_number,
- real x,
- real y,
- real z,
- real occupancy,
- real b_factor)
+static int gmx_fprintf_pqr_atomline(FILE* fp,
+ enum PDB_record record,
+ int atom_seq_number,
+ const char* atom_name,
+ const char* res_name,
+ char chain_id,
+ int res_seq_number,
+ real x,
+ real y,
+ real z,
+ real occupancy,
+ real b_factor)
{
GMX_RELEASE_ASSERT(record == epdbATOM || record == epdbHETATM,
"Can only print PQR atom lines as ATOM or HETATM records");
/* Check atom name */
- GMX_RELEASE_ASSERT(atom_name != nullptr,
- "Need atom information to print pqr");
+ GMX_RELEASE_ASSERT(atom_name != nullptr, "Need atom information to print pqr");
/* Check residue name */
- GMX_RELEASE_ASSERT(res_name != nullptr,
- "Need residue information to print pqr");
+ GMX_RELEASE_ASSERT(res_name != nullptr, "Need residue information to print pqr");
/* Truncate integers so they fit */
atom_seq_number = atom_seq_number % 100000;
res_seq_number = res_seq_number % 10000;
- int n = fprintf(fp,
- "%-6s%5d %-4.4s%4.4s%c%4d %8.3f %8.3f %8.3f %6.2f %6.2f\n",
- pdbtp[record],
- atom_seq_number,
- atom_name,
- res_name,
- chain_id,
- res_seq_number,
- x, y, z,
- occupancy,
- b_factor);
+ int n = fprintf(fp, "%-6s%5d %-4.4s%4.4s%c%4d %8.3f %8.3f %8.3f %6.2f %6.2f\n", pdbtp[record],
+ atom_seq_number, atom_name, res_name, chain_id, res_seq_number, x, y, z,
+ occupancy, b_factor);
return n;
}
-void write_pdbfile_indexed(FILE *out, const char *title,
- const t_atoms *atoms, const rvec x[],
- int ePBC, const matrix box, char chainid,
- int model_nr, int nindex, const int index[],
- gmx_conect conect, gmx_bool bTerSepChains,
- bool usePqrFormat)
+void write_pdbfile_indexed(FILE* out,
+ const char* title,
+ const t_atoms* atoms,
+ const rvec x[],
+ int ePBC,
+ const matrix box,
+ char chainid,
+ int model_nr,
+ int nindex,
+ const int index[],
+ gmx_conect conect,
+ bool usePqrFormat)
{
- gmx_conect_t *gc = static_cast<gmx_conect_t *>(conect);
- int i, ii;
- int resind, resnr;
- enum PDB_record type;
- unsigned char resic, ch;
- char altloc;
- real occup, bfac;
- gmx_bool bOccup;
- int chainnum, lastchainnum;
- gmx_residuetype_t*rt;
- const char *p_restype;
- const char *p_lastrestype;
-
- gmx_residuetype_init(&rt);
+ gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
+ enum PDB_record type;
+ char altloc;
+ real occup, bfac;
+ gmx_bool bOccup;
+
fprintf(out, "TITLE %s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
- if (box && ( (norm2(box[XX]) != 0.0f) || (norm2(box[YY]) != 0.0f) || (norm2(box[ZZ]) != 0.0f) ) )
+ if (box && ((norm2(box[XX]) != 0.0F) || (norm2(box[YY]) != 0.0F) || (norm2(box[ZZ]) != 0.0F)))
{
gmx_write_pdb_box(out, ePBC, box);
}
* otherwise set them all to one
*/
bOccup = TRUE;
- for (ii = 0; (ii < nindex) && bOccup; ii++)
+ for (int ii = 0; (ii < nindex) && bOccup; ii++)
{
- i = index[ii];
+ int i = index[ii];
bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
}
}
fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
- lastchainnum = -1;
- p_restype = nullptr;
-
- for (ii = 0; ii < nindex; ii++)
+ ResidueType rt;
+ for (int ii = 0; ii < nindex; ii++)
{
- i = index[ii];
- resind = atoms->atom[i].resind;
- chainnum = atoms->resinfo[resind].chainnum;
- p_lastrestype = p_restype;
- gmx_residuetype_get_type(rt, *atoms->resinfo[resind].name, &p_restype);
-
- /* Add a TER record if we changed chain, and if either the previous or this chain is protein/DNA/RNA. */
- if (bTerSepChains && ii > 0 && chainnum != lastchainnum)
- {
- /* Only add TER if the previous chain contained protein/DNA/RNA. */
- if (gmx_residuetype_is_protein(rt, p_lastrestype) || gmx_residuetype_is_dna(rt, p_lastrestype) || gmx_residuetype_is_rna(rt, p_lastrestype))
- {
- fprintf(out, "TER\n");
- }
- lastchainnum = chainnum;
- }
-
- std::string resnm = *atoms->resinfo[resind].name;
- std::string nm = *atoms->atomname[i];
+ int i = index[ii];
+ int resind = atoms->atom[i].resind;
+ std::string resnm = *atoms->resinfo[resind].name;
+ std::string nm = *atoms->atomname[i];
/* rename HG12 to 2HG1, etc. */
- nm = xlate_atomname_gmx2pdb(nm);
- resnr = atoms->resinfo[resind].nr;
- resic = atoms->resinfo[resind].ic;
+ nm = xlate_atomname_gmx2pdb(nm);
+ int resnr = atoms->resinfo[resind].nr;
+ unsigned char resic = atoms->resinfo[resind].ic;
+ unsigned char ch;
if (chainid != ' ')
{
ch = chainid;
bfac = pdbinfo.bfac;
if (!usePqrFormat)
{
- gmx_fprintf_pdb_atomline(out,
- type,
- i+1,
- nm.c_str(),
- altloc,
- resnm.c_str(),
- ch,
- resnr,
- resic,
- 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ],
- occup,
- bfac,
- atoms->atom[i].elem);
+ gmx_fprintf_pdb_atomline(out, type, i + 1, nm.c_str(), altloc, resnm.c_str(), ch, resnr,
+ resic, 10 * x[i][XX], 10 * x[i][YY], 10 * x[i][ZZ], occup,
+ bfac, atoms->atom[i].elem);
if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
{
- fprintf(out, "ANISOU%5d %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n",
- (i+1)%100000, nm.c_str(), resnm.c_str(), ch, resnr,
- (resic == '\0') ? ' ' : resic,
- atoms->pdbinfo[i].uij[0], atoms->pdbinfo[i].uij[1],
- atoms->pdbinfo[i].uij[2], atoms->pdbinfo[i].uij[3],
- atoms->pdbinfo[i].uij[4], atoms->pdbinfo[i].uij[5]);
+ fprintf(out, "ANISOU%5d %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n", (i + 1) % 100000,
+ nm.c_str(), resnm.c_str(), ch, resnr, (resic == '\0') ? ' ' : resic,
+ atoms->pdbinfo[i].uij[0], atoms->pdbinfo[i].uij[1], atoms->pdbinfo[i].uij[2],
+ atoms->pdbinfo[i].uij[3], atoms->pdbinfo[i].uij[4], atoms->pdbinfo[i].uij[5]);
}
}
else
{
- gmx_fprintf_pqr_atomline(out,
- type,
- i+1,
- nm.c_str(),
- resnm.c_str(),
- ch,
- resnr,
- 10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ],
- occup,
- bfac);
+ gmx_fprintf_pqr_atomline(out, type, i + 1, nm.c_str(), resnm.c_str(), ch, resnr,
+ 10 * x[i][XX], 10 * x[i][YY], 10 * x[i][ZZ], occup, bfac);
}
}
if (nullptr != gc)
{
/* Write conect records */
- for (i = 0; (i < gc->nconect); i++)
+ for (int i = 0; (i < gc->nconect); i++)
{
- fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai+1, gc->conect[i].aj+1);
+ fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai + 1, gc->conect[i].aj + 1);
}
}
-
- gmx_residuetype_destroy(rt);
}
-void write_pdbfile(FILE *out, const char *title, const t_atoms *atoms, const rvec x[],
- int ePBC, const matrix box, char chainid, int model_nr, gmx_conect conect, gmx_bool bTerSepChains)
+void write_pdbfile(FILE* out,
+ const char* title,
+ const t_atoms* atoms,
+ const rvec x[],
+ int ePBC,
+ const matrix box,
+ char chainid,
+ int model_nr,
+ gmx_conect conect)
{
int i, *index;
{
index[i] = i;
}
- write_pdbfile_indexed(out, title, atoms, x, ePBC, box, chainid, model_nr,
- atoms->nr, index, conect, bTerSepChains, false);
+ write_pdbfile_indexed(out, title, atoms, x, ePBC, box, chainid, model_nr, atoms->nr, index,
+ conect, false);
sfree(index);
}
-static int line2type(const char *line)
+static int line2type(const char* line)
{
int k;
char type[8];
return k;
}
-static void read_anisou(char line[], int natom, t_atoms *atoms)
+static void read_anisou(char line[], int natom, t_atoms* atoms)
{
int i, j, k, atomnr;
char nc = '\0';
/* Search backwards for number and name only */
atomnr = std::strtol(anr, nullptr, 10);
- for (i = natom-1; (i >= 0); i--)
+ for (i = natom - 1; (i >= 0); i--)
{
- if ((std::strcmp(anm, *(atoms->atomname[i])) == 0) &&
- (atomnr == atoms->pdbinfo[i].atomnr))
+ if ((std::strcmp(anm, *(atoms->atomname[i])) == 0) && (atomnr == atoms->pdbinfo[i].atomnr))
{
break;
}
}
if (i < 0)
{
- fprintf(stderr, "Skipping ANISOU record (atom %s %d not found)\n",
- anm, atomnr);
+ fprintf(stderr, "Skipping ANISOU record (atom %s %d not found)\n", anm, atomnr);
}
else
{
- if (sscanf(line+29, "%d%d%d%d%d%d",
- &atoms->pdbinfo[i].uij[U11], &atoms->pdbinfo[i].uij[U22],
+ if (sscanf(line + 29, "%d%d%d%d%d%d", &atoms->pdbinfo[i].uij[U11], &atoms->pdbinfo[i].uij[U22],
&atoms->pdbinfo[i].uij[U33], &atoms->pdbinfo[i].uij[U12],
&atoms->pdbinfo[i].uij[U13], &atoms->pdbinfo[i].uij[U23])
== 6)
}
}
-void get_pdb_atomnumber(const t_atoms *atoms, gmx_atomprop_t aps)
+void get_pdb_atomnumber(const t_atoms* atoms, AtomProperties* aps)
{
int i, atomnumber, len;
size_t k;
- char anm[6], anm_copy[6], *ptr;
+ char anm[6], anm_copy[6];
char nc = '\0';
real eval;
std::strcpy(anm, atoms->pdbinfo[i].atomnm);
std::strcpy(anm_copy, atoms->pdbinfo[i].atomnm);
bool atomNumberSet = false;
- len = strlen(anm);
+ len = strlen(anm);
if ((anm[0] != ' ') && ((len <= 2) || !std::isdigit(anm[2])))
{
anm_copy[2] = nc;
- if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
+ if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
{
atomnumber = gmx::roundToInt(eval);
atomNumberSet = true;
else
{
anm_copy[1] = nc;
- if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
+ if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
{
atomnumber = gmx::roundToInt(eval);
atomNumberSet = true;
}
anm_copy[0] = anm[k];
anm_copy[1] = nc;
- if (gmx_atomprop_query(aps, epropElement, "???", anm_copy, &eval))
+ if (aps->setAtomProperty(epropElement, "???", anm_copy, &eval))
{
atomnumber = gmx::roundToInt(eval);
atomNumberSet = true;
}
}
+ std::string buf;
if (atomNumberSet)
{
atoms->atom[i].atomnumber = atomnumber;
- ptr = gmx_atomprop_element(aps, atomnumber);
+ buf = aps->elementFromAtomNumber(atomnumber);
if (debug)
{
- fprintf(debug, "Atomnumber for atom '%s' is %d\n",
- anm, atomnumber);
+ fprintf(debug, "Atomnumber for atom '%s' is %d\n", anm, atomnumber);
}
}
- else
- {
- ptr = nullptr;
- }
- std::strncpy(atoms->atom[i].elem, ptr == nullptr ? "" : ptr, 4);
+ buf.resize(3);
+ std::strncpy(atoms->atom[i].elem, buf.c_str(), 4);
}
}
-static int read_atom(t_symtab *symtab,
- const char line[], int type, int natom,
- t_atoms *atoms, rvec x[], int chainnum, gmx_bool bChange)
+static int
+read_atom(t_symtab* symtab, const char line[], int type, int natom, t_atoms* atoms, rvec x[], int chainnum, gmx_bool bChange)
{
- t_atom *atomn;
+ t_atom* atomn;
int j, k;
char nc = '\0';
char anr[12], anm[12], anm_copy[12], altloc, resnm[12], rnr[12], elem[3];
if (natom >= atoms->nr)
{
- gmx_fatal(FARGS, "\nFound more atoms (%d) in pdb file than expected (%d)",
- natom+1, atoms->nr);
+ gmx_fatal(FARGS, "\nFound more atoms (%d) in pdb file than expected (%d)", natom + 1, atoms->nr);
}
/* Skip over type */
trim(rnr);
resnr = std::strtol(rnr, nullptr, 10);
resic = line[j];
- j += 4;
+ j += 4;
/* X,Y,Z Coordinate */
for (k = 0; (k < 8); k++, j++)
if (atoms->atom)
{
atomn = &(atoms->atom[natom]);
- if ((natom == 0) ||
- atoms->resinfo[atoms->atom[natom-1].resind].nr != resnr ||
- atoms->resinfo[atoms->atom[natom-1].resind].ic != resic ||
- (strcmp(*atoms->resinfo[atoms->atom[natom-1].resind].name, resnm) != 0))
+ if ((natom == 0) || atoms->resinfo[atoms->atom[natom - 1].resind].nr != resnr
+ || atoms->resinfo[atoms->atom[natom - 1].resind].ic != resic
+ || (strcmp(*atoms->resinfo[atoms->atom[natom - 1].resind].name, resnm) != 0))
{
if (natom == 0)
{
}
else
{
- atomn->resind = atoms->atom[natom-1].resind + 1;
+ atomn->resind = atoms->atom[natom - 1].resind + 1;
}
atoms->nres = atomn->resind + 1;
t_atoms_set_resinfo(atoms, natom, symtab, resnm, resnr, resic, chainnum, chainid);
}
else
{
- atomn->resind = atoms->atom[natom-1].resind;
+ atomn->resind = atoms->atom[natom - 1].resind;
}
if (bChange)
{
atomn->atomnumber = atomnumber;
strncpy(atomn->elem, elem, 4);
}
- x[natom][XX] = strtod(xc, nullptr)*0.1;
- x[natom][YY] = strtod(yc, nullptr)*0.1;
- x[natom][ZZ] = strtod(zc, nullptr)*0.1;
+ x[natom][XX] = strtod(xc, nullptr) * 0.1;
+ x[natom][YY] = strtod(yc, nullptr) * 0.1;
+ x[natom][ZZ] = strtod(zc, nullptr) * 0.1;
if (atoms->pdbinfo)
{
atoms->pdbinfo[natom].type = type;
return natom;
}
-gmx_bool is_hydrogen(const char *nm)
+gmx_bool is_hydrogen(const char* nm)
{
char buf[30];
return FALSE;
}
-gmx_bool is_dummymass(const char *nm)
+gmx_bool is_dummymass(const char* nm)
{
char buf[30];
std::strcpy(buf, nm);
trim(buf);
- return (buf[0] == 'M') && (std::isdigit(buf[strlen(buf)-1]) != 0);
+ return (buf[0] == 'M') && (std::isdigit(buf[strlen(buf) - 1]) != 0);
}
-static void gmx_conect_addline(gmx_conect_t *con, char *line)
+static void gmx_conect_addline(gmx_conect_t* con, char* line)
{
- int n, ai, aj;
+ int n, ai, aj;
- std::string form2 = "%%*s";
- std::string format = form2 + "%%d";
+ std::string form2 = "%*s";
+ std::string format = form2 + "%d";
if (sscanf(line, format.c_str(), &ai) == 1)
{
do
{
form2 += "%*s";
- format = form2 + "%%d";
+ format = form2 + "%d";
n = sscanf(line, format.c_str(), &aj);
if (n == 1)
{
gmx_conect_add(con, ai - 1, aj - 1); /* to prevent duplicated records */
}
- }
- while (n == 1);
+ } while (n == 1);
}
}
-void gmx_conect_dump(FILE *fp, gmx_conect conect)
+void gmx_conect_dump(FILE* fp, gmx_conect conect)
{
- gmx_conect_t *gc = static_cast<gmx_conect_t *>(conect);
+ gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
int i;
for (i = 0; (i < gc->nconect); i++)
{
- fprintf(fp, "%6s%5d%5d\n", "CONECT",
- gc->conect[i].ai+1, gc->conect[i].aj+1);
+ fprintf(fp, "%6s%5d%5d\n", "CONECT", gc->conect[i].ai + 1, gc->conect[i].aj + 1);
}
}
gmx_conect gmx_conect_init()
{
- gmx_conect_t *gc;
+ gmx_conect_t* gc;
snew(gc, 1);
void gmx_conect_done(gmx_conect conect)
{
- gmx_conect_t *gc = conect;
+ gmx_conect_t* gc = conect;
sfree(gc->conect);
}
gmx_bool gmx_conect_exist(gmx_conect conect, int ai, int aj)
{
- gmx_conect_t *gc = conect;
+ gmx_conect_t* gc = conect;
int i;
/* if (!gc->bSorted)
for (i = 0; (i < gc->nconect); i++)
{
- if (((gc->conect[i].ai == ai) &&
- (gc->conect[i].aj == aj)) ||
- ((gc->conect[i].aj == ai) &&
- (gc->conect[i].ai == aj)))
+ if (((gc->conect[i].ai == ai) && (gc->conect[i].aj == aj))
+ || ((gc->conect[i].aj == ai) && (gc->conect[i].ai == aj)))
{
return TRUE;
}
void gmx_conect_add(gmx_conect conect, int ai, int aj)
{
- gmx_conect_t *gc = static_cast<gmx_conect_t *>(conect);
+ gmx_conect_t* gc = static_cast<gmx_conect_t*>(conect);
/* if (!gc->bSorted)
sort_conect(gc);*/
if (!gmx_conect_exist(conect, ai, aj))
{
srenew(gc->conect, ++gc->nconect);
- gc->conect[gc->nconect-1].ai = ai;
- gc->conect[gc->nconect-1].aj = aj;
+ gc->conect[gc->nconect - 1].ai = ai;
+ gc->conect[gc->nconect - 1].aj = aj;
}
}
-int read_pdbfile(FILE *in, char *title, int *model_nr,
- t_atoms *atoms, t_symtab *symtab, rvec x[], int *ePBC,
- matrix box, gmx_bool bChange, gmx_conect conect)
+int read_pdbfile(FILE* in,
+ char* title,
+ int* model_nr,
+ t_atoms* atoms,
+ t_symtab* symtab,
+ rvec x[],
+ int* ePBC,
+ matrix box,
+ gmx_bool bChange,
+ gmx_conect conect)
{
- gmx_conect_t *gc = conect;
+ gmx_conect_t* gc = conect;
gmx_bool bCOMPND;
gmx_bool bConnWarn = FALSE;
- char line[STRLEN+1];
+ char line[STRLEN + 1];
int line_type;
- char *c, *d;
+ char * c, *d;
int natom, chainnum;
- gmx_bool bStop = FALSE;
+ gmx_bool bStop = FALSE;
if (ePBC)
{
}
break;
- case epdbCRYST1:
- read_cryst1(line, ePBC, box);
- break;
+ case epdbCRYST1: read_cryst1(line, ePBC, box); break;
case epdbTITLE:
case epdbHEADER:
if (std::strlen(line) > 6)
{
- c = line+6;
+ c = line + 6;
/* skip HEADER or TITLE and spaces */
while (c[0] != ' ')
{
break;
case epdbCOMPND:
- if ((!std::strstr(line, ": ")) || (std::strstr(line+6, "MOLECULE:")))
+ if ((!std::strstr(line, ": ")) || (std::strstr(line + 6, "MOLECULE:")))
{
- if (!(c = std::strstr(line+6, "MOLECULE:")) )
+ if (!(c = std::strstr(line + 6, "MOLECULE:")))
{
c = line;
}
d = strstr(c, " ");
if (d)
{
- while ( (d[-1] == ';') && d > c)
+ while ((d[-1] == ';') && d > c)
{
d--;
}
}
break;
- case epdbTER:
- chainnum++;
- break;
+ case epdbTER: chainnum++; break;
case epdbMODEL:
if (model_nr)
}
break;
- case epdbENDMDL:
- bStop = TRUE;
- break;
+ case epdbENDMDL: bStop = TRUE; break;
case epdbCONECT:
if (gc)
{
}
break;
- default:
- break;
+ default: break;
}
}
return natom;
}
-void get_pdb_coordnum(FILE *in, int *natoms)
+void get_pdb_coordnum(FILE* in, int* natoms)
{
char line[STRLEN];
}
}
-void gmx_pdb_read_conf(const char *infile,
- t_symtab *symtab, char **name, t_atoms *atoms,
- rvec x[], int *ePBC, matrix box)
+void gmx_pdb_read_conf(const char* infile, t_symtab* symtab, char** name, t_atoms* atoms, rvec x[], int* ePBC, matrix box)
{
- FILE *in = gmx_fio_fopen(infile, "r");
+ FILE* in = gmx_fio_fopen(infile, "r");
char title[STRLEN];
read_pdbfile(in, title, nullptr, atoms, symtab, x, ePBC, box, TRUE, nullptr);
if (name != nullptr)
gmx_fio_fclose(in);
}
-gmx_conect gmx_conect_generate(const t_topology *top)
+gmx_conect gmx_conect_generate(const t_topology* top)
{
int f, i;
gmx_conect gc;
/* Fill the conect records */
- gc = gmx_conect_init();
+ gc = gmx_conect_init();
for (f = 0; (f < F_NRE); f++)
{
if (IS_CHEMBOND(f))
{
- for (i = 0; (i < top->idef.il[f].nr); i += interaction_function[f].nratoms+1)
+ for (i = 0; (i < top->idef.il[f].nr); i += interaction_function[f].nratoms + 1)
{
- gmx_conect_add(gc, top->idef.il[f].iatoms[i+1],
- top->idef.il[f].iatoms[i+2]);
+ gmx_conect_add(gc, top->idef.il[f].iatoms[i + 1], top->idef.il[f].iatoms[i + 2]);
}
}
}
return gc;
}
-int
-gmx_fprintf_pdb_atomline(FILE * fp,
- enum PDB_record record,
- int atom_seq_number,
- const char * atom_name,
- char alternate_location,
- const char * res_name,
- char chain_id,
- int res_seq_number,
- char res_insertion_code,
- real x,
- real y,
- real z,
- real occupancy,
- real b_factor,
- const char * element)
+int gmx_fprintf_pdb_atomline(FILE* fp,
+ enum PDB_record record,
+ int atom_seq_number,
+ const char* atom_name,
+ char alternate_location,
+ const char* res_name,
+ char chain_id,
+ int res_seq_number,
+ char res_insertion_code,
+ real x,
+ real y,
+ real z,
+ real occupancy,
+ real b_factor,
+ const char* element)
{
char tmp_atomname[6], tmp_resname[6];
gmx_bool start_name_in_col13;
/* If the atom name is an element name with two chars, it should start already in column 13.
* Otherwise it should start in column 14, unless the name length is 4 chars.
*/
- if ( (element != nullptr) && (std::strlen(element) >= 2) && (gmx_strncasecmp(atom_name, element, 2) == 0) )
+ if ((element != nullptr) && (std::strlen(element) >= 2)
+ && (gmx_strncasecmp(atom_name, element, 2) == 0))
{
start_name_in_col13 = TRUE;
}
atom_seq_number = atom_seq_number % 100000;
res_seq_number = res_seq_number % 10000;
- n = fprintf(fp,
- "%-6s%5d %-4.4s%c%4.4s%c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %2s\n",
- pdbtp[record],
- atom_seq_number,
- tmp_atomname,
- alternate_location,
- tmp_resname,
- chain_id,
- res_seq_number,
- res_insertion_code,
- x, y, z,
- occupancy,
- b_factor,
+ n = fprintf(fp, "%-6s%5d %-4.4s%c%4.4s%c%4d%c %8.3f%8.3f%8.3f%6.2f%6.2f %2s\n",
+ pdbtp[record], atom_seq_number, tmp_atomname, alternate_location, tmp_resname,
+ chain_id, res_seq_number, res_insertion_code, x, y, z, occupancy, b_factor,
(element != nullptr) ? element : "");
return n;
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
+ #include "gromacs/gmxana/angle_correction.h"
#include "gromacs/gmxana/gstat.h"
-#include "gromacs/listed-forces/bonded.h"
+#include "gromacs/listed_forces/bonded.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-void print_one(const gmx_output_env_t *oenv, const char *base, const char *name,
- const char *title, const char *ylabel, int nf, real time[],
- real data[])
+void print_one(const gmx_output_env_t* oenv,
+ const char* base,
+ const char* name,
+ const char* title,
+ const char* ylabel,
+ int nf,
+ real time[],
+ real data[])
{
- FILE *fp;
+ FILE* fp;
char buf[256], t2[256];
int k;
{
/* multiplicity and core_frac NOT used,
* just given to enable use of pt-to-fn in caller low_ana_dih_trans*/
- static const real r30 = M_PI/6.0;
- static const real r90 = M_PI/2.0;
- static const real r150 = M_PI*5.0/6.0;
+ static const real r30 = M_PI / 6.0;
+ static const real r90 = M_PI / 2.0;
+ static const real r150 = M_PI * 5.0 / 6.0;
if ((phi < r30) && (phi > -r30))
{
static int calc_Nbin(real phi, int multiplicity, real core_frac)
{
- static const real r360 = 360*DEG2RAD;
+ static const real r360 = 360 * DEG2RAD;
real rot_width, core_width, core_offset, low, hi;
int bin;
/* with multiplicity 3 and core_frac 0.5
phi += r360;
}
- rot_width = 360./multiplicity;
+ rot_width = 360. / multiplicity;
core_width = core_frac * rot_width;
- core_offset = (rot_width - core_width)/2.0;
+ core_offset = (rot_width - core_width) / 2.0;
for (bin = 1; bin <= multiplicity; bin++)
{
- low = ((bin - 1) * rot_width ) + core_offset;
- hi = ((bin - 1) * rot_width ) + core_offset + core_width;
+ low = ((bin - 1) * rot_width) + core_offset;
+ hi = ((bin - 1) * rot_width) + core_offset + core_width;
low *= DEG2RAD;
- hi *= DEG2RAD;
+ hi *= DEG2RAD;
if ((phi > low) && (phi < hi))
{
return bin;
return 0;
}
-void ana_dih_trans(const char *fn_trans, const char *fn_histo,
- real **dih, int nframes, int nangles,
- const char *grpname, real *time, gmx_bool bRb,
- const gmx_output_env_t *oenv)
+void ana_dih_trans(const char* fn_trans,
+ const char* fn_histo,
+ real** dih,
+ int nframes,
+ int nangles,
+ const char* grpname,
+ real* time,
+ gmx_bool bRb,
+ const gmx_output_env_t* oenv)
{
/* just a wrapper; declare extra args, then chuck away at end. */
int maxchi = 0;
- t_dlist *dlist;
- int *multiplicity;
+ t_dlist* dlist;
+ int* multiplicity;
int nlist = nangles;
int k;
multiplicity[k] = 3;
}
- low_ana_dih_trans(TRUE, fn_trans, TRUE, fn_histo, maxchi,
- dih, nlist, dlist, nframes,
- nangles, grpname, multiplicity, time, bRb, 0.5, oenv);
+ low_ana_dih_trans(TRUE, fn_trans, TRUE, fn_histo, maxchi, dih, nlist, dlist, nframes, nangles,
+ grpname, multiplicity, time, bRb, 0.5, oenv);
sfree(dlist);
sfree(multiplicity);
-
}
-void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
- gmx_bool bHisto, const char *fn_histo, int maxchi,
- real **dih, int nlist, t_dlist dlist[], int nframes,
- int nangles, const char *grpname, int multiplicity[],
- real *time, gmx_bool bRb, real core_frac,
- const gmx_output_env_t *oenv)
+void low_ana_dih_trans(gmx_bool bTrans,
+ const char* fn_trans,
+ gmx_bool bHisto,
+ const char* fn_histo,
+ int maxchi,
+ real** dih,
+ int nlist,
+ t_dlist dlist[],
+ int nframes,
+ int nangles,
+ const char* grpname,
+ int multiplicity[],
+ real* time,
+ gmx_bool bRb,
+ real core_frac,
+ const gmx_output_env_t* oenv)
{
- FILE *fp;
- int *tr_f, *tr_h;
+ FILE* fp;
+ int * tr_f, *tr_h;
char title[256];
int i, j, k, Dih, ntrans;
int cur_bin, new_bin;
real ttime;
- real *rot_occ[NROT];
- int (*calc_bin)(real, int, real);
- real dt;
+ real* rot_occ[NROT];
+ int (*calc_bin)(real, int, real);
+ real dt;
if (1 <= nframes)
{
return;
}
/* Assumes the frames are equally spaced in time */
- dt = (time[nframes-1]-time[0])/(nframes-1);
+ dt = (time[nframes - 1] - time[0]) / (nframes - 1);
/* Analysis of dihedral transitions */
fprintf(stderr, "Now calculating transitions...\n");
}
#else
/* why is all this md rubbish periodic? Remove 360 degree periodicity */
- if ( (dih[i][j] - prev) > M_PI)
+ if ((dih[i][j] - prev) > M_PI)
{
- dih[i][j] -= 2*M_PI;
+ dih[i][j] -= 2 * M_PI;
}
- else if ( (dih[i][j] - prev) < -M_PI)
+ else if ((dih[i][j] - prev) < -M_PI)
{
- dih[i][j] += 2*M_PI;
+ dih[i][j] += 2 * M_PI;
}
prev = dih[i][j];
mind = std::min(mind, dih[i][j]);
maxd = std::max(maxd, dih[i][j]);
- if ( (maxd - mind) > 2*M_PI/3) /* or 120 degrees, assuming */
- { /* multiplicity 3. Not so general.*/
+ if ((maxd - mind) > 2 * M_PI / 3) /* or 120 degrees, assuming */
+ { /* multiplicity 3. Not so general.*/
tr_f[j]++;
tr_h[i]++;
maxd = mind = dih[i][j]; /* get ready for next transition */
fprintf(stderr, "Total number of transitions: %10d\n", ntrans);
if (ntrans > 0)
{
- ttime = (dt*nframes*nangles)/ntrans;
+ ttime = (dt * nframes * nangles) / ntrans;
fprintf(stderr, "Time between transitions: %10.3f ps\n", ttime);
}
* based on fn histogramming in g_chi. diff roles for i and j here */
j = 0;
- for (Dih = 0; (Dih < NONCHI+maxchi); Dih++)
+ for (Dih = 0; (Dih < NONCHI + maxchi); Dih++)
{
for (i = 0; (i < nlist); i++)
{
- if (((Dih < edOmega) ) ||
- ((Dih == edOmega) && (has_dihedral(edOmega, &(dlist[i])))) ||
- ((Dih > edOmega) && (dlist[i].atm.Cn[Dih-NONCHI+3] != -1)))
+ if (((Dih < edOmega)) || ((Dih == edOmega) && (has_dihedral(edOmega, &(dlist[i]))))
+ || ((Dih > edOmega) && (dlist[i].atm.Cn[Dih - NONCHI + 3] != -1)))
{
/* grs debug printf("Not OK? i %d j %d Dih %d \n", i, j, Dih) ; */
dlist[i].ntr[Dih] = tr_h[j];
{
tr_f[tr_h[i]]++;
}
- for (j = nframes; ((tr_f[j-1] == 0) && (j > 0)); j--)
- {
- ;
- }
+ for (j = nframes; ((tr_f[j - 1] == 0) && (j > 0)); j--) {}
- ttime = dt*nframes;
+ ttime = dt * nframes;
if (bHisto)
{
sprintf(title, "Transition time: %s", grpname);
fp = xvgropen(fn_histo, title, "Time (ps)", "#", oenv);
- for (i = j-1; (i > 0); i--)
+ for (i = j - 1; (i > 0); i--)
{
if (tr_f[i] != 0)
{
- fprintf(fp, "%10.3f %10d\n", ttime/i, tr_f[i]);
+ fprintf(fp, "%10.3f %10d\n", ttime / i, tr_f[i]);
}
}
xvgrclose(fp);
{
sfree(rot_occ[k]);
}
-
}
-void mk_multiplicity_lookup (int *multiplicity, int maxchi,
- int nlist, t_dlist dlist[], int nangles)
+void mk_multiplicity_lookup(int* multiplicity, int maxchi, int nlist, t_dlist dlist[], int nangles)
{
/* new by grs - for dihedral j (as in dih[j]) get multiplicity from dlist
* and store in multiplicity[j]
char name[4];
j = 0;
- for (Dih = 0; (Dih < NONCHI+maxchi); Dih++)
+ for (Dih = 0; (Dih < NONCHI + maxchi); Dih++)
{
for (i = 0; (i < nlist); i++)
{
std::strncpy(name, dlist[i].name, 3);
name[3] = '\0';
- if (((Dih < edOmega) ) ||
- ((Dih == edOmega) && (has_dihedral(edOmega, &(dlist[i])))) ||
- ((Dih > edOmega) && (dlist[i].atm.Cn[Dih-NONCHI+3] != -1)))
+ if (((Dih < edOmega)) || ((Dih == edOmega) && (has_dihedral(edOmega, &(dlist[i]))))
+ || ((Dih > edOmega) && (dlist[i].atm.Cn[Dih - NONCHI + 3] != -1)))
{
/* default - we will correct the rest below */
multiplicity[j] = 3;
}
/* dihedrals to aromatic rings, COO, CONH2 or guanidinium are 2fold*/
- if (Dih > edOmega && (dlist[i].atm.Cn[Dih-NONCHI+3] != -1))
+ if (Dih > edOmega && (dlist[i].atm.Cn[Dih - NONCHI + 3] != -1))
{
- if ( ((std::strstr(name, "PHE") != nullptr) && (Dih == edChi2)) ||
- ((std::strstr(name, "TYR") != nullptr) && (Dih == edChi2)) ||
- ((std::strstr(name, "PTR") != nullptr) && (Dih == edChi2)) ||
- ((std::strstr(name, "TRP") != nullptr) && (Dih == edChi2)) ||
- ((std::strstr(name, "HIS") != nullptr) && (Dih == edChi2)) ||
- ((std::strstr(name, "GLU") != nullptr) && (Dih == edChi3)) ||
- ((std::strstr(name, "ASP") != nullptr) && (Dih == edChi2)) ||
- ((std::strstr(name, "GLN") != nullptr) && (Dih == edChi3)) ||
- ((std::strstr(name, "ASN") != nullptr) && (Dih == edChi2)) ||
- ((std::strstr(name, "ARG") != nullptr) && (Dih == edChi4)) )
+ if (((std::strstr(name, "PHE") != nullptr) && (Dih == edChi2))
+ || ((std::strstr(name, "TYR") != nullptr) && (Dih == edChi2))
+ || ((std::strstr(name, "PTR") != nullptr) && (Dih == edChi2))
+ || ((std::strstr(name, "TRP") != nullptr) && (Dih == edChi2))
+ || ((std::strstr(name, "HIS") != nullptr) && (Dih == edChi2))
+ || ((std::strstr(name, "GLU") != nullptr) && (Dih == edChi3))
+ || ((std::strstr(name, "ASP") != nullptr) && (Dih == edChi2))
+ || ((std::strstr(name, "GLN") != nullptr) && (Dih == edChi3))
+ || ((std::strstr(name, "ASN") != nullptr) && (Dih == edChi2))
+ || ((std::strstr(name, "ARG") != nullptr) && (Dih == edChi4)))
{
multiplicity[j] = 2;
}
}
if (j < nangles)
{
- fprintf(stderr, "WARNING: not all dihedrals found in topology (only %d out of %d)!\n",
- j, nangles);
+ fprintf(stderr, "WARNING: not all dihedrals found in topology (only %d out of %d)!\n", j, nangles);
}
/* Check for remaining dihedrals */
for (; (j < nangles); j++)
{
multiplicity[j] = 3;
}
-
}
-void mk_chi_lookup (int **lookup, int maxchi,
- int nlist, t_dlist dlist[])
+void mk_chi_lookup(int** lookup, int maxchi, int nlist, t_dlist dlist[])
{
/* by grs. should rewrite everything to use this. (but haven't,
j = 0;
/* NONCHI points to chi1, therefore we have to start counting there. */
- for (Dih = NONCHI; (Dih < NONCHI+maxchi); Dih++)
+ for (Dih = NONCHI; (Dih < NONCHI + maxchi); Dih++)
{
for (i = 0; (i < nlist); i++)
{
Chi = Dih - NONCHI;
- if (((Dih < edOmega) ) ||
- ((Dih == edOmega) && (has_dihedral(edOmega, &(dlist[i])))) ||
- ((Dih > edOmega) && (dlist[i].atm.Cn[Dih-NONCHI+3] != -1)))
+ if (((Dih < edOmega)) || ((Dih == edOmega) && (has_dihedral(edOmega, &(dlist[i]))))
+ || ((Dih > edOmega) && (dlist[i].atm.Cn[Dih - NONCHI + 3] != -1)))
{
/* grs debug printf("Not OK? i %d j %d Dih %d \n", i, j, Dih) ; */
if (Dih > edOmega)
}
}
}
-
}
-void get_chi_product_traj (real **dih, int nframes, int nlist,
- int maxchi, t_dlist dlist[], real time[],
- int **lookup, int *multiplicity, gmx_bool bRb, gmx_bool bNormalize,
- real core_frac, gmx_bool bAll, const char *fnall,
- const gmx_output_env_t *oenv)
+void get_chi_product_traj(real** dih,
+ int nframes,
+ int nlist,
+ int maxchi,
+ t_dlist dlist[],
+ real time[],
+ int** lookup,
+ int* multiplicity,
+ gmx_bool bRb,
+ gmx_bool bNormalize,
+ real core_frac,
+ gmx_bool bAll,
+ const char* fnall,
+ const gmx_output_env_t* oenv)
{
gmx_bool bRotZero, bHaveChi = FALSE;
int accum = 0, index, i, j, k, Xi, n, b;
- real *chi_prtrj;
- int *chi_prhist;
+ real* chi_prtrj;
+ int* chi_prhist;
int nbin;
- FILE *fp, *fpall;
+ FILE * fp, *fpall;
char hisfile[256], histitle[256], *namept;
- int (*calc_bin)(real, int, real);
+ int (*calc_bin)(real, int, real);
/* Analysis of dihedral transitions */
fprintf(stderr, "Now calculating Chi product trajectories...\n");
if (index >= 0)
{
n = multiplicity[index];
- nbin = n*nbin;
+ nbin = n * nbin;
}
}
nbin += 1; /* for the "zero rotamer", outside the core region */
else
{
chi_prtrj[j] = accum;
- if (accum+1 > nbin)
+ if (accum + 1 > nbin)
{
- nbin = accum+1;
+ nbin = accum + 1;
}
}
}
{
if (bNormalize)
{
- fprintf(fp, "%5d %10g\n", k, (1.0*chi_prhist[k])/nframes);
+ fprintf(fp, "%5d %10g\n", k, (1.0 * chi_prhist[k]) / nframes);
}
else
{
{
if (bNormalize)
{
- fprintf(fpall, " %10g", (1.0*chi_prhist[k])/nframes);
+ fprintf(fpall, " %10g", (1.0 * chi_prhist[k]) / nframes);
}
else
{
sfree(chi_prtrj);
xvgrclose(fpall);
fprintf(stderr, "\n");
-
}
-void calc_distribution_props(int nh, const int histo[], real start,
- int nkkk, t_karplus kkk[],
- real *S2)
+void calc_distribution_props(int nh, const int histo[], real start, int nkkk, t_karplus kkk[], real* S2)
{
real d, dc, ds, c1, c2, tdc, tds;
real fac, ang, invth, Jc;
{
gmx_fatal(FARGS, "No points in histogram (%s, %d)", __FILE__, __LINE__);
}
- fac = 2*M_PI/nh;
+ fac = 2 * M_PI / nh;
/* Compute normalisation factor */
th = 0;
{
th += histo[j];
}
- invth = 1.0/th;
+ invth = 1.0 / th;
for (i = 0; (i < nkkk); i++)
{
kkk[i].Jc = 0;
kkk[i].Jcsig = 0;
}
- tdc = 0; tds = 0;
+ tdc = 0;
+ tds = 0;
for (j = 0; (j < nh); j++)
{
- d = invth*histo[j];
- ang = j*fac-start;
- c1 = std::cos(ang);
- dc = d*c1;
- ds = d*std::sin(ang);
+ d = invth * histo[j];
+ ang = j * fac - start;
+ c1 = std::cos(ang);
+ dc = d * c1;
+ ds = d * std::sin(ang);
tdc += dc;
tds += ds;
for (i = 0; (i < nkkk); i++)
{
- c1 = std::cos(ang+kkk[i].offset);
- c2 = c1*c1;
- Jc = (kkk[i].A*c2 + kkk[i].B*c1 + kkk[i].C);
- kkk[i].Jc += histo[j]*Jc;
- kkk[i].Jcsig += histo[j]*gmx::square(Jc);
+ c1 = std::cos(ang + kkk[i].offset);
+ c2 = c1 * c1;
+ Jc = (kkk[i].A * c2 + kkk[i].B * c1 + kkk[i].C);
+ kkk[i].Jc += histo[j] * Jc;
+ kkk[i].Jcsig += histo[j] * gmx::square(Jc);
}
}
for (i = 0; (i < nkkk); i++)
{
- kkk[i].Jc /= th;
- kkk[i].Jcsig = std::sqrt(kkk[i].Jcsig/th-gmx::square(kkk[i].Jc));
+ kkk[i].Jc /= th;
+ kkk[i].Jcsig = std::sqrt(kkk[i].Jcsig / th - gmx::square(kkk[i].Jc));
}
- *S2 = tdc*tdc+tds*tds;
+ *S2 = tdc * tdc + tds * tds;
}
-static void calc_angles(struct t_pbc *pbc,
- int n3, int index[], real ang[], rvec x_s[])
+static void calc_angles(struct t_pbc* pbc, int n3, int index[], real ang[], rvec x_s[])
{
int i, ix, t1, t2;
rvec r_ij, r_kj;
for (i = ix = 0; (ix < n3); i++, ix += 3)
{
- ang[i] = bond_angle(x_s[index[ix]], x_s[index[ix+1]], x_s[index[ix+2]],
- pbc, r_ij, r_kj, &costh, &t1, &t2);
+ ang[i] = bond_angle(x_s[index[ix]], x_s[index[ix + 1]], x_s[index[ix + 2]], pbc, r_ij, r_kj,
+ &costh, &t1, &t2);
}
if (debug)
{
- fprintf(debug, "Angle[0]=%g, costh=%g, index0 = %d, %d, %d\n",
- ang[0], costh, index[0], index[1], index[2]);
+ fprintf(debug, "Angle[0]=%g, costh=%g, index0 = %d, %d, %d\n", ang[0], costh, index[0],
+ index[1], index[2]);
pr_rvec(debug, 0, "rij", r_ij, DIM, TRUE);
pr_rvec(debug, 0, "rkj", r_kj, DIM, TRUE);
}
gauche += 1.0;
}
}
- if (trans+gauche > 0)
+ if (trans + gauche > 0)
{
- return trans/(trans+gauche);
+ return trans / (trans + gauche);
}
else
{
}
}
-static void calc_dihs(struct t_pbc *pbc,
- int n4, const int index[], real ang[], rvec x_s[])
+static void calc_dihs(struct t_pbc* pbc, int n4, const int index[], real ang[], rvec x_s[])
{
int i, ix, t1, t2, t3;
rvec r_ij, r_kj, r_kl, m, n;
for (i = ix = 0; (ix < n4); i++, ix += 4)
{
- aaa = dih_angle(x_s[index[ix]], x_s[index[ix+1]], x_s[index[ix+2]],
- x_s[index[ix+3]], pbc,
- r_ij, r_kj, r_kl, m, n,
- &t1, &t2, &t3);
+ aaa = dih_angle(x_s[index[ix]], x_s[index[ix + 1]], x_s[index[ix + 2]], x_s[index[ix + 3]],
+ pbc, r_ij, r_kj, r_kl, m, n, &t1, &t2, &t3);
ang[i] = aaa; /* not taking into account ryckaert bellemans yet */
}
}
-void make_histo(FILE *log,
- int ndata, real data[], int npoints, int histo[],
- real minx, real maxx)
+void make_histo(FILE* log, int ndata, real data[], int npoints, int histo[], real minx, real maxx)
{
double dx;
int i, ind;
}
fprintf(log, "Min data: %10g Max data: %10g\n", minx, maxx);
}
- dx = npoints/(maxx-minx);
+ dx = npoints / (maxx - minx);
if (debug)
{
- fprintf(debug,
- "Histogramming: ndata=%d, nhisto=%d, minx=%g,maxx=%g,dx=%g\n",
- ndata, npoints, minx, maxx, dx);
+ fprintf(debug, "Histogramming: ndata=%d, nhisto=%d, minx=%g,maxx=%g,dx=%g\n", ndata,
+ npoints, minx, maxx, dx);
}
for (i = 0; (i < ndata); i++)
{
- ind = static_cast<int>((data[i]-minx)*dx);
+ ind = static_cast<int>((data[i] - minx) * dx);
if ((ind >= 0) && (ind < npoints))
{
histo[ind]++;
d = 0;
for (i = 0; (i < npoints); i++)
{
- d += dx*histo[i];
+ d += dx * histo[i];
}
if (d == 0)
{
fprintf(stderr, "Empty histogram!\n");
return;
}
- fac = 1.0/d;
+ fac = 1.0 / d;
for (i = 0; (i < npoints); i++)
{
- normhisto[i] = fac*histo[i];
+ normhisto[i] = fac * histo[i];
}
}
-void read_ang_dih(const char *trj_fn,
- gmx_bool bAngles, gmx_bool bSaveAll, gmx_bool bRb, gmx_bool bPBC,
- int maxangstat, int angstat[],
- int *nframes, real **time,
- int isize, int index[],
- real **trans_frac,
- real **aver_angle,
- real *dih[],
- const gmx_output_env_t *oenv)
+void read_ang_dih(const char* trj_fn,
+ gmx_bool bAngles,
+ gmx_bool bSaveAll,
+ gmx_bool bRb,
+ gmx_bool bPBC,
+ int maxangstat,
+ int angstat[],
+ int* nframes,
+ real** time,
+ int isize,
+ int index[],
+ real** trans_frac,
+ real** aver_angle,
+ real* dih[],
+ const gmx_output_env_t* oenv)
{
- struct t_pbc *pbc;
- t_trxstatus *status;
+ struct t_pbc* pbc;
+ t_trxstatus* status;
int i, angind, total, teller;
int nangles, n_alloc;
- real t, fraction, pifac, aa, angle;
+ real t, fraction, pifac, angle;
- real *angles[2];
+ real* angles[2];
matrix box;
- rvec *x;
+ rvec* x;
int cur = 0;
-#define prev (1-cur)
+#define prev (1 - cur)
snew(pbc, 1);
read_first_x(oenv, &status, trj_fn, &t, &x, box);
if (bAngles)
{
- nangles = isize/3;
+ nangles = isize / 3;
pifac = M_PI;
}
else
{
- nangles = isize/4;
- pifac = 2.0*M_PI;
+ nangles = isize / 4;
+ pifac = 2.0 * M_PI;
}
snew(angles[cur], nangles);
snew(angles[prev], nangles);
{
if (angles[cur][i] <= 0.0)
{
- angles[cur][i] += 2*M_PI;
+ angles[cur][i] += 2 * M_PI;
}
}
}
{
for (i = 0; (i < nangles); i++)
{
- real dd = angles[cur][i];
+ real dd = angles[cur][i];
angles[cur][i] = std::atan2(std::sin(dd), std::cos(dd));
}
}
{
while (angles[cur][i] <= angles[prev][i] - M_PI)
{
- angles[cur][i] += 2*M_PI;
+ angles[cur][i] += 2 * M_PI;
}
while (angles[cur][i] > angles[prev][i] + M_PI)
{
- angles[cur][i] -= 2*M_PI;
+ angles[cur][i] -= 2 * M_PI;
}
}
}
}
/* Average angles */
- aa = 0;
+ double aa = 0;
for (i = 0; (i < nangles); i++)
{
- real diffa = angles[cur][i] - angles[cur][i-1];
+ if (!bAngles && i > 0)
+ {
- angles[cur][i] = angles[cur][i-1] + diffa;
++ real diffa = angles[cur][i] - angles[cur][i - 1];
+ diffa = correctRadianAngleRange(diffa);
++ angles[cur][i] = angles[cur][i - 1] + diffa;
+ }
+
aa = aa + angles[cur][i];
/* angle in rad / 2Pi * max determines bin. bins go from 0 to maxangstat,
angle = angles[cur][i];
if (!bAngles)
{
- while (angle < -M_PI)
- {
- angle += 2 * M_PI;
- }
- while (angle >= M_PI)
- {
- angle -= 2 * M_PI;
- }
-
- angle = correctRadianAngleRange(angle);
++ angle = correctRadianAngleRange(angle);
angle += M_PI;
}
/* Update the distribution histogram */
- angind = gmx::roundToInt((angle*maxangstat)/pifac);
+ angind = gmx::roundToInt((angle * maxangstat) / pifac);
if (angind == maxangstat)
{
angind = 0;
}
- if ( (angind < 0) || (angind >= maxangstat) )
+ if ((angind < 0) || (angind >= maxangstat))
{
/* this will never happen */
- gmx_fatal(FARGS, "angle (%f) index out of range (0..%d) : %d\n",
- angle, maxangstat, angind);
+ gmx_fatal(FARGS, "angle (%f) index out of range (0..%d) : %d\n", angle, maxangstat, angind);
}
angstat[angind]++;
}
/* average over all angles */
- (*aver_angle)[teller] = (aa / nangles);
- aa = correctRadianAngleRange(aa/nangles);
++ aa = correctRadianAngleRange(aa / nangles);
+ (*aver_angle)[teller] = (aa);
/* this copies all current dih. angles to dih[i], teller is frame */
if (bSaveAll)
{
for (i = 0; i < nangles; i++)
{
- dih[i][teller] = angles[cur][i];
+ if (!bAngles)
+ {
+ dih[i][teller] = correctRadianAngleRange(angles[cur][i]);
+ }
+ else
+ {
+ dih[i][teller] = angles[cur][i];
+ }
}
}
/* Increment loop counter */
teller++;
- }
- while (read_next_x(oenv, status, &t, x, box));
+ } while (read_next_x(oenv, status, &t, x, box));
close_trx(status);
sfree(x);
#include "gromacs/correlationfunctions/autocorr.h"
#include "gromacs/fileio/trrio.h"
#include "gromacs/fileio/xvgr.h"
+ #include "gromacs/gmxana/angle_correction.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/gstat.h"
#include "gromacs/math/functions.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
-static void dump_dih_trr(int nframes, int nangles, real **dih, const char *fn,
- real *time)
+static void dump_dih_trr(int nframes, int nangles, real** dih, const char* fn, real* time)
{
int i, j, k, l, m, na;
- struct t_fileio *fio;
- rvec *x;
- matrix box = {{2, 0, 0}, {0, 2, 0}, {0, 0, 2}};
+ struct t_fileio* fio;
+ rvec* x;
+ matrix box = { { 2, 0, 0 }, { 0, 2, 0 }, { 0, 0, 2 } };
- na = (nangles*2);
+ na = (nangles * 2);
if ((na % 3) != 0)
{
- na = 1+na/3;
+ na = 1 + na / 3;
}
else
{
- na = na/3;
+ na = na / 3;
}
- printf("There are %d dihedrals. Will fill %d atom positions with cos/sin\n",
- nangles, na);
+ printf("There are %d dihedrals. Will fill %d atom positions with cos/sin\n", nangles, na);
snew(x, na);
fio = gmx_trr_open(fn, "w");
for (i = 0; (i < nframes); i++)
sfree(x);
}
-int gmx_g_angle(int argc, char *argv[])
+int gmx_g_angle(int argc, char* argv[])
{
- static const char *desc[] = {
+ static const char* desc[] = {
"[THISMODULE] computes the angle distribution for a number of angles",
"or dihedrals.[PAR]",
"With option [TT]-ov[tt], you can plot the average angle of",
"records a histogram of the times between such transitions,",
"assuming the input trajectory frames are equally spaced in time."
};
- static const char *opt[] = { nullptr, "angle", "dihedral", "improper", "ryckaert-bellemans", nullptr };
- static gmx_bool bALL = FALSE, bChandler = FALSE, bAverCorr = FALSE, bPBC = TRUE;
+ static const char* opt[] = { nullptr, "angle", "dihedral", "improper", "ryckaert-bellemans",
+ nullptr };
+ static gmx_bool bALL = FALSE, bChandler = FALSE, bAverCorr = FALSE, bPBC = TRUE;
static real binwidth = 1;
t_pargs pa[] = {
- { "-type", FALSE, etENUM, {opt},
- "Type of angle to analyse" },
- { "-all", FALSE, etBOOL, {&bALL},
- "Plot all angles separately in the averages file, in the order of appearance in the index file." },
- { "-binwidth", FALSE, etREAL, {&binwidth},
+ { "-type", FALSE, etENUM, { opt }, "Type of angle to analyse" },
+ { "-all",
+ FALSE,
+ etBOOL,
+ { &bALL },
+ "Plot all angles separately in the averages file, in the order of appearance in the "
+ "index file." },
+ { "-binwidth",
+ FALSE,
+ etREAL,
+ { &binwidth },
"binwidth (degrees) for calculating the distribution" },
- { "-periodic", FALSE, etBOOL, {&bPBC},
- "Print dihedral angles modulo 360 degrees" },
- { "-chandler", FALSE, etBOOL, {&bChandler},
- "Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi < -60 or phi > 60." },
- { "-avercorr", FALSE, etBOOL, {&bAverCorr},
+ { "-periodic", FALSE, etBOOL, { &bPBC }, "Print dihedral angles modulo 360 degrees" },
+ { "-chandler",
+ FALSE,
+ etBOOL,
+ { &bChandler },
+ "Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine "
+ "correlation function. Trans is defined as phi < -60 or phi > 60." },
+ { "-avercorr",
+ FALSE,
+ etBOOL,
+ { &bAverCorr },
"Average the correlation functions for the individual angles/dihedrals" }
};
- static const char *bugs[] = {
+ static const char* bugs[] = {
"Counting transitions only works for dihedrals with multiplicity 3"
};
- FILE *out;
- real dt;
- int isize;
- int *index;
- char *grpname;
- real maxang, S2, norm_fac, maxstat;
- unsigned long mode;
- int nframes, maxangstat, mult, *angstat;
- int i, j, nangles, first, last;
- gmx_bool bAver, bRb, bPeriodic,
- bFrac, /* calculate fraction too? */
- bTrans, /* worry about transtions too? */
- bCorr; /* correlation function ? */
- double tfrac = 0;
- char title[256];
- real **dih = nullptr; /* mega array with all dih. angles at all times*/
- real *time, *trans_frac, *aver_angle;
- t_filenm fnm[] = {
- { efTRX, "-f", nullptr, ffREAD },
- { efNDX, nullptr, "angle", ffREAD },
- { efXVG, "-od", "angdist", ffWRITE },
- { efXVG, "-ov", "angaver", ffOPTWR },
- { efXVG, "-of", "dihfrac", ffOPTWR },
- { efXVG, "-ot", "dihtrans", ffOPTWR },
- { efXVG, "-oh", "trhisto", ffOPTWR },
- { efXVG, "-oc", "dihcorr", ffOPTWR },
- { efTRR, "-or", nullptr, ffOPTWR }
- };
+ FILE* out;
+ real dt;
+ int isize;
+ int* index;
+ char* grpname;
+ real maxang, S2, norm_fac, maxstat;
+ unsigned long mode;
+ int nframes, maxangstat, mult, *angstat;
+ int i, j, nangles, first, last;
+ gmx_bool bAver, bRb, bPeriodic, bFrac, /* calculate fraction too? */
+ bTrans, /* worry about transtions too? */
+ bCorr; /* correlation function ? */
- real aver, aver2, aversig; /* fraction trans dihedrals */
+ double tfrac = 0;
+ char title[256];
+ real** dih = nullptr; /* mega array with all dih. angles at all times*/
+ real * time, *trans_frac, *aver_angle;
+ t_filenm fnm[] = { { efTRX, "-f", nullptr, ffREAD }, { efNDX, nullptr, "angle", ffREAD },
+ { efXVG, "-od", "angdist", ffWRITE }, { efXVG, "-ov", "angaver", ffOPTWR },
+ { efXVG, "-of", "dihfrac", ffOPTWR }, { efXVG, "-ot", "dihtrans", ffOPTWR },
+ { efXVG, "-oh", "trhisto", ffOPTWR }, { efXVG, "-oc", "dihcorr", ffOPTWR },
+ { efTRR, "-or", nullptr, ffOPTWR } };
#define NFILE asize(fnm)
- int npargs;
- t_pargs *ppa;
- gmx_output_env_t *oenv;
+ int npargs;
+ t_pargs* ppa;
+ gmx_output_env_t* oenv;
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
- &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, NFILE, fnm, npargs, ppa,
+ asize(desc), desc, asize(bugs), bugs, &oenv))
{
sfree(ppa);
return 0;
maxang = 360.0;
bRb = FALSE;
- GMX_RELEASE_ASSERT(opt[0] != nullptr, "Internal option inconsistency; opt[0]==NULL after processing");
+ GMX_RELEASE_ASSERT(opt[0] != nullptr,
+ "Internal option inconsistency; opt[0]==NULL after processing");
switch (opt[0][0])
{
mult = 3;
maxang = 180.0;
break;
- case 'd':
- break;
- case 'i':
- break;
- case 'r':
- bRb = TRUE;
- break;
+ case 'd': break;
+ case 'i': break;
+ case 'r': bRb = TRUE; break;
}
if (opt2bSet("-or", NFILE, fnm))
}
/* Calculate bin size */
- maxangstat = gmx::roundToInt(maxang/binwidth);
- binwidth = maxang/maxangstat;
+ maxangstat = gmx::roundToInt(maxang / binwidth);
+ binwidth = maxang / maxangstat;
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
- nangles = isize/mult;
+ nangles = isize / mult;
if ((isize % mult) != 0)
{
- gmx_fatal(FARGS, "number of index elements not multiple of %d, "
+ gmx_fatal(FARGS,
+ "number of index elements not multiple of %d, "
"these can not be %s\n",
mult, (mult == 3) ? "angle triplets" : "dihedral quadruplets");
}
if (bFrac && !bRb)
{
- fprintf(stderr, "Warning:"
+ fprintf(stderr,
+ "Warning:"
" calculating fractions as defined in this program\n"
"makes sense for Ryckaert Bellemans dihs. only. Ignoring -of\n\n");
bFrac = FALSE;
}
- if ( (bTrans || bFrac || bCorr) && mult == 3)
+ if ((bTrans || bFrac || bCorr) && mult == 3)
{
- gmx_fatal(FARGS, "Can only do transition, fraction or correlation\n"
+ gmx_fatal(FARGS,
+ "Can only do transition, fraction or correlation\n"
"on dihedrals. Select -d\n");
}
* We need to know the nr of frames so we can allocate memory for an array
* with all dihedral angles at all timesteps. Works for me.
*/
- if (bTrans || bCorr || bALL || opt2bSet("-or", NFILE, fnm))
+ if (bTrans || bCorr || bALL || opt2bSet("-or", NFILE, fnm))
{
snew(dih, nangles);
}
snew(angstat, maxangstat);
read_ang_dih(ftp2fn(efTRX, NFILE, fnm), (mult == 3),
- bALL || bCorr || bTrans || opt2bSet("-or", NFILE, fnm),
- bRb, bPBC, maxangstat, angstat,
- &nframes, &time, isize, index, &trans_frac, &aver_angle, dih,
- oenv);
+ bALL || bCorr || bTrans || opt2bSet("-or", NFILE, fnm), bRb, bPBC, maxangstat,
+ angstat, &nframes, &time, isize, index, &trans_frac, &aver_angle, dih, oenv);
- dt = (time[nframes-1]-time[0])/(nframes-1);
+ dt = (time[nframes - 1] - time[0]) / (nframes - 1);
if (bAver)
{
sprintf(title, "Average Angle: %s", grpname);
- out = xvgropen(opt2fn("-ov", NFILE, fnm),
- title, "Time (ps)", "Angle (degrees)", oenv);
+ out = xvgropen(opt2fn("-ov", NFILE, fnm), title, "Time (ps)", "Angle (degrees)", oenv);
for (i = 0; (i < nframes); i++)
{
- fprintf(out, "%10.5f %8.3f", time[i], aver_angle[i]*RAD2DEG);
+ fprintf(out, "%10.5f %8.3f", time[i], aver_angle[i] * RAD2DEG);
if (bALL)
{
for (j = 0; (j < nangles); j++)
if (bPBC)
{
real dd = dih[j][i];
- fprintf(out, " %8.3f", std::atan2(std::sin(dd), std::cos(dd))*RAD2DEG);
+ fprintf(out, " %8.3f", std::atan2(std::sin(dd), std::cos(dd)) * RAD2DEG);
}
else
{
- fprintf(out, " %8.3f", dih[j][i]*RAD2DEG);
+ fprintf(out, " %8.3f", dih[j][i] * RAD2DEG);
}
}
}
if (bFrac)
{
sprintf(title, "Trans fraction: %s", grpname);
- out = xvgropen(opt2fn("-of", NFILE, fnm),
- title, "Time (ps)", "Fraction", oenv);
+ out = xvgropen(opt2fn("-of", NFILE, fnm), title, "Time (ps)", "Fraction", oenv);
tfrac = 0.0;
for (i = 0; (i < nframes); i++)
{
if (bTrans)
{
- ana_dih_trans(opt2fn("-ot", NFILE, fnm), opt2fn("-oh", NFILE, fnm),
- dih, nframes, nangles, grpname, time, bRb, oenv);
+ ana_dih_trans(opt2fn("-ot", NFILE, fnm), opt2fn("-oh", NFILE, fnm), dih, nframes, nangles,
+ grpname, time, bRb, oenv);
}
if (bCorr)
if (bChandler)
{
- real dval, sixty = DEG2RAD*60;
+ real dval, sixty = DEG2RAD * 60;
gmx_bool bTest;
for (i = 0; (i < nangles); i++)
}
if (bTest)
{
- dih[i][j] = dval-tfrac;
+ dih[i][j] = dval - tfrac;
}
else
{
{
mode = eacCos;
}
- do_autocorr(opt2fn("-oc", NFILE, fnm), oenv,
- "Dihedral Autocorrelation Function",
+ do_autocorr(opt2fn("-oc", NFILE, fnm), oenv, "Dihedral Autocorrelation Function",
nframes, nangles, dih, dt, mode, bAverCorr);
}
}
/* Determine the non-zero part of the distribution */
- for (first = 0; (first < maxangstat-1) && (angstat[first+1] == 0); first++)
- {
- ;
- }
- for (last = maxangstat-1; (last > 0) && (angstat[last-1] == 0); last--)
- {
- ;
- }
+ for (first = 0; (first < maxangstat - 1) && (angstat[first + 1] == 0); first++) {}
+ for (last = maxangstat - 1; (last > 0) && (angstat[last - 1] == 0); last--) {}
- aver = aver2 = 0;
- for (i = 0; (i < nframes); i++)
- {
- aver += RAD2DEG * aver_angle[i];
- aver2 += gmx::square(RAD2DEG * aver_angle[i]);
- double aver = 0;
- printf("Found points in the range from %d to %d (max %d)\n",
- first, last, maxangstat);
- if (bTrans || bCorr || bALL || opt2bSet("-or", NFILE, fnm))
- { /* It's better to re-calculate Std. Dev per sample */
++ double aver = 0;
++ printf("Found points in the range from %d to %d (max %d)\n", first, last, maxangstat);
++ if (bTrans || bCorr || bALL || opt2bSet("-or", NFILE, fnm))
++ { /* It's better to re-calculate Std. Dev per sample */
+ real b_aver = aver_angle[0];
+ real b = dih[0][0];
+ real delta;
+ for (int i = 0; (i < nframes); i++)
+ {
- delta = correctRadianAngleRange(aver_angle[i] - b_aver);
++ delta = correctRadianAngleRange(aver_angle[i] - b_aver);
+ b_aver += delta;
- aver += b_aver;
++ aver += b_aver;
+ for (int j = 0; (j < nangles); j++)
+ {
- delta = correctRadianAngleRange(dih[j][i] - b);
- b += delta;
++ delta = correctRadianAngleRange(dih[j][i] - b);
++ b += delta;
+ }
+ }
+ }
+ else
- { /* Incorrect for Std. Dev. */
++ { /* Incorrect for Std. Dev. */
+ real delta, b_aver = aver_angle[0];
+ for (i = 0; (i < nframes); i++)
+ {
- delta = correctRadianAngleRange(aver_angle[i] - b_aver);
++ delta = correctRadianAngleRange(aver_angle[i] - b_aver);
+ b_aver += delta;
- aver += b_aver;
++ aver += b_aver;
+ }
}
- aver /= nframes;
+ aver /= nframes;
- aver2 /= nframes;
- aversig = std::sqrt(aver2 - gmx::square(aver));
- printf("Found points in the range from %d to %d (max %d)\n", first, last, maxangstat);
- printf(" < angle > = %g\n", aver);
- printf("< angle^2 > = %g\n", aver2);
- printf("Std. Dev. = %g\n", aversig);
+ double aversig = correctRadianAngleRange(aver);
+ aversig *= RAD2DEG;
- aver *= RAD2DEG;
++ aver *= RAD2DEG;
+ printf(" < angle > = %g\n", aversig);
if (mult == 3)
{
fprintf(stderr, "Order parameter S^2 = %g\n", S2);
}
- bPeriodic = (mult == 4) && (first == 0) && (last == maxangstat-1);
+ bPeriodic = (mult == 4) && (first == 0) && (last == maxangstat - 1);
out = xvgropen(opt2fn("-od", NFILE, fnm), title, "Degrees", "", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(out, "@ subtitle \"average angle: %g\\So\\N\"\n", aver);
}
- norm_fac = 1.0/(nangles*nframes*binwidth);
+ norm_fac = 1.0 / (nangles * nframes * binwidth);
if (bPeriodic)
{
maxstat = 0;
for (i = first; (i <= last); i++)
{
- maxstat = std::max(maxstat, angstat[i]*norm_fac);
+ maxstat = std::max(maxstat, angstat[i] * norm_fac);
}
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(out, "@ world xmin -180\n");
fprintf(out, "@ world xmax 180\n");
fprintf(out, "@ world ymin 0\n");
- fprintf(out, "@ world ymax %g\n", maxstat*1.05);
+ fprintf(out, "@ world ymax %g\n", maxstat * 1.05);
fprintf(out, "@ xaxis tick major 60\n");
fprintf(out, "@ xaxis tick minor 30\n");
fprintf(out, "@ yaxis tick major 0.005\n");
}
for (i = first; (i <= last); i++)
{
- fprintf(out, "%10g %10f\n", i*binwidth+180.0-maxang, angstat[i]*norm_fac);
+ fprintf(out, "%10g %10f\n", i * binwidth + 180.0 - maxang, angstat[i] * norm_fac);
}
if (bPeriodic)
{
/* print first bin again as last one */
- fprintf(out, "%10g %10f\n", 180.0, angstat[0]*norm_fac);
+ fprintf(out, "%10g %10f\n", 180.0, angstat[0] * norm_fac);
}
xvgrclose(out);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013-2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <algorithm>
+#include <memory>
#include "gromacs/commandline/filenm.h"
-#include "gromacs/compat/make_unique.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/ewald/ewald.h"
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
+#include "gromacs/ewald/pme_pp_comm_gpu.h"
#include "gromacs/fileio/filetypes.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nonbonded/nonbonded.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/hardware/hw_info.h"
-#include "gromacs/listed-forces/gpubonded.h"
-#include "gromacs/listed-forces/manage-threading.h"
-#include "gromacs/listed-forces/pairs.h"
+#include "gromacs/listed_forces/gpubonded.h"
+#include "gromacs/listed_forces/manage_threading.h"
+#include "gromacs/listed_forces/pairs.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/dispersioncorrection.h"
#include "gromacs/mdlib/force.h"
-#include "gromacs/mdlib/forcerec-threading.h"
+#include "gromacs/mdlib/forcerec_threading.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/md_support.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/mdlib/nbnxn_atomdata.h"
-#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
-#include "gromacs/mdlib/nbnxn_grid.h"
-#include "gromacs/mdlib/nbnxn_internal.h"
-#include "gromacs/mdlib/nbnxn_search.h"
-#include "gromacs/mdlib/nbnxn_simd.h"
-#include "gromacs/mdlib/nbnxn_tuning.h"
-#include "gromacs/mdlib/nbnxn_util.h"
-#include "gromacs/mdlib/ns.h"
#include "gromacs/mdlib/qmmm.h"
#include "gromacs/mdlib/rf_util.h"
-#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdlib/wall.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/iforceprovider.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/nbnxm/gpu_data_mgmt.h"
+#include "gromacs/nbnxm/nbnxm.h"
+#include "gromacs/nbnxm/nbnxm_geometry.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/simd/simd.h"
#include "gromacs/tables/forcetable.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"
-#include "nbnxn_gpu_jit_support.h"
+/*! \brief environment variable to enable GPU P2P communication */
+static const bool c_enableGpuPmePpComms =
+ (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
-t_forcerec *mk_forcerec()
+static real* mk_nbfp(const gmx_ffparams_t* idef, gmx_bool bBHAM)
{
- t_forcerec *fr;
-
- snew(fr, 1);
-
- return fr;
-}
-
-static real *mk_nbfp(const gmx_ffparams_t *idef, gmx_bool bBHAM)
-{
- real *nbfp;
+ real* nbfp;
int i, j, k, atnr;
atnr = idef->atnr;
if (bBHAM)
{
- snew(nbfp, 3*atnr*atnr);
+ snew(nbfp, 3 * atnr * atnr);
for (i = k = 0; (i < atnr); i++)
{
for (j = 0; (j < atnr); j++, k++)
BHAMA(nbfp, atnr, i, j) = idef->iparams[k].bham.a;
BHAMB(nbfp, atnr, i, j) = idef->iparams[k].bham.b;
/* nbfp now includes the 6.0 derivative prefactor */
- BHAMC(nbfp, atnr, i, j) = idef->iparams[k].bham.c*6.0;
+ BHAMC(nbfp, atnr, i, j) = idef->iparams[k].bham.c * 6.0;
}
}
}
else
{
- snew(nbfp, 2*atnr*atnr);
+ snew(nbfp, 2 * atnr * atnr);
for (i = k = 0; (i < atnr); i++)
{
for (j = 0; (j < atnr); j++, k++)
{
/* nbfp now includes the 6.0/12.0 derivative prefactors */
- C6(nbfp, atnr, i, j) = idef->iparams[k].lj.c6*6.0;
- C12(nbfp, atnr, i, j) = idef->iparams[k].lj.c12*12.0;
+ C6(nbfp, atnr, i, j) = idef->iparams[k].lj.c6 * 6.0;
+ C12(nbfp, atnr, i, j) = idef->iparams[k].lj.c12 * 12.0;
}
}
}
return nbfp;
}
-static real *make_ljpme_c6grid(const gmx_ffparams_t *idef, t_forcerec *fr)
+static real* make_ljpme_c6grid(const gmx_ffparams_t* idef, t_forcerec* fr)
{
- int i, j, k, atnr;
- real c6, c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
- real *grid;
+ int i, j, k, atnr;
+ real c6, c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
+ real* grid;
/* For LJ-PME simulations, we correct the energies with the reciprocal space
* inside of the cut-off. To do this the non-bonded kernels needs to have
*/
atnr = idef->atnr;
- snew(grid, 2*atnr*atnr);
+ snew(grid, 2 * atnr * atnr);
for (i = k = 0; (i < atnr); i++)
{
for (j = 0; (j < atnr); j++, k++)
{
- c6i = idef->iparams[i*(atnr+1)].lj.c6;
- c12i = idef->iparams[i*(atnr+1)].lj.c12;
- c6j = idef->iparams[j*(atnr+1)].lj.c6;
- c12j = idef->iparams[j*(atnr+1)].lj.c12;
+ c6i = idef->iparams[i * (atnr + 1)].lj.c6;
+ c12i = idef->iparams[i * (atnr + 1)].lj.c12;
+ c6j = idef->iparams[j * (atnr + 1)].lj.c6;
+ c12j = idef->iparams[j * (atnr + 1)].lj.c12;
c6 = std::sqrt(c6i * c6j);
- if (fr->ljpme_combination_rule == eljpmeLB
- && !gmx_numzero(c6) && !gmx_numzero(c12i) && !gmx_numzero(c12j))
+ if (fr->ljpme_combination_rule == eljpmeLB && !gmx_numzero(c6) && !gmx_numzero(c12i)
+ && !gmx_numzero(c12j))
{
sigmai = gmx::sixthroot(c12i / c6i);
sigmaj = gmx::sixthroot(c12j / c6j);
epsi = c6i * c6i / c12i;
epsj = c6j * c6j / c12j;
- c6 = std::sqrt(epsi * epsj) * gmx::power6(0.5*(sigmai+sigmaj));
+ c6 = std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
}
/* Store the elements at the same relative positions as C6 in nbfp in order
* to simplify access in the kernels
*/
- grid[2*(atnr*i+j)] = c6*6.0;
+ grid[2 * (atnr * i + j)] = c6 * 6.0;
}
}
return grid;
}
-static real *mk_nbfp_combination_rule(const gmx_ffparams_t *idef, int comb_rule)
-{
- real *nbfp;
- int i, j, atnr;
- real c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
- real c6, c12;
-
- atnr = idef->atnr;
- snew(nbfp, 2*atnr*atnr);
- for (i = 0; i < atnr; ++i)
- {
- for (j = 0; j < atnr; ++j)
- {
- c6i = idef->iparams[i*(atnr+1)].lj.c6;
- c12i = idef->iparams[i*(atnr+1)].lj.c12;
- c6j = idef->iparams[j*(atnr+1)].lj.c6;
- c12j = idef->iparams[j*(atnr+1)].lj.c12;
- c6 = std::sqrt(c6i * c6j);
- c12 = std::sqrt(c12i * c12j);
- if (comb_rule == eCOMB_ARITHMETIC
- && !gmx_numzero(c6) && !gmx_numzero(c12))
- {
- sigmai = gmx::sixthroot(c12i / c6i);
- sigmaj = gmx::sixthroot(c12j / c6j);
- epsi = c6i * c6i / c12i;
- epsj = c6j * c6j / c12j;
- c6 = std::sqrt(epsi * epsj) * gmx::power6(0.5*(sigmai+sigmaj));
- c12 = std::sqrt(epsi * epsj) * gmx::power12(0.5*(sigmai+sigmaj));
- }
- C6(nbfp, atnr, i, j) = c6*6.0;
- C12(nbfp, atnr, i, j) = c12*12.0;
- }
- }
- return nbfp;
-}
-
-/* This routine sets fr->solvent_opt to the most common solvent in the
- * system, e.g. esolSPC or esolTIP4P. It will also mark each charge group in
- * the fr->solvent_type array with the correct type (or esolNO).
- *
- * Charge groups that fulfill the conditions but are not identical to the
- * most common one will be marked as esolNO in the solvent_type array.
- *
- * TIP3p is identical to SPC for these purposes, so we call it
- * SPC in the arrays (Apologies to Bill Jorgensen ;-)
- *
- * NOTE: QM particle should not
- * become an optimized solvent. Not even if there is only one charge
- * group in the Qm
- */
-
-typedef struct
-{
- int model;
- int count;
- int vdwtype[4];
- real charge[4];
-} solvent_parameters_t;
-
-static void
-check_solvent_cg(const gmx_moltype_t *molt,
- int cg0,
- int nmol,
- const unsigned char *qm_grpnr,
- const t_grps *qm_grps,
- t_forcerec * fr,
- int *n_solvent_parameters,
- solvent_parameters_t **solvent_parameters_p,
- int cginfo,
- int *cg_sp)
-{
- t_atom *atom;
- int j, k;
- int j0, j1, nj;
- gmx_bool perturbed;
- gmx_bool has_vdw[4];
- gmx_bool match;
- real tmp_charge[4] = { 0.0 }; /* init to zero to make gcc4.8 happy */
- int tmp_vdwtype[4] = { 0 }; /* init to zero to make gcc4.8 happy */
- int tjA;
- gmx_bool qm;
- solvent_parameters_t *solvent_parameters;
-
- /* We use a list with parameters for each solvent type.
- * Every time we discover a new molecule that fulfills the basic
- * conditions for a solvent we compare with the previous entries
- * in these lists. If the parameters are the same we just increment
- * the counter for that type, and otherwise we create a new type
- * based on the current molecule.
- *
- * Once we've finished going through all molecules we check which
- * solvent is most common, and mark all those molecules while we
- * clear the flag on all others.
- */
-
- solvent_parameters = *solvent_parameters_p;
-
- /* Mark the cg first as non optimized */
- *cg_sp = -1;
-
- /* Check if this cg has no exclusions with atoms in other charge groups
- * and all atoms inside the charge group excluded.
- * We only have 3 or 4 atom solvent loops.
- */
- if (GET_CGINFO_EXCL_INTER(cginfo) ||
- !GET_CGINFO_EXCL_INTRA(cginfo))
- {
- return;
- }
-
- /* Get the indices of the first atom in this charge group */
- j0 = molt->cgs.index[cg0];
- j1 = molt->cgs.index[cg0+1];
-
- /* Number of atoms in our molecule */
- nj = j1 - j0;
-
- if (debug)
- {
- fprintf(debug,
- "Moltype '%s': there are %d atoms in this charge group\n",
- *molt->name, nj);
- }
-
- /* Check if it could be an SPC (3 atoms) or TIP4p (4) water,
- * otherwise skip it.
- */
- if (nj < 3 || nj > 4)
- {
- return;
- }
-
- /* Check if we are doing QM on this group */
- qm = FALSE;
- if (qm_grpnr != nullptr)
- {
- for (j = j0; j < j1 && !qm; j++)
- {
- qm = (qm_grpnr[j] < qm_grps->nr - 1);
- }
- }
- /* Cannot use solvent optimization with QM */
- if (qm)
- {
- return;
- }
-
- atom = molt->atoms.atom;
-
- /* Still looks like a solvent, time to check parameters */
-
- /* If it is perturbed (free energy) we can't use the solvent loops,
- * so then we just skip to the next molecule.
- */
- perturbed = FALSE;
-
- for (j = j0; j < j1 && !perturbed; j++)
- {
- perturbed = PERTURBED(atom[j]);
- }
-
- if (perturbed)
- {
- return;
- }
-
- /* Now it's only a question if the VdW and charge parameters
- * are OK. Before doing the check we compare and see if they are
- * identical to a possible previous solvent type.
- * First we assign the current types and charges.
- */
- for (j = 0; j < nj; j++)
- {
- tmp_vdwtype[j] = atom[j0+j].type;
- tmp_charge[j] = atom[j0+j].q;
- }
-
- /* Does it match any previous solvent type? */
- for (k = 0; k < *n_solvent_parameters; k++)
- {
- match = TRUE;
-
-
- /* We can only match SPC with 3 atoms and TIP4p with 4 atoms */
- if ( (solvent_parameters[k].model == esolSPC && nj != 3) ||
- (solvent_parameters[k].model == esolTIP4P && nj != 4) )
- {
- match = FALSE;
- }
-
- /* Check that types & charges match for all atoms in molecule */
- for (j = 0; j < nj && match; j++)
- {
- if (tmp_vdwtype[j] != solvent_parameters[k].vdwtype[j])
- {
- match = FALSE;
- }
- if (tmp_charge[j] != solvent_parameters[k].charge[j])
- {
- match = FALSE;
- }
- }
- if (match)
- {
- /* Congratulations! We have a matched solvent.
- * Flag it with this type for later processing.
- */
- *cg_sp = k;
- solvent_parameters[k].count += nmol;
-
- /* We are done with this charge group */
- return;
- }
- }
-
- /* If we get here, we have a tentative new solvent type.
- * Before we add it we must check that it fulfills the requirements
- * of the solvent optimized loops. First determine which atoms have
- * VdW interactions.
- */
- for (j = 0; j < nj; j++)
- {
- has_vdw[j] = FALSE;
- tjA = tmp_vdwtype[j];
-
- /* Go through all other tpes and see if any have non-zero
- * VdW parameters when combined with this one.
- */
- for (k = 0; k < fr->ntype && (!has_vdw[j]); k++)
- {
- /* We already checked that the atoms weren't perturbed,
- * so we only need to check state A now.
- */
- if (fr->bBHAM)
- {
- has_vdw[j] = (has_vdw[j] ||
- (BHAMA(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
- (BHAMB(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
- (BHAMC(fr->nbfp, fr->ntype, tjA, k) != 0.0));
- }
- else
- {
- /* Standard LJ */
- has_vdw[j] = (has_vdw[j] ||
- (C6(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
- (C12(fr->nbfp, fr->ntype, tjA, k) != 0.0));
- }
- }
- }
-
- /* Now we know all we need to make the final check and assignment. */
- if (nj == 3)
- {
- /* So, is it an SPC?
- * For this we require thatn all atoms have charge,
- * the charges on atom 2 & 3 should be the same, and only
- * atom 1 might have VdW.
- */
- if (!has_vdw[1] &&
- !has_vdw[2] &&
- tmp_charge[0] != 0 &&
- tmp_charge[1] != 0 &&
- tmp_charge[2] == tmp_charge[1])
- {
- srenew(solvent_parameters, *n_solvent_parameters+1);
- solvent_parameters[*n_solvent_parameters].model = esolSPC;
- solvent_parameters[*n_solvent_parameters].count = nmol;
- for (k = 0; k < 3; k++)
- {
- solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
- solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
- }
-
- *cg_sp = *n_solvent_parameters;
- (*n_solvent_parameters)++;
- }
- }
- else if (nj == 4)
- {
- /* Or could it be a TIP4P?
- * For this we require thatn atoms 2,3,4 have charge, but not atom 1.
- * Only atom 1 mght have VdW.
- */
- if (!has_vdw[1] &&
- !has_vdw[2] &&
- !has_vdw[3] &&
- tmp_charge[0] == 0 &&
- tmp_charge[1] != 0 &&
- tmp_charge[2] == tmp_charge[1] &&
- tmp_charge[3] != 0)
- {
- srenew(solvent_parameters, *n_solvent_parameters+1);
- solvent_parameters[*n_solvent_parameters].model = esolTIP4P;
- solvent_parameters[*n_solvent_parameters].count = nmol;
- for (k = 0; k < 4; k++)
- {
- solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
- solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
- }
-
- *cg_sp = *n_solvent_parameters;
- (*n_solvent_parameters)++;
- }
- }
-
- *solvent_parameters_p = solvent_parameters;
-}
-
-static void
-check_solvent(FILE * fp,
- const gmx_mtop_t * mtop,
- t_forcerec * fr,
- cginfo_mb_t *cginfo_mb)
+enum
{
- const t_block * cgs;
- const gmx_moltype_t *molt;
- int mol, cg_mol, at_offset, am, cgm, i, nmol_ch, nmol;
- int n_solvent_parameters;
- solvent_parameters_t *solvent_parameters;
- int **cg_sp;
- int bestsp, bestsol;
-
- if (debug)
- {
- fprintf(debug, "Going to determine what solvent types we have.\n");
- }
-
- n_solvent_parameters = 0;
- solvent_parameters = nullptr;
- /* Allocate temporary array for solvent type */
- snew(cg_sp, mtop->molblock.size());
-
- at_offset = 0;
- for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
- {
- molt = &mtop->moltype[mtop->molblock[mb].type];
- cgs = &molt->cgs;
- /* Here we have to loop over all individual molecules
- * because we need to check for QMMM particles.
- */
- snew(cg_sp[mb], cginfo_mb[mb].cg_mod);
- nmol_ch = cginfo_mb[mb].cg_mod/cgs->nr;
- nmol = mtop->molblock[mb].nmol/nmol_ch;
- for (mol = 0; mol < nmol_ch; mol++)
- {
- cgm = mol*cgs->nr;
- am = mol*cgs->index[cgs->nr];
- for (cg_mol = 0; cg_mol < cgs->nr; cg_mol++)
- {
- check_solvent_cg(molt, cg_mol, nmol,
- mtop->groups.grpnr[egcQMMM] ?
- mtop->groups.grpnr[egcQMMM]+at_offset+am : nullptr,
- &mtop->groups.grps[egcQMMM],
- fr,
- &n_solvent_parameters, &solvent_parameters,
- cginfo_mb[mb].cginfo[cgm+cg_mol],
- &cg_sp[mb][cgm+cg_mol]);
- }
- }
- at_offset += cgs->index[cgs->nr];
- }
-
- /* Puh! We finished going through all charge groups.
- * Now find the most common solvent model.
- */
-
- /* Most common solvent this far */
- bestsp = -2;
- for (i = 0; i < n_solvent_parameters; i++)
- {
- if (bestsp == -2 ||
- solvent_parameters[i].count > solvent_parameters[bestsp].count)
- {
- bestsp = i;
- }
- }
-
- if (bestsp >= 0)
- {
- bestsol = solvent_parameters[bestsp].model;
- }
- else
- {
- bestsol = esolNO;
- }
-
- fr->nWatMol = 0;
- for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
- {
- cgs = &mtop->moltype[mtop->molblock[mb].type].cgs;
- nmol = (mtop->molblock[mb].nmol*cgs->nr)/cginfo_mb[mb].cg_mod;
- for (i = 0; i < cginfo_mb[mb].cg_mod; i++)
- {
- if (cg_sp[mb][i] == bestsp)
- {
- SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], bestsol);
- fr->nWatMol += nmol;
- }
- else
- {
- SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], esolNO);
- }
- }
- sfree(cg_sp[mb]);
- }
- sfree(cg_sp);
-
- if (bestsol != esolNO && fp != nullptr)
- {
- fprintf(fp, "\nEnabling %s-like water optimization for %d molecules.\n\n",
- esol_names[bestsol],
- solvent_parameters[bestsp].count);
- }
-
- sfree(solvent_parameters);
- fr->solvent_opt = bestsol;
-}
-
-enum {
- acNONE = 0, acCONSTRAINT, acSETTLE
+ acNONE = 0,
+ acCONSTRAINT,
+ acSETTLE
};
-static cginfo_mb_t *init_cginfo_mb(FILE *fplog, const gmx_mtop_t *mtop,
- t_forcerec *fr, gmx_bool bNoSolvOpt,
- gmx_bool *bFEP_NonBonded,
- gmx_bool *bExcl_IntraCGAll_InterCGNone)
+static cginfo_mb_t* init_cginfo_mb(const gmx_mtop_t* mtop, const t_forcerec* fr, gmx_bool* bFEP_NonBonded)
{
- const t_block *cgs;
- const t_blocka *excl;
- const gmx_moltype_t *molt;
- const gmx_molblock_t *molb;
- cginfo_mb_t *cginfo_mb;
- gmx_bool *type_VDW;
- int *cginfo;
- int cg_offset, a_offset;
- int m, cg, a0, a1, gid, ai, j, aj, excl_nalloc;
- int *a_con;
- int ftype;
- int ia;
- gmx_bool bId, *bExcl, bExclIntraAll, bExclInter, bHaveVDW, bHaveQ, bHavePerturbedAtoms;
+ cginfo_mb_t* cginfo_mb;
+ gmx_bool* type_VDW;
+ int* cginfo;
+ int* a_con;
snew(cginfo_mb, mtop->molblock.size());
snew(type_VDW, fr->ntype);
- for (ai = 0; ai < fr->ntype; ai++)
+ for (int ai = 0; ai < fr->ntype; ai++)
{
type_VDW[ai] = FALSE;
- for (j = 0; j < fr->ntype; j++)
+ for (int j = 0; j < fr->ntype; j++)
{
- type_VDW[ai] = type_VDW[ai] ||
- fr->bBHAM ||
- C6(fr->nbfp, fr->ntype, ai, j) != 0 ||
- C12(fr->nbfp, fr->ntype, ai, j) != 0;
+ type_VDW[ai] = type_VDW[ai] || fr->bBHAM || C6(fr->nbfp, fr->ntype, ai, j) != 0
+ || C12(fr->nbfp, fr->ntype, ai, j) != 0;
}
}
- *bFEP_NonBonded = FALSE;
- *bExcl_IntraCGAll_InterCGNone = TRUE;
+ *bFEP_NonBonded = FALSE;
- excl_nalloc = 10;
- snew(bExcl, excl_nalloc);
- cg_offset = 0;
- a_offset = 0;
+ int a_offset = 0;
for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
{
- molb = &mtop->molblock[mb];
- molt = &mtop->moltype[molb->type];
- cgs = &molt->cgs;
- excl = &molt->excls;
+ const gmx_molblock_t& molb = mtop->molblock[mb];
+ const gmx_moltype_t& molt = mtop->moltype[molb.type];
+ const t_blocka& excl = molt.excls;
/* Check if the cginfo is identical for all molecules in this block.
* If so, we only need an array of the size of one molecule.
* Otherwise we make an array of #mol times #cgs per molecule.
*/
- bId = TRUE;
- for (m = 0; m < molb->nmol; m++)
+ gmx_bool bId = TRUE;
+ for (int m = 0; m < molb.nmol; m++)
{
- int am = m*cgs->index[cgs->nr];
- for (cg = 0; cg < cgs->nr; cg++)
+ const int am = m * molt.atoms.nr;
+ for (int a = 0; a < molt.atoms.nr; a++)
{
- a0 = cgs->index[cg];
- a1 = cgs->index[cg+1];
- if (getGroupType(&mtop->groups, egcENER, a_offset+am+a0) !=
- getGroupType(&mtop->groups, egcENER, a_offset +a0))
+ if (getGroupType(mtop->groups, SimulationAtomGroupType::QuantumMechanics, a_offset + am + a)
+ != getGroupType(mtop->groups, SimulationAtomGroupType::QuantumMechanics, a_offset + a))
{
bId = FALSE;
}
- if (mtop->groups.grpnr[egcQMMM] != nullptr)
+ if (!mtop->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics].empty())
{
- for (ai = a0; ai < a1; ai++)
+ if (mtop->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][a_offset + am + a]
+ != mtop->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][a_offset + a])
{
- if (mtop->groups.grpnr[egcQMMM][a_offset+am+ai] !=
- mtop->groups.grpnr[egcQMMM][a_offset +ai])
- {
- bId = FALSE;
- }
+ bId = FALSE;
}
}
}
}
- cginfo_mb[mb].cg_start = cg_offset;
- cginfo_mb[mb].cg_end = cg_offset + molb->nmol*cgs->nr;
- cginfo_mb[mb].cg_mod = (bId ? 1 : molb->nmol)*cgs->nr;
+ cginfo_mb[mb].cg_start = a_offset;
+ cginfo_mb[mb].cg_end = a_offset + molb.nmol * molt.atoms.nr;
+ cginfo_mb[mb].cg_mod = (bId ? 1 : molb.nmol) * molt.atoms.nr;
snew(cginfo_mb[mb].cginfo, cginfo_mb[mb].cg_mod);
cginfo = cginfo_mb[mb].cginfo;
/* Set constraints flags for constrained atoms */
- snew(a_con, molt->atoms.nr);
- for (ftype = 0; ftype < F_NRE; ftype++)
+ snew(a_con, molt.atoms.nr);
+ for (int ftype = 0; ftype < F_NRE; ftype++)
{
if (interaction_function[ftype].flags & IF_CONSTRAINT)
{
- int nral;
-
- nral = NRAL(ftype);
- for (ia = 0; ia < molt->ilist[ftype].size(); ia += 1+nral)
+ const int nral = NRAL(ftype);
+ for (int ia = 0; ia < molt.ilist[ftype].size(); ia += 1 + nral)
{
int a;
for (a = 0; a < nral; a++)
{
- a_con[molt->ilist[ftype].iatoms[ia+1+a]] =
- (ftype == F_SETTLE ? acSETTLE : acCONSTRAINT);
+ a_con[molt.ilist[ftype].iatoms[ia + 1 + a]] =
+ (ftype == F_SETTLE ? acSETTLE : acCONSTRAINT);
}
}
}
}
- for (m = 0; m < (bId ? 1 : molb->nmol); m++)
+ for (int m = 0; m < (bId ? 1 : molb.nmol); m++)
{
- int cgm = m*cgs->nr;
- int am = m*cgs->index[cgs->nr];
- for (cg = 0; cg < cgs->nr; cg++)
+ const int molculeOffsetInBlock = m * molt.atoms.nr;
+ for (int a = 0; a < molt.atoms.nr; a++)
{
- a0 = cgs->index[cg];
- a1 = cgs->index[cg+1];
+ const t_atom& atom = molt.atoms.atom[a];
+ int& atomInfo = cginfo[molculeOffsetInBlock + a];
/* Store the energy group in cginfo */
- gid = getGroupType(&mtop->groups, egcENER, a_offset+am+a0);
- SET_CGINFO_GID(cginfo[cgm+cg], gid);
+ int gid = getGroupType(mtop->groups, SimulationAtomGroupType::EnergyOutput,
+ a_offset + molculeOffsetInBlock + a);
+ SET_CGINFO_GID(atomInfo, gid);
- /* Check the intra/inter charge group exclusions */
- if (a1-a0 > excl_nalloc)
- {
- excl_nalloc = a1 - a0;
- srenew(bExcl, excl_nalloc);
- }
- /* bExclIntraAll: all intra cg interactions excluded
- * bExclInter: any inter cg interactions excluded
- */
- bExclIntraAll = TRUE;
- bExclInter = FALSE;
- bHaveVDW = FALSE;
- bHaveQ = FALSE;
- bHavePerturbedAtoms = FALSE;
- for (ai = a0; ai < a1; ai++)
- {
- /* Check VDW and electrostatic interactions */
- bHaveVDW = bHaveVDW || (type_VDW[molt->atoms.atom[ai].type] ||
- type_VDW[molt->atoms.atom[ai].typeB]);
- bHaveQ = bHaveQ || (molt->atoms.atom[ai].q != 0 ||
- molt->atoms.atom[ai].qB != 0);
-
- bHavePerturbedAtoms = bHavePerturbedAtoms || (PERTURBED(molt->atoms.atom[ai]) != 0);
-
- /* Clear the exclusion list for atom ai */
- for (aj = a0; aj < a1; aj++)
- {
- bExcl[aj-a0] = FALSE;
- }
- /* Loop over all the exclusions of atom ai */
- for (j = excl->index[ai]; j < excl->index[ai+1]; j++)
- {
- aj = excl->a[j];
- if (aj < a0 || aj >= a1)
- {
- bExclInter = TRUE;
- }
- else
- {
- bExcl[aj-a0] = TRUE;
- }
- }
- /* Check if ai excludes a0 to a1 */
- for (aj = a0; aj < a1; aj++)
- {
- if (!bExcl[aj-a0])
- {
- bExclIntraAll = FALSE;
- }
- }
+ bool bHaveVDW = (type_VDW[atom.type] || type_VDW[atom.typeB]);
+ bool bHaveQ = (atom.q != 0 || atom.qB != 0);
- switch (a_con[ai])
+ bool haveExclusions = false;
+ /* Loop over all the exclusions of atom ai */
+ for (int j = excl.index[a]; j < excl.index[a + 1]; j++)
+ {
+ if (excl.a[j] != a)
{
- case acCONSTRAINT:
- SET_CGINFO_CONSTR(cginfo[cgm+cg]);
- break;
- case acSETTLE:
- SET_CGINFO_SETTLE(cginfo[cgm+cg]);
- break;
- default:
- break;
+ haveExclusions = true;
+ break;
}
}
- if (bExclIntraAll)
- {
- SET_CGINFO_EXCL_INTRA(cginfo[cgm+cg]);
- }
- if (bExclInter)
+
+ switch (a_con[a])
{
- SET_CGINFO_EXCL_INTER(cginfo[cgm+cg]);
+ case acCONSTRAINT: SET_CGINFO_CONSTR(atomInfo); break;
+ case acSETTLE: SET_CGINFO_SETTLE(atomInfo); break;
+ default: break;
}
- if (a1 - a0 > MAX_CHARGEGROUP_SIZE)
+ if (haveExclusions)
{
- /* The size in cginfo is currently only read with DD */
- gmx_fatal(FARGS, "A charge group has size %d which is larger than the limit of %d atoms", a1-a0, MAX_CHARGEGROUP_SIZE);
+ SET_CGINFO_EXCL_INTER(atomInfo);
}
if (bHaveVDW)
{
- SET_CGINFO_HAS_VDW(cginfo[cgm+cg]);
+ SET_CGINFO_HAS_VDW(atomInfo);
}
if (bHaveQ)
{
- SET_CGINFO_HAS_Q(cginfo[cgm+cg]);
+ SET_CGINFO_HAS_Q(atomInfo);
}
- if (bHavePerturbedAtoms && fr->efep != efepNO)
+ if (fr->efep != efepNO && PERTURBED(atom))
{
- SET_CGINFO_FEP(cginfo[cgm+cg]);
+ SET_CGINFO_FEP(atomInfo);
*bFEP_NonBonded = TRUE;
}
- /* Store the charge group size */
- SET_CGINFO_NATOMS(cginfo[cgm+cg], a1-a0);
-
- if (!bExclIntraAll || bExclInter)
- {
- *bExcl_IntraCGAll_InterCGNone = FALSE;
- }
}
}
sfree(a_con);
- cg_offset += molb->nmol*cgs->nr;
- a_offset += molb->nmol*cgs->index[cgs->nr];
+ a_offset += molb.nmol * molt.atoms.nr;
}
sfree(type_VDW);
- sfree(bExcl);
-
- /* the solvent optimizer is called after the QM is initialized,
- * because we don't want to have the QM subsystemto become an
- * optimized solvent
- */
-
- check_solvent(fplog, mtop, fr, cginfo_mb);
-
- if (getenv("GMX_NO_SOLV_OPT"))
- {
- if (fplog)
- {
- fprintf(fplog, "Found environment variable GMX_NO_SOLV_OPT.\n"
- "Disabling all solvent optimization\n");
- }
- fr->solvent_opt = esolNO;
- }
- if (bNoSolvOpt)
- {
- fr->solvent_opt = esolNO;
- }
- if (!fr->solvent_opt)
- {
- for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
- {
- for (cg = 0; cg < cginfo_mb[mb].cg_mod; cg++)
- {
- SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[cg], esolNO);
- }
- }
- }
return cginfo_mb;
}
-static int *cginfo_expand(int nmb, cginfo_mb_t *cgi_mb)
+static std::vector<int> cginfo_expand(const int nmb, const cginfo_mb_t* cgi_mb)
{
- int ncg, mb, cg;
- int *cginfo;
+ const int ncg = cgi_mb[nmb - 1].cg_end;
- ncg = cgi_mb[nmb-1].cg_end;
- snew(cginfo, ncg);
- mb = 0;
- for (cg = 0; cg < ncg; cg++)
+ std::vector<int> cginfo(ncg);
+
+ int mb = 0;
+ for (int cg = 0; cg < ncg; cg++)
{
while (cg >= cgi_mb[mb].cg_end)
{
mb++;
}
- cginfo[cg] =
- cgi_mb[mb].cginfo[(cg - cgi_mb[mb].cg_start) % cgi_mb[mb].cg_mod];
+ cginfo[cg] = cgi_mb[mb].cginfo[(cg - cgi_mb[mb].cg_start) % cgi_mb[mb].cg_mod];
}
return cginfo;
}
-static void done_cginfo_mb(cginfo_mb_t *cginfo_mb, int numMolBlocks)
+static void done_cginfo_mb(cginfo_mb_t* cginfo_mb, int numMolBlocks)
{
if (cginfo_mb == nullptr)
{
/* Sets the sum of charges (squared) and C6 in the system in fr.
* Returns whether the system has a net charge.
*/
-static bool set_chargesum(FILE *log, t_forcerec *fr, const gmx_mtop_t *mtop)
+static bool set_chargesum(FILE* log, t_forcerec* fr, const gmx_mtop_t* mtop)
{
/*This now calculates sum for q and c6*/
- double qsum, q2sum, q, c6sum, c6;
+ double qsum, q2sum, q, c6sum, c6;
- qsum = 0;
- q2sum = 0;
- c6sum = 0;
- for (const gmx_molblock_t &molb : mtop->molblock)
+ qsum = 0;
+ q2sum = 0;
+ c6sum = 0;
+ for (const gmx_molblock_t& molb : mtop->molblock)
{
int nmol = molb.nmol;
- const t_atoms *atoms = &mtop->moltype[molb.type].atoms;
+ const t_atoms* atoms = &mtop->moltype[molb.type].atoms;
for (int i = 0; i < atoms->nr; i++)
{
- q = atoms->atom[i].q;
- qsum += nmol*q;
- q2sum += nmol*q*q;
- c6 = mtop->ffparams.iparams[atoms->atom[i].type*(mtop->ffparams.atnr+1)].lj.c6;
- c6sum += nmol*c6;
+ q = atoms->atom[i].q;
+ qsum += nmol * q;
+ q2sum += nmol * q * q;
+ c6 = mtop->ffparams.iparams[atoms->atom[i].type * (mtop->ffparams.atnr + 1)].lj.c6;
+ c6sum += nmol * c6;
}
}
- fr->qsum[0] = qsum;
- fr->q2sum[0] = q2sum;
- fr->c6sum[0] = c6sum;
+ fr->qsum[0] = qsum;
+ fr->q2sum[0] = q2sum;
+ fr->c6sum[0] = c6sum;
if (fr->efep != efepNO)
{
- qsum = 0;
- q2sum = 0;
- c6sum = 0;
- for (const gmx_molblock_t &molb : mtop->molblock)
+ qsum = 0;
+ q2sum = 0;
+ c6sum = 0;
+ for (const gmx_molblock_t& molb : mtop->molblock)
{
int nmol = molb.nmol;
- const t_atoms *atoms = &mtop->moltype[molb.type].atoms;
+ const t_atoms* atoms = &mtop->moltype[molb.type].atoms;
for (int i = 0; i < atoms->nr; i++)
{
- q = atoms->atom[i].qB;
- qsum += nmol*q;
- q2sum += nmol*q*q;
- c6 = mtop->ffparams.iparams[atoms->atom[i].typeB*(mtop->ffparams.atnr+1)].lj.c6;
- c6sum += nmol*c6;
+ q = atoms->atom[i].qB;
+ qsum += nmol * q;
+ q2sum += nmol * q * q;
+ c6 = mtop->ffparams.iparams[atoms->atom[i].typeB * (mtop->ffparams.atnr + 1)].lj.c6;
+ c6sum += nmol * c6;
}
- fr->qsum[1] = qsum;
- fr->q2sum[1] = q2sum;
- fr->c6sum[1] = c6sum;
+ fr->qsum[1] = qsum;
+ fr->q2sum[1] = q2sum;
+ fr->c6sum[1] = c6sum;
}
}
else
{
- fr->qsum[1] = fr->qsum[0];
- fr->q2sum[1] = fr->q2sum[0];
- fr->c6sum[1] = fr->c6sum[0];
+ fr->qsum[1] = fr->qsum[0];
+ fr->q2sum[1] = fr->q2sum[0];
+ fr->c6sum[1] = fr->c6sum[0];
}
if (log)
{
}
else
{
- fprintf(log, "System total charge, top. A: %.3f top. B: %.3f\n",
- fr->qsum[0], fr->qsum[1]);
+ fprintf(log, "System total charge, top. A: %.3f top. B: %.3f\n", fr->qsum[0], fr->qsum[1]);
}
}
/* A cut-off of 1e-4 is used to catch rounding errors due to ascii input */
- return (std::abs(fr->qsum[0]) > 1e-4 ||
- std::abs(fr->qsum[1]) > 1e-4);
-}
-
-void update_forcerec(t_forcerec *fr, matrix box)
-{
- if (fr->ic->eeltype == eelGRF)
- {
- calc_rffac(nullptr, fr->ic->eeltype, fr->ic->epsilon_r, fr->ic->epsilon_rf,
- fr->ic->rcoulomb, fr->temp, fr->zsquare, box,
- &fr->ic->k_rf, &fr->ic->c_rf);
- }
+ return (std::abs(fr->qsum[0]) > 1e-4 || std::abs(fr->qsum[1]) > 1e-4);
}
-void set_avcsixtwelve(FILE *fplog, t_forcerec *fr, const gmx_mtop_t *mtop)
-{
- const t_atoms *atoms, *atoms_tpi;
- const t_blocka *excl;
- int nmolc, i, j, tpi, tpj, j1, j2, k, nexcl, q;
- int64_t npair, npair_ij, tmpi, tmpj;
- double csix, ctwelve;
- int ntp, *typecount;
- gmx_bool bBHAM;
- real *nbfp;
- real *nbfp_comb = nullptr;
-
- ntp = fr->ntype;
- bBHAM = fr->bBHAM;
- nbfp = fr->nbfp;
-
- /* For LJ-PME, we want to correct for the difference between the
- * actual C6 values and the C6 values used by the LJ-PME based on
- * combination rules. */
-
- if (EVDW_PME(fr->ic->vdwtype))
- {
- nbfp_comb = mk_nbfp_combination_rule(&mtop->ffparams,
- (fr->ljpme_combination_rule == eljpmeLB) ? eCOMB_ARITHMETIC : eCOMB_GEOMETRIC);
- for (tpi = 0; tpi < ntp; ++tpi)
- {
- for (tpj = 0; tpj < ntp; ++tpj)
- {
- C6(nbfp_comb, ntp, tpi, tpj) =
- C6(nbfp, ntp, tpi, tpj) - C6(nbfp_comb, ntp, tpi, tpj);
- C12(nbfp_comb, ntp, tpi, tpj) = C12(nbfp, ntp, tpi, tpj);
- }
- }
- nbfp = nbfp_comb;
- }
- for (q = 0; q < (fr->efep == efepNO ? 1 : 2); q++)
- {
- csix = 0;
- ctwelve = 0;
- npair = 0;
- nexcl = 0;
- if (!fr->n_tpi)
- {
- /* Count the types so we avoid natoms^2 operations */
- snew(typecount, ntp);
- gmx_mtop_count_atomtypes(mtop, q, typecount);
-
- for (tpi = 0; tpi < ntp; tpi++)
- {
- for (tpj = tpi; tpj < ntp; tpj++)
- {
- tmpi = typecount[tpi];
- tmpj = typecount[tpj];
- if (tpi != tpj)
- {
- npair_ij = tmpi*tmpj;
- }
- else
- {
- npair_ij = tmpi*(tmpi - 1)/2;
- }
- if (bBHAM)
- {
- /* nbfp now includes the 6.0 derivative prefactor */
- csix += npair_ij*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
- }
- else
- {
- /* nbfp now includes the 6.0/12.0 derivative prefactors */
- csix += npair_ij* C6(nbfp, ntp, tpi, tpj)/6.0;
- ctwelve += npair_ij* C12(nbfp, ntp, tpi, tpj)/12.0;
- }
- npair += npair_ij;
- }
- }
- sfree(typecount);
- /* Subtract the excluded pairs.
- * The main reason for substracting exclusions is that in some cases
- * some combinations might never occur and the parameters could have
- * any value. These unused values should not influence the dispersion
- * correction.
- */
- for (const gmx_molblock_t &molb : mtop->molblock)
- {
- int nmol = molb.nmol;
- atoms = &mtop->moltype[molb.type].atoms;
- excl = &mtop->moltype[molb.type].excls;
- for (int i = 0; (i < atoms->nr); i++)
- {
- if (q == 0)
- {
- tpi = atoms->atom[i].type;
- }
- else
- {
- tpi = atoms->atom[i].typeB;
- }
- j1 = excl->index[i];
- j2 = excl->index[i+1];
- for (j = j1; j < j2; j++)
- {
- k = excl->a[j];
- if (k > i)
- {
- if (q == 0)
- {
- tpj = atoms->atom[k].type;
- }
- else
- {
- tpj = atoms->atom[k].typeB;
- }
- if (bBHAM)
- {
- /* nbfp now includes the 6.0 derivative prefactor */
- csix -= nmol*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
- }
- else
- {
- /* nbfp now includes the 6.0/12.0 derivative prefactors */
- csix -= nmol*C6 (nbfp, ntp, tpi, tpj)/6.0;
- ctwelve -= nmol*C12(nbfp, ntp, tpi, tpj)/12.0;
- }
- nexcl += molb.nmol;
- }
- }
- }
- }
- }
- else
- {
- /* Only correct for the interaction of the test particle
- * with the rest of the system.
- */
- atoms_tpi =
- &mtop->moltype[mtop->molblock.back().type].atoms;
-
- npair = 0;
- for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
- {
- const gmx_molblock_t &molb = mtop->molblock[mb];
- atoms = &mtop->moltype[molb.type].atoms;
- for (j = 0; j < atoms->nr; j++)
- {
- nmolc = molb.nmol;
- /* Remove the interaction of the test charge group
- * with itself.
- */
- if (mb == mtop->molblock.size() - 1)
- {
- nmolc--;
-
- if (mb == 0 && molb.nmol == 1)
- {
- gmx_fatal(FARGS, "Old format tpr with TPI, please generate a new tpr file");
- }
- }
- if (q == 0)
- {
- tpj = atoms->atom[j].type;
- }
- else
- {
- tpj = atoms->atom[j].typeB;
- }
- for (i = 0; i < fr->n_tpi; i++)
- {
- if (q == 0)
- {
- tpi = atoms_tpi->atom[i].type;
- }
- else
- {
- tpi = atoms_tpi->atom[i].typeB;
- }
- if (bBHAM)
- {
- /* nbfp now includes the 6.0 derivative prefactor */
- csix += nmolc*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
- }
- else
- {
- /* nbfp now includes the 6.0/12.0 derivative prefactors */
- csix += nmolc*C6 (nbfp, ntp, tpi, tpj)/6.0;
- ctwelve += nmolc*C12(nbfp, ntp, tpi, tpj)/12.0;
- }
- npair += nmolc;
- }
- }
- }
- }
- if (npair - nexcl <= 0 && fplog)
- {
- fprintf(fplog, "\nWARNING: There are no atom pairs for dispersion correction\n\n");
- csix = 0;
- ctwelve = 0;
- }
- else
- {
- csix /= npair - nexcl;
- ctwelve /= npair - nexcl;
- }
- if (debug)
- {
- fprintf(debug, "Counted %d exclusions\n", nexcl);
- fprintf(debug, "Average C6 parameter is: %10g\n", csix);
- fprintf(debug, "Average C12 parameter is: %10g\n", ctwelve);
- }
- fr->avcsix[q] = csix;
- fr->avctwelve[q] = ctwelve;
- }
-
- if (EVDW_PME(fr->ic->vdwtype))
- {
- sfree(nbfp_comb);
- }
-
- if (fplog != nullptr)
- {
- if (fr->eDispCorr == edispcAllEner ||
- fr->eDispCorr == edispcAllEnerPres)
- {
- fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
- fr->avcsix[0], fr->avctwelve[0]);
- }
- else
- {
- fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e\n", fr->avcsix[0]);
- }
- }
-}
-
-
-static real calcBuckinghamBMax(FILE *fplog, const gmx_mtop_t *mtop)
+static real calcBuckinghamBMax(FILE* fplog, const gmx_mtop_t* mtop)
{
const t_atoms *at1, *at2;
int i, j, tpi, tpj, ntypes;
{
gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", j, tpj, ntypes);
}
- b = mtop->ffparams.iparams[tpi*ntypes + tpj].bham.b;
+ b = mtop->ffparams.iparams[tpi * ntypes + tpj].bham.b;
if (b > bham_b_max)
{
bham_b_max = b;
}
if (fplog)
{
- fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n",
- bmin, bham_b_max);
+ fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n", bmin, bham_b_max);
}
return bham_b_max;
}
-static void make_nbf_tables(FILE *fp,
- const interaction_const_t *ic, real rtab,
- const char *tabfn, char *eg1, char *eg2,
- t_nblists *nbl)
-{
- char buf[STRLEN];
- int i, j;
-
- if (tabfn == nullptr)
- {
- if (debug)
- {
- fprintf(debug, "No table file name passed, can not read table, can not do non-bonded interactions\n");
- }
- return;
- }
-
- sprintf(buf, "%s", tabfn);
- if (eg1 && eg2)
- {
- /* Append the two energy group names */
- sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
- eg1, eg2, ftp2ext(efXVG));
- }
- nbl->table_elec_vdw = make_tables(fp, ic, buf, rtab, 0);
- /* Copy the contents of the table to separate coulomb and LJ tables too,
- * to improve cache performance.
- */
- /* For performance reasons we want
- * the table data to be aligned to 16-byte. The pointers could be freed
- * but currently aren't.
- */
- snew(nbl->table_elec, 1);
- nbl->table_elec->interaction = GMX_TABLE_INTERACTION_ELEC;
- nbl->table_elec->format = nbl->table_elec_vdw->format;
- nbl->table_elec->r = nbl->table_elec_vdw->r;
- nbl->table_elec->n = nbl->table_elec_vdw->n;
- nbl->table_elec->scale = nbl->table_elec_vdw->scale;
- nbl->table_elec->formatsize = nbl->table_elec_vdw->formatsize;
- nbl->table_elec->ninteractions = 1;
- nbl->table_elec->stride = nbl->table_elec->formatsize * nbl->table_elec->ninteractions;
- snew_aligned(nbl->table_elec->data, nbl->table_elec->stride*(nbl->table_elec->n+1), 32);
-
- snew(nbl->table_vdw, 1);
- nbl->table_vdw->interaction = GMX_TABLE_INTERACTION_VDWREP_VDWDISP;
- nbl->table_vdw->format = nbl->table_elec_vdw->format;
- nbl->table_vdw->r = nbl->table_elec_vdw->r;
- nbl->table_vdw->n = nbl->table_elec_vdw->n;
- nbl->table_vdw->scale = nbl->table_elec_vdw->scale;
- nbl->table_vdw->formatsize = nbl->table_elec_vdw->formatsize;
- nbl->table_vdw->ninteractions = 2;
- nbl->table_vdw->stride = nbl->table_vdw->formatsize * nbl->table_vdw->ninteractions;
- snew_aligned(nbl->table_vdw->data, nbl->table_vdw->stride*(nbl->table_vdw->n+1), 32);
-
- /* NOTE: Using a single i-loop here leads to mix-up of data in table_vdw
- * with (at least) gcc 6.2, 6.3 and 6.4 when compiled with -O3 and AVX
- */
- for (i = 0; i <= nbl->table_elec_vdw->n; i++)
- {
- for (j = 0; j < 4; j++)
- {
- nbl->table_elec->data[4*i+j] = nbl->table_elec_vdw->data[12*i+j];
- }
- }
- for (i = 0; i <= nbl->table_elec_vdw->n; i++)
- {
- for (j = 0; j < 8; j++)
- {
- nbl->table_vdw->data[8*i+j] = nbl->table_elec_vdw->data[12*i+4+j];
- }
- }
-}
-
/*!\brief If there's bonded interactions of type \c ftype1 or \c
* ftype2 present in the topology, build an array of the number of
* interactions present for each bonded interaction index found in the
* \c ncount. It will contain zero for every bonded interaction index
* for which no interactions are present in the topology.
*/
-static void count_tables(int ftype1, int ftype2, const gmx_mtop_t *mtop,
- int *ncount, int **count)
+static void count_tables(int ftype1, int ftype2, const gmx_mtop_t* mtop, int* ncount, int** count)
{
- int ftype, i, j, tabnr;
+ int ftype, i, j, tabnr;
// Loop over all moleculetypes
- for (const gmx_moltype_t &molt : mtop->moltype)
+ for (const gmx_moltype_t& molt : mtop->moltype)
{
// Loop over all interaction types
for (ftype = 0; ftype < F_NRE; ftype++)
// If the current interaction type is one of the types whose tables we're trying to count...
if (ftype == ftype1 || ftype == ftype2)
{
- const InteractionList &il = molt.ilist[ftype];
+ const InteractionList& il = molt.ilist[ftype];
const int stride = 1 + NRAL(ftype);
// ... and there are actually some interactions for this type
for (i = 0; i < il.size(); i += stride)
// Make room for this index in the data structure
if (tabnr >= *ncount)
{
- srenew(*count, tabnr+1);
- for (j = *ncount; j < tabnr+1; j++)
+ srenew(*count, tabnr + 1);
+ for (j = *ncount; j < tabnr + 1; j++)
{
(*count)[j] = 0;
}
- *ncount = tabnr+1;
+ *ncount = tabnr + 1;
}
// Record that this table index is used and must have a valid file
(*count)[tabnr]++;
*
* A fatal error occurs if no matching filename is found.
*/
-static bondedtable_t *make_bonded_tables(FILE *fplog,
- int ftype1, int ftype2,
- const gmx_mtop_t *mtop,
+static bondedtable_t* make_bonded_tables(FILE* fplog,
+ int ftype1,
+ int ftype2,
+ const gmx_mtop_t* mtop,
gmx::ArrayRef<const std::string> tabbfnm,
- const char *tabext)
+ const char* tabext)
{
int ncount, *count;
- bondedtable_t *tab;
+ bondedtable_t* tab;
tab = nullptr;
// being recognized and used for table 1.
std::string patternToFind = gmx::formatString("_%s%d.%s", tabext, i, ftp2ext(efXVG));
bool madeTable = false;
- for (gmx::index j = 0; j < tabbfnm.size() && !madeTable; ++j)
+ for (gmx::index j = 0; j < tabbfnm.ssize() && !madeTable; ++j)
{
if (gmx::endsWith(tabbfnm[j], patternToFind))
{
// Finally read the table from the file found
- tab[i] = make_bonded_table(fplog, tabbfnm[j].c_str(), NRAL(ftype1)-2);
+ tab[i] = make_bonded_table(fplog, tabbfnm[j].c_str(), NRAL(ftype1) - 2);
madeTable = true;
}
}
if (!madeTable)
{
bool isPlural = (ftype2 != -1);
- gmx_fatal(FARGS, "Tabulated interaction of type '%s%s%s' with index %d cannot be used because no table file whose name matched '%s' was passed via the gmx mdrun -tableb command-line option.",
- interaction_function[ftype1].longname,
- isPlural ? "' or '" : "",
- isPlural ? interaction_function[ftype2].longname : "",
- i,
+ gmx_fatal(FARGS,
+ "Tabulated interaction of type '%s%s%s' with index %d cannot be used "
+ "because no table file whose name matched '%s' was passed via the "
+ "gmx mdrun -tableb command-line option.",
+ interaction_function[ftype1].longname, isPlural ? "' or '" : "",
+ isPlural ? interaction_function[ftype2].longname : "", i,
patternToFind.c_str());
}
}
return tab;
}
-void forcerec_set_ranges(t_forcerec *fr,
- int ncg_home, int ncg_force,
- int natoms_force,
- int natoms_force_constr, int natoms_f_novirsum)
+void forcerec_set_ranges(t_forcerec* fr, int natoms_force, int natoms_force_constr, int natoms_f_novirsum)
{
- fr->cg0 = 0;
- fr->hcg = ncg_home;
-
- /* fr->ncg_force is unused in the standard code,
- * but it can be useful for modified code dealing with charge groups.
- */
- fr->ncg_force = ncg_force;
fr->natoms_force = natoms_force;
fr->natoms_force_constr = natoms_force_constr;
if (fr->haveDirectVirialContributions)
{
- fr->forceBufferForDirectVirialContributions->resize(natoms_f_novirsum);
+ fr->forceBufferForDirectVirialContributions.resize(natoms_f_novirsum);
}
}
static real cutoff_inf(real cutoff)
-{
- if (cutoff == 0)
- {
- cutoff = GMX_CUTOFF_INF;
- }
-
- return cutoff;
-}
-
-gmx_bool can_use_allvsall(const t_inputrec *ir, gmx_bool bPrintNote, const t_commrec *cr, FILE *fp)
-{
- gmx_bool bAllvsAll;
-
- bAllvsAll =
- (
- ir->rlist == 0 &&
- ir->rcoulomb == 0 &&
- ir->rvdw == 0 &&
- ir->ePBC == epbcNONE &&
- ir->vdwtype == evdwCUT &&
- ir->coulombtype == eelCUT &&
- ir->efep == efepNO &&
- getenv("GMX_NO_ALLVSALL") == nullptr
- );
-
- if (bAllvsAll && ir->opts.ngener > 1)
- {
- const char *note = "NOTE: Can not use all-vs-all force loops, because there are multiple energy monitor groups; you might get significantly higher performance when using only a single energy monitor group.\n";
-
- if (bPrintNote)
- {
- if (fp != nullptr)
- {
- fprintf(fp, "\n%s\n", note);
- }
- }
- bAllvsAll = FALSE;
- }
-
- if (bAllvsAll && fp && MASTER(cr))
- {
- fprintf(fp, "\nUsing SIMD all-vs-all kernels.\n\n");
- }
-
- return bAllvsAll;
-}
-
-
-gmx_bool nbnxn_simd_supported(const gmx::MDLogger &mdlog,
- const t_inputrec *ir)
-{
- if (ir->vdwtype == evdwPME && ir->ljpme_combination_rule == eljpmeLB)
- {
- /* LJ PME with LB combination rule does 7 mesh operations.
- * This so slow that we don't compile SIMD non-bonded kernels
- * for that. */
- GMX_LOG(mdlog.warning).asParagraph().appendText("LJ-PME with Lorentz-Berthelot is not supported with SIMD kernels, falling back to plain C kernels");
- return FALSE;
- }
-
- return TRUE;
-}
-
-
-static void pick_nbnxn_kernel_cpu(const t_inputrec gmx_unused *ir,
- int *kernel_type,
- int *ewald_excl,
- const gmx_hw_info_t gmx_unused &hardwareInfo)
-{
- *kernel_type = nbnxnk4x4_PlainC;
- *ewald_excl = ewaldexclTable;
-
-#if GMX_SIMD
- {
-#ifdef GMX_NBNXN_SIMD_4XN
- *kernel_type = nbnxnk4xN_SIMD_4xN;
-#endif
-#ifdef GMX_NBNXN_SIMD_2XNN
- *kernel_type = nbnxnk4xN_SIMD_2xNN;
-#endif
-
-#if defined GMX_NBNXN_SIMD_2XNN && defined GMX_NBNXN_SIMD_4XN
- /* We need to choose if we want 2x(N+N) or 4xN kernels.
- * This is based on the SIMD acceleration choice and CPU information
- * detected at runtime.
- *
- * 4xN calculates more (zero) interactions, but has less pair-search
- * work and much better kernel instruction scheduling.
- *
- * Up till now we have only seen that on Intel Sandy/Ivy Bridge,
- * which doesn't have FMA, both the analytical and tabulated Ewald
- * kernels have similar pair rates for 4x8 and 2x(4+4), so we choose
- * 2x(4+4) because it results in significantly fewer pairs.
- * For RF, the raw pair rate of the 4x8 kernel is higher than 2x(4+4),
- * 10% with HT, 50% without HT. As we currently don't detect the actual
- * use of HT, use 4x8 to avoid a potential performance hit.
- * On Intel Haswell 4x8 is always faster.
- */
- *kernel_type = nbnxnk4xN_SIMD_4xN;
-
-#if !GMX_SIMD_HAVE_FMA
- if (EEL_PME_EWALD(ir->coulombtype) ||
- EVDW_PME(ir->vdwtype))
- {
- /* We have Ewald kernels without FMA (Intel Sandy/Ivy Bridge).
- * There are enough instructions to make 2x(4+4) efficient.
- */
- *kernel_type = nbnxnk4xN_SIMD_2xNN;
- }
-#endif
- if (hardwareInfo.haveAmdZen1Cpu)
- {
- /* One 256-bit FMA per cycle makes 2xNN faster */
- *kernel_type = nbnxnk4xN_SIMD_2xNN;
- }
-#endif /* GMX_NBNXN_SIMD_2XNN && GMX_NBNXN_SIMD_4XN */
-
-
- if (getenv("GMX_NBNXN_SIMD_4XN") != nullptr)
- {
-#ifdef GMX_NBNXN_SIMD_4XN
- *kernel_type = nbnxnk4xN_SIMD_4xN;
-#else
- gmx_fatal(FARGS, "SIMD 4xN kernels requested, but GROMACS has been compiled without support for these kernels");
-#endif
- }
- if (getenv("GMX_NBNXN_SIMD_2XNN") != nullptr)
- {
-#ifdef GMX_NBNXN_SIMD_2XNN
- *kernel_type = nbnxnk4xN_SIMD_2xNN;
-#else
- gmx_fatal(FARGS, "SIMD 2x(N+N) kernels requested, but GROMACS has been compiled without support for these kernels");
-#endif
- }
-
- /* Analytical Ewald exclusion correction is only an option in
- * the SIMD kernel.
- * Since table lookup's don't parallelize with SIMD, analytical
- * will probably always be faster for a SIMD width of 8 or more.
- * With FMA analytical is sometimes faster for a width if 4 as well.
- * In single precision, this is faster on Bulldozer.
- */
-#if GMX_SIMD_REAL_WIDTH >= 8 || \
- (GMX_SIMD_REAL_WIDTH >= 4 && GMX_SIMD_HAVE_FMA && !GMX_DOUBLE)
- /* On AMD Zen, tabulated Ewald kernels are faster on all 4 combinations
- * of single or double precision and 128 or 256-bit AVX2.
- */
- if (!hardwareInfo.haveAmdZen1Cpu)
- {
- *ewald_excl = ewaldexclAnalytical;
- }
-#endif
- if (getenv("GMX_NBNXN_EWALD_TABLE") != nullptr)
- {
- *ewald_excl = ewaldexclTable;
- }
- if (getenv("GMX_NBNXN_EWALD_ANALYTICAL") != nullptr)
- {
- *ewald_excl = ewaldexclAnalytical;
- }
-
- }
-#endif // GMX_SIMD
-}
-
-
-const char *lookup_nbnxn_kernel_name(int kernel_type)
-{
- const char *returnvalue = nullptr;
- switch (kernel_type)
- {
- case nbnxnkNotSet:
- returnvalue = "not set";
- break;
- case nbnxnk4x4_PlainC:
- returnvalue = "plain C";
- break;
- case nbnxnk4xN_SIMD_4xN:
- case nbnxnk4xN_SIMD_2xNN:
-#if GMX_SIMD
- returnvalue = "SIMD";
-#else // GMX_SIMD
- returnvalue = "not available";
-#endif // GMX_SIMD
- break;
- case nbnxnk8x8x8_GPU: returnvalue = "GPU"; break;
- case nbnxnk8x8x8_PlainC: returnvalue = "plain C"; break;
-
- case nbnxnkNR:
- default:
- gmx_fatal(FARGS, "Illegal kernel type selected");
- }
- return returnvalue;
-};
-
-static void pick_nbnxn_kernel(const gmx::MDLogger &mdlog,
- gmx_bool use_simd_kernels,
- const gmx_hw_info_t &hardwareInfo,
- gmx_bool bUseGPU,
- EmulateGpuNonbonded emulateGpu,
- const t_inputrec *ir,
- int *kernel_type,
- int *ewald_excl,
- gmx_bool bDoNonbonded)
-{
- assert(kernel_type);
-
- *kernel_type = nbnxnkNotSet;
- *ewald_excl = ewaldexclTable;
-
- if (emulateGpu == EmulateGpuNonbonded::Yes)
- {
- *kernel_type = nbnxnk8x8x8_PlainC;
-
- if (bDoNonbonded)
- {
- GMX_LOG(mdlog.warning).asParagraph().appendText("Emulating a GPU run on the CPU (slow)");
- }
- }
- else if (bUseGPU)
- {
- *kernel_type = nbnxnk8x8x8_GPU;
- }
-
- if (*kernel_type == nbnxnkNotSet)
- {
- if (use_simd_kernels &&
- nbnxn_simd_supported(mdlog, ir))
- {
- pick_nbnxn_kernel_cpu(ir, kernel_type, ewald_excl, hardwareInfo);
- }
- else
- {
- *kernel_type = nbnxnk4x4_PlainC;
- }
- }
-
- if (bDoNonbonded)
+{
+ if (cutoff == 0)
{
- GMX_LOG(mdlog.info).asParagraph().appendTextFormatted(
- "Using %s %dx%d nonbonded short-range kernels",
- lookup_nbnxn_kernel_name(*kernel_type),
- nbnxn_kernel_to_cluster_i_size(*kernel_type),
- nbnxn_kernel_to_cluster_j_size(*kernel_type));
-
- if (nbnxnk4x4_PlainC == *kernel_type ||
- nbnxnk8x8x8_PlainC == *kernel_type)
- {
- GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
- "WARNING: Using the slow %s kernels. This should\n"
- "not happen during routine usage on supported platforms.",
- lookup_nbnxn_kernel_name(*kernel_type));
- }
+ cutoff = GMX_CUTOFF_INF;
}
+
+ return cutoff;
}
/*! \brief Print Coulomb Ewald citations and set ewald coefficients */
-static void initCoulombEwaldParameters(FILE *fp, const t_inputrec *ir,
- bool systemHasNetCharge,
- interaction_const_t *ic)
+static void initCoulombEwaldParameters(FILE* fp,
+ const t_inputrec* ir,
+ bool systemHasNetCharge,
+ interaction_const_t* ic)
{
if (!EEL_PME_EWALD(ir->coulombtype))
{
ic->ewaldcoeff_q = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
if (fp)
{
- fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n",
- 1/ic->ewaldcoeff_q);
+ fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n", 1 / ic->ewaldcoeff_q);
}
if (ic->coulomb_modifier == eintmodPOTSHIFT)
{
GMX_RELEASE_ASSERT(ic->rcoulomb != 0, "Cutoff radius cannot be zero");
- ic->sh_ewald = std::erfc(ic->ewaldcoeff_q*ic->rcoulomb) / ic->rcoulomb;
+ ic->sh_ewald = std::erfc(ic->ewaldcoeff_q * ic->rcoulomb) / ic->rcoulomb;
}
else
{
}
/*! \brief Print Van der Waals Ewald citations and set ewald coefficients */
-static void initVdwEwaldParameters(FILE *fp, const t_inputrec *ir,
- interaction_const_t *ic)
+static void initVdwEwaldParameters(FILE* fp, const t_inputrec* ir, interaction_const_t* ic)
{
if (!EVDW_PME(ir->vdwtype))
{
ic->ewaldcoeff_lj = calc_ewaldcoeff_lj(ir->rvdw, ir->ewald_rtol_lj);
if (fp)
{
- fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for LJ Ewald\n",
- 1/ic->ewaldcoeff_lj);
+ fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for LJ Ewald\n", 1 / ic->ewaldcoeff_lj);
}
if (ic->vdw_modifier == eintmodPOTSHIFT)
{
- real crc2 = gmx::square(ic->ewaldcoeff_lj*ic->rvdw);
- ic->sh_lj_ewald = (std::exp(-crc2)*(1 + crc2 + 0.5*crc2*crc2) - 1)/gmx::power6(ic->rvdw);
+ real crc2 = gmx::square(ic->ewaldcoeff_lj * ic->rvdw);
+ ic->sh_lj_ewald = (std::exp(-crc2) * (1 + crc2 + 0.5 * crc2 * crc2) - 1) / gmx::power6(ic->rvdw);
}
else
{
}
}
-gmx_bool uses_simple_tables(int cutoff_scheme,
- nonbonded_verlet_t *nbv,
- int group)
-{
- gmx_bool bUsesSimpleTables = TRUE;
- int grp_index;
-
- switch (cutoff_scheme)
- {
- case ecutsGROUP:
- bUsesSimpleTables = TRUE;
- break;
- case ecutsVERLET:
- assert(nullptr != nbv);
- grp_index = (group < 0) ? 0 : (nbv->ngrp - 1);
- bUsesSimpleTables = nbnxn_kernel_pairlist_simple(nbv->grp[grp_index].kernel_type);
- break;
- default:
- gmx_incons("unimplemented");
- }
- return bUsesSimpleTables;
-}
-
-static void init_ewald_f_table(interaction_const_t *ic,
- real rtab)
+/* Generate Coulomb and/or Van der Waals Ewald long-range correction tables
+ *
+ * Tables are generated for one or both, depending on if the pointers
+ * are non-null. The spacing for both table sets is the same and obeys
+ * both accuracy requirements, when relevant.
+ */
+static void init_ewald_f_table(const interaction_const_t& ic,
+ EwaldCorrectionTables* coulombTables,
+ EwaldCorrectionTables* vdwTables)
{
- real maxr;
+ const bool useCoulombTable = (EEL_PME_EWALD(ic.eeltype) && coulombTables != nullptr);
+ const bool useVdwTable = (EVDW_PME(ic.vdwtype) && vdwTables != nullptr);
/* Get the Ewald table spacing based on Coulomb and/or LJ
* Ewald coefficients and rtol.
*/
- ic->tabq_scale = ewald_spline3_table_scale(ic);
-
- if (ic->cutoff_scheme == ecutsVERLET)
- {
- maxr = ic->rcoulomb;
- }
- else
- {
- maxr = std::max(ic->rcoulomb, rtab);
- }
- ic->tabq_size = static_cast<int>(maxr*ic->tabq_scale) + 2;
-
- sfree_aligned(ic->tabq_coul_FDV0);
- sfree_aligned(ic->tabq_coul_F);
- sfree_aligned(ic->tabq_coul_V);
+ const real tableScale = ewald_spline3_table_scale(ic, useCoulombTable, useVdwTable);
- sfree_aligned(ic->tabq_vdw_FDV0);
- sfree_aligned(ic->tabq_vdw_F);
- sfree_aligned(ic->tabq_vdw_V);
+ const int tableSize = static_cast<int>(ic.rcoulomb * tableScale) + 2;
- if (EEL_PME_EWALD(ic->eeltype))
+ if (useCoulombTable)
{
- /* Create the original table data in FDV0 */
- snew_aligned(ic->tabq_coul_FDV0, ic->tabq_size*4, 32);
- snew_aligned(ic->tabq_coul_F, ic->tabq_size, 32);
- snew_aligned(ic->tabq_coul_V, ic->tabq_size, 32);
- table_spline3_fill_ewald_lr(ic->tabq_coul_F, ic->tabq_coul_V, ic->tabq_coul_FDV0,
- ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff_q, v_q_ewald_lr);
+ *coulombTables =
+ generateEwaldCorrectionTables(tableSize, tableScale, ic.ewaldcoeff_q, v_q_ewald_lr);
}
- if (EVDW_PME(ic->vdwtype))
+ if (useVdwTable)
{
- snew_aligned(ic->tabq_vdw_FDV0, ic->tabq_size*4, 32);
- snew_aligned(ic->tabq_vdw_F, ic->tabq_size, 32);
- snew_aligned(ic->tabq_vdw_V, ic->tabq_size, 32);
- table_spline3_fill_ewald_lr(ic->tabq_vdw_F, ic->tabq_vdw_V, ic->tabq_vdw_FDV0,
- ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff_lj, v_lj_ewald_lr);
+ *vdwTables = generateEwaldCorrectionTables(tableSize, tableScale, ic.ewaldcoeff_lj, v_lj_ewald_lr);
}
}
-void init_interaction_const_tables(FILE *fp,
- interaction_const_t *ic,
- real rtab)
+void init_interaction_const_tables(FILE* fp, interaction_const_t* ic)
{
- if (EEL_PME_EWALD(ic->eeltype) || EVDW_PME(ic->vdwtype))
+ if (EEL_PME_EWALD(ic->eeltype))
{
- init_ewald_f_table(ic, rtab);
-
+ init_ewald_f_table(*ic, ic->coulombEwaldTables.get(), nullptr);
if (fp != nullptr)
{
- fprintf(fp, "Initialized non-bonded Ewald correction tables, spacing: %.2e size: %d\n\n",
- 1/ic->tabq_scale, ic->tabq_size);
+ fprintf(fp, "Initialized non-bonded Coulomb Ewald tables, spacing: %.2e size: %zu\n\n",
+ 1 / ic->coulombEwaldTables->scale, ic->coulombEwaldTables->tableF.size());
}
}
}
-static void clear_force_switch_constants(shift_consts_t *sc)
+static void clear_force_switch_constants(shift_consts_t* sc)
{
sc->c2 = 0;
sc->c3 = 0;
sc->cpot = 0;
}
-static void force_switch_constants(real p,
- real rsw, real rc,
- shift_consts_t *sc)
+static void force_switch_constants(real p, real rsw, real rc, shift_consts_t* sc)
{
/* Here we determine the coefficient for shifting the force to zero
* between distance rsw and the cut-off rc.
* force/p = r^-(p+1) + c2*r^2 + c3*r^3
* potential = r^-p + c2/3*r^3 + c3/4*r^4 + cpot
*/
- sc->c2 = ((p + 1)*rsw - (p + 4)*rc)/(pow(rc, p + 2)*gmx::square(rc - rsw));
- sc->c3 = -((p + 1)*rsw - (p + 3)*rc)/(pow(rc, p + 2)*gmx::power3(rc - rsw));
- sc->cpot = -pow(rc, -p) + p*sc->c2/3*gmx::power3(rc - rsw) + p*sc->c3/4*gmx::power4(rc - rsw);
+ sc->c2 = ((p + 1) * rsw - (p + 4) * rc) / (pow(rc, p + 2) * gmx::square(rc - rsw));
+ sc->c3 = -((p + 1) * rsw - (p + 3) * rc) / (pow(rc, p + 2) * gmx::power3(rc - rsw));
+ sc->cpot = -pow(rc, -p) + p * sc->c2 / 3 * gmx::power3(rc - rsw)
+ + p * sc->c3 / 4 * gmx::power4(rc - rsw);
}
-static void potential_switch_constants(real rsw, real rc,
- switch_consts_t *sc)
+static void potential_switch_constants(real rsw, real rc, switch_consts_t* sc)
{
/* The switch function is 1 at rsw and 0 at rc.
* The derivative and second derivate are zero at both ends.
* force = force*dsw - potential*sw
* potential *= sw
*/
- sc->c3 = -10/gmx::power3(rc - rsw);
- sc->c4 = 15/gmx::power4(rc - rsw);
- sc->c5 = -6/gmx::power5(rc - rsw);
+ sc->c3 = -10 / gmx::power3(rc - rsw);
+ sc->c4 = 15 / gmx::power4(rc - rsw);
+ sc->c5 = -6 / gmx::power5(rc - rsw);
}
/*! \brief Construct interaction constants
* short-range interactions. Many of these are constant for the whole
* simulation; some are constant only after PME tuning completes.
*/
-static void
-init_interaction_const(FILE *fp,
- interaction_const_t **interaction_const,
- const t_inputrec *ir,
- const gmx_mtop_t *mtop,
- bool systemHasNetCharge)
+static void init_interaction_const(FILE* fp,
+ interaction_const_t** interaction_const,
+ const t_inputrec* ir,
+ const gmx_mtop_t* mtop,
+ bool systemHasNetCharge)
{
- interaction_const_t *ic;
-
- snew(ic, 1);
+ interaction_const_t* ic = new interaction_const_t;
- ic->cutoff_scheme = ir->cutoff_scheme;
+ ic->cutoff_scheme = ir->cutoff_scheme;
- /* Just allocate something so we can free it */
- snew_aligned(ic->tabq_coul_FDV0, 16, 32);
- snew_aligned(ic->tabq_coul_F, 16, 32);
- snew_aligned(ic->tabq_coul_V, 16, 32);
+ ic->coulombEwaldTables = std::make_unique<EwaldCorrectionTables>();
/* Lennard-Jones */
ic->vdwtype = ir->vdwtype;
{
case eintmodPOTSHIFT:
/* Only shift the potential, don't touch the force */
- ic->dispersion_shift.cpot = -1.0/gmx::power6(ic->rvdw);
- ic->repulsion_shift.cpot = -1.0/gmx::power12(ic->rvdw);
+ ic->dispersion_shift.cpot = -1.0 / gmx::power6(ic->rvdw);
+ ic->repulsion_shift.cpot = -1.0 / gmx::power12(ic->rvdw);
break;
case eintmodFORCESWITCH:
/* Switch the force, switch and shift the potential */
- force_switch_constants(6.0, ic->rvdw_switch, ic->rvdw,
- &ic->dispersion_shift);
- force_switch_constants(12.0, ic->rvdw_switch, ic->rvdw,
- &ic->repulsion_shift);
+ force_switch_constants(6.0, ic->rvdw_switch, ic->rvdw, &ic->dispersion_shift);
+ force_switch_constants(12.0, ic->rvdw_switch, ic->rvdw, &ic->repulsion_shift);
break;
case eintmodPOTSWITCH:
/* Switch the potential and force */
- potential_switch_constants(ic->rvdw_switch, ic->rvdw,
- &ic->vdw_switch);
+ potential_switch_constants(ic->rvdw_switch, ic->rvdw, &ic->vdw_switch);
break;
case eintmodNONE:
case eintmodEXACTCUTOFF:
/* Nothing to do here */
break;
- default:
- gmx_incons("unimplemented potential modifier");
+ default: gmx_incons("unimplemented potential modifier");
}
- ic->sh_invrc6 = -ic->dispersion_shift.cpot;
-
/* Electrostatics */
ic->eeltype = ir->coulombtype;
ic->coulomb_modifier = ir->coulomb_modifier;
/* Set the Coulomb energy conversion factor */
if (ic->epsilon_r != 0)
{
- ic->epsfac = ONE_4PI_EPS0/ic->epsilon_r;
+ ic->epsfac = ONE_4PI_EPS0 / ic->epsilon_r;
}
else
{
/* Reaction-field */
if (EEL_RF(ic->eeltype))
{
+ GMX_RELEASE_ASSERT(ic->eeltype != eelGRF_NOTUSED, "GRF is no longer supported");
ic->epsilon_rf = ir->epsilon_rf;
- /* Generalized reaction field parameters are updated every step */
- if (ic->eeltype != eelGRF)
- {
- calc_rffac(fp, ic->eeltype, ic->epsilon_r, ic->epsilon_rf,
- ic->rcoulomb, 0, 0, nullptr,
- &ic->k_rf, &ic->c_rf);
- }
- if (ir->cutoff_scheme == ecutsGROUP && ic->eeltype == eelRF_ZERO)
- {
- /* grompp should have done this, but this scheme is obsolete */
- ic->coulomb_modifier = eintmodEXACTCUTOFF;
- }
+ calc_rffac(fp, ic->epsilon_r, ic->epsilon_rf, ic->rcoulomb, &ic->k_rf, &ic->c_rf);
}
else
{
ic->k_rf = 0;
if (ir->coulomb_modifier == eintmodPOTSHIFT)
{
- ic->c_rf = 1/ic->rcoulomb;
+ ic->c_rf = 1 / ic->rcoulomb;
}
else
{
- ic->c_rf = 0;
+ ic->c_rf = 0;
}
}
{
dispersion_shift -= ic->sh_lj_ewald;
}
- fprintf(fp, "Potential shift: LJ r^-12: %.3e r^-6: %.3e",
- ic->repulsion_shift.cpot, dispersion_shift);
+ fprintf(fp, "Potential shift: LJ r^-12: %.3e r^-6: %.3e", ic->repulsion_shift.cpot, dispersion_shift);
if (ic->eeltype == eelCUT)
{
*interaction_const = ic;
}
-static void
-done_interaction_const(interaction_const_t *interaction_const)
-{
- sfree_aligned(interaction_const->tabq_coul_FDV0);
- sfree_aligned(interaction_const->tabq_coul_F);
- sfree_aligned(interaction_const->tabq_coul_V);
- sfree(interaction_const);
-}
-
-static void init_nb_verlet(const gmx::MDLogger &mdlog,
- nonbonded_verlet_t **nb_verlet,
- gmx_bool bFEP_NonBonded,
- const t_inputrec *ir,
- const t_forcerec *fr,
- const t_commrec *cr,
- const gmx_hw_info_t &hardwareInfo,
- const gmx_device_info_t *deviceInfo,
- const gmx_mtop_t *mtop,
- matrix box)
-{
- nonbonded_verlet_t *nbv;
- char *env;
-
- nbnxn_alloc_t *nb_alloc;
- nbnxn_free_t *nb_free;
-
- nbv = new nonbonded_verlet_t();
-
- nbv->emulateGpu = ((getenv("GMX_EMULATE_GPU") != nullptr) ? EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
- nbv->bUseGPU = deviceInfo != nullptr;
-
- GMX_RELEASE_ASSERT(!(nbv->emulateGpu == EmulateGpuNonbonded::Yes && nbv->bUseGPU), "When GPU emulation is active, there cannot be a GPU assignment");
-
- nbv->nbs = nullptr;
- nbv->min_ci_balanced = 0;
-
- nbv->ngrp = (DOMAINDECOMP(cr) ? 2 : 1);
- for (int i = 0; i < nbv->ngrp; i++)
- {
- nbv->grp[i].nbl_lists.nnbl = 0;
- nbv->grp[i].kernel_type = nbnxnkNotSet;
-
- if (i == 0) /* local */
- {
- pick_nbnxn_kernel(mdlog, fr->use_simd_kernels, hardwareInfo,
- nbv->bUseGPU, nbv->emulateGpu, ir,
- &nbv->grp[i].kernel_type,
- &nbv->grp[i].ewald_excl,
- fr->bNonbonded);
- }
- else /* non-local */
- {
- /* Use the same kernel for local and non-local interactions */
- nbv->grp[i].kernel_type = nbv->grp[0].kernel_type;
- nbv->grp[i].ewald_excl = nbv->grp[0].ewald_excl;
- }
- }
-
- nbv->listParams = gmx::compat::make_unique<NbnxnListParameters>(ir->rlist);
- setupDynamicPairlistPruning(mdlog, ir, mtop, box, nbv->grp[0].kernel_type, fr->ic,
- nbv->listParams.get());
-
- nbv->nbs = gmx::compat::make_unique<nbnxn_search>(DOMAINDECOMP(cr) ? &cr->dd->nc : nullptr,
- DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : nullptr,
- bFEP_NonBonded,
- gmx_omp_nthreads_get(emntPairsearch));
-
- gpu_set_host_malloc_and_free(nbv->grp[0].kernel_type == nbnxnk8x8x8_GPU,
- &nb_alloc, &nb_free);
-
- for (int i = 0; i < nbv->ngrp; i++)
- {
- nbnxn_init_pairlist_set(&nbv->grp[i].nbl_lists,
- nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
- /* 8x8x8 "non-simple" lists are ATM always combined */
- !nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
- nb_alloc, nb_free);
- }
-
- int enbnxninitcombrule;
- if (fr->ic->vdwtype == evdwCUT &&
- (fr->ic->vdw_modifier == eintmodNONE ||
- fr->ic->vdw_modifier == eintmodPOTSHIFT) &&
- getenv("GMX_NO_LJ_COMB_RULE") == nullptr)
- {
- /* Plain LJ cut-off: we can optimize with combination rules */
- enbnxninitcombrule = enbnxninitcombruleDETECT;
- }
- else if (fr->ic->vdwtype == evdwPME)
- {
- /* LJ-PME: we need to use a combination rule for the grid */
- if (fr->ljpme_combination_rule == eljpmeGEOM)
- {
- enbnxninitcombrule = enbnxninitcombruleGEOM;
- }
- else
- {
- enbnxninitcombrule = enbnxninitcombruleLB;
- }
- }
- else
- {
- /* We use a full combination matrix: no rule required */
- enbnxninitcombrule = enbnxninitcombruleNONE;
- }
-
- snew(nbv->nbat, 1);
- int mimimumNumEnergyGroupNonbonded = ir->opts.ngener;
- if (ir->opts.ngener - ir->nwall == 1)
- {
- /* We have only one non-wall energy group, we do not need energy group
- * support in the non-bondeds kernels, since all non-bonded energy
- * contributions go to the first element of the energy group matrix.
- */
- mimimumNumEnergyGroupNonbonded = 1;
- }
- bool bSimpleList = nbnxn_kernel_pairlist_simple(nbv->grp[0].kernel_type);
- nbnxn_atomdata_init(mdlog,
- nbv->nbat,
- nbv->grp[0].kernel_type,
- enbnxninitcombrule,
- fr->ntype, fr->nbfp,
- mimimumNumEnergyGroupNonbonded,
- bSimpleList ? gmx_omp_nthreads_get(emntNonbonded) : 1,
- nb_alloc, nb_free);
-
- if (nbv->bUseGPU)
- {
- /* init the NxN GPU data; the last argument tells whether we'll have
- * both local and non-local NB calculation on GPU */
- nbnxn_gpu_init(&nbv->gpu_nbv,
- deviceInfo,
- fr->ic,
- nbv->listParams.get(),
- nbv->nbat,
- cr->nodeid,
- (nbv->ngrp > 1));
-
- if ((env = getenv("GMX_NB_MIN_CI")) != nullptr)
- {
- char *end;
-
- nbv->min_ci_balanced = strtol(env, &end, 10);
- if (!end || (*end != 0) || nbv->min_ci_balanced < 0)
- {
- gmx_fatal(FARGS, "Invalid value passed in GMX_NB_MIN_CI=%s, non-negative integer required", env);
- }
-
- if (debug)
- {
- fprintf(debug, "Neighbor-list balancing parameter: %d (passed as env. var.)\n",
- nbv->min_ci_balanced);
- }
- }
- else
- {
- nbv->min_ci_balanced = nbnxn_gpu_min_ci_balanced(nbv->gpu_nbv);
- if (debug)
- {
- fprintf(debug, "Neighbor-list balancing parameter: %d (auto-adjusted to the number of GPU multi-processors)\n",
- nbv->min_ci_balanced);
- }
- }
-
- }
-
- *nb_verlet = nbv;
-}
-
-gmx_bool usingGpu(nonbonded_verlet_t *nbv)
-{
- return nbv != nullptr && nbv->bUseGPU;
-}
-
-void init_forcerec(FILE *fp,
- const gmx::MDLogger &mdlog,
- t_forcerec *fr,
- t_fcdata *fcd,
- const t_inputrec *ir,
- const gmx_mtop_t *mtop,
- const t_commrec *cr,
- matrix box,
- const char *tabfn,
- const char *tabpfn,
- gmx::ArrayRef<const std::string> tabbfnm,
- const gmx_hw_info_t &hardwareInfo,
- const gmx_device_info_t *deviceInfo,
- const bool useGpuForBonded,
- gmx_bool bNoSolvOpt,
- real print_force)
+void init_forcerec(FILE* fp,
+ const gmx::MDLogger& mdlog,
+ t_forcerec* fr,
+ t_fcdata* fcd,
+ const t_inputrec* ir,
+ const gmx_mtop_t* mtop,
+ const t_commrec* cr,
+ matrix box,
+ const char* tabfn,
+ const char* tabpfn,
+ gmx::ArrayRef<const std::string> tabbfnm,
+ const gmx_hw_info_t& hardwareInfo,
+ const gmx_device_info_t* deviceInfo,
+ const bool useGpuForBonded,
+ const bool pmeOnlyRankUsesGpu,
+ real print_force,
+ gmx_wallcycle* wcycle)
{
- int m, negp_pp, negptable, egi, egj;
- real rtab;
- char *env;
- double dbl;
- const t_block *cgs;
- gmx_bool bGenericKernelOnly;
- gmx_bool needGroupSchemeTables, bSomeNormalNbListsAreInUse;
- gmx_bool bFEP_NonBonded;
- int *nm_ind, egp_flags;
+ real rtab;
+ char* env;
+ double dbl;
+ gmx_bool bFEP_NonBonded;
/* By default we turn SIMD kernels on, but it might be turned off further down... */
fr->use_simd_kernels = TRUE;
if (EI_TPI(ir->eI))
{
/* Set to the size of the molecule to be inserted (the last one) */
- /* Because of old style topologies, we have to use the last cg
- * instead of the last molecule type.
- */
- cgs = &mtop->moltype[mtop->molblock.back().type].cgs;
- fr->n_tpi = cgs->index[cgs->nr] - cgs->index[cgs->nr-1];
gmx::RangePartitioning molecules = gmx_mtop_molecules(*mtop);
- if (fr->n_tpi != molecules.block(molecules.numBlocks() - 1).size())
- {
- gmx_fatal(FARGS, "The molecule to insert can not consist of multiple charge groups.\nMake it a single charge group.");
- }
+ fr->n_tpi = molecules.block(molecules.numBlocks() - 1).size();
}
else
{
fr->n_tpi = 0;
}
- if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
+ if (ir->coulombtype == eelRF_NEC_UNSUPPORTED || ir->coulombtype == eelGRF_NOTUSED)
{
- gmx_fatal(FARGS, "%s electrostatics is no longer supported",
- eel_names[ir->coulombtype]);
+ gmx_fatal(FARGS, "%s electrostatics is no longer supported", eel_names[ir->coulombtype]);
}
if (ir->bAdress)
{
/* turn off non-bonded calculations */
fr->bNonbonded = FALSE;
- GMX_LOG(mdlog.warning).asParagraph().appendText(
- "Found environment variable GMX_NO_NONBONDED.\n"
- "Disabling nonbonded calculations.");
- }
-
- bGenericKernelOnly = FALSE;
-
- /* We now check in the NS code whether a particular combination of interactions
- * can be used with water optimization, and disable it if that is not the case.
- */
-
- if (getenv("GMX_NB_GENERIC") != nullptr)
- {
- if (fp != nullptr)
- {
- fprintf(fp,
- "Found environment variable GMX_NB_GENERIC.\n"
- "Disabling all interaction-specific nonbonded kernels, will only\n"
- "use the slow generic ones in src/gmxlib/nonbonded/nb_generic.c\n\n");
- }
- bGenericKernelOnly = TRUE;
- }
-
- if (bGenericKernelOnly)
- {
- bNoSolvOpt = TRUE;
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendText(
+ "Found environment variable GMX_NO_NONBONDED.\n"
+ "Disabling nonbonded calculations.");
}
- if ( (getenv("GMX_DISABLE_SIMD_KERNELS") != nullptr) || (getenv("GMX_NOOPTIMIZEDKERNELS") != nullptr) )
+ if ((getenv("GMX_DISABLE_SIMD_KERNELS") != nullptr) || (getenv("GMX_NOOPTIMIZEDKERNELS") != nullptr))
{
fr->use_simd_kernels = FALSE;
if (fp != nullptr)
fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
- /* Check if we can/should do all-vs-all kernels */
- fr->bAllvsAll = can_use_allvsall(ir, FALSE, nullptr, nullptr);
- fr->AllvsAll_work = nullptr;
-
- /* All-vs-all kernels have not been implemented in 4.6 and later.
- * See Redmine #1249. */
- if (fr->bAllvsAll)
- {
- fr->bAllvsAll = FALSE;
- if (fp != nullptr)
- {
- fprintf(fp,
- "\nYour simulation settings would have triggered the efficient all-vs-all\n"
- "kernels in GROMACS 4.5, but these have not been implemented in GROMACS\n"
- "4.6 and 5.x. If performance is important, please use GROMACS 4.5.7\n"
- "or try cutoff-scheme = Verlet.\n\n");
- }
- }
-
/* Neighbour searching stuff */
fr->cutoff_scheme = ir->cutoff_scheme;
- fr->bGrid = (ir->ns_type == ensGRID);
fr->ePBC = ir->ePBC;
- if (fr->cutoff_scheme == ecutsGROUP)
- {
- const char *note = "NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be\n"
- "removed in a future release when 'verlet' supports all interaction forms.\n";
-
- if (MASTER(cr))
- {
- fprintf(stderr, "\n%s\n", note);
- }
- if (fp != nullptr)
- {
- fprintf(fp, "\n%s\n", note);
- }
- }
-
/* Determine if we will do PBC for distances in bonded interactions */
if (fr->ePBC == epbcNONE)
{
}
else
{
+ const bool useEwaldSurfaceCorrection =
+ (EEL_PME_EWALD(ir->coulombtype) && ir->epsilon_surface != 0);
if (!DOMAINDECOMP(cr))
{
gmx_bool bSHAKE;
- bSHAKE = (ir->eConstrAlg == econtSHAKE &&
- (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0 ||
- gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0));
+ bSHAKE = (ir->eConstrAlg == econtSHAKE
+ && (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0
+ || gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0));
/* The group cut-off scheme and SHAKE assume charge groups
* are whole, but not using molpbc is faster in most cases.
* With intermolecular interactions we need PBC for calculating
* distances between atoms in different molecules.
*/
- if ((fr->cutoff_scheme == ecutsGROUP || bSHAKE) &&
- !mtop->bIntermolecularInteractions)
+ if (bSHAKE && !mtop->bIntermolecularInteractions)
{
fr->bMolPBC = ir->bPeriodicMols;
else
{
/* Not making molecules whole is faster in most cases,
- * but With orientation restraints we need whole molecules.
+ * but with orientation restraints or non-tinfoil boundary
+ * conditions we need whole molecules.
*/
- fr->bMolPBC = (fcd->orires.nr == 0);
+ fr->bMolPBC = (fcd->orires.nr == 0 && !useEwaldSurfaceCorrection);
if (getenv("GMX_USE_GRAPH") != nullptr)
{
fr->bMolPBC = FALSE;
if (fp)
{
- GMX_LOG(mdlog.warning).asParagraph().appendText("GMX_USE_GRAPH is set, using the graph for bonded interactions");
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendText(
+ "GMX_USE_GRAPH is set, using the graph for bonded "
+ "interactions");
}
if (mtop->bIntermolecularInteractions)
{
- GMX_LOG(mdlog.warning).asParagraph().appendText("WARNING: Molecules linked by intermolecular interactions have to reside in the same periodic image, otherwise artifacts will occur!");
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendText(
+ "WARNING: Molecules linked by intermolecular interactions "
+ "have to reside in the same periodic image, otherwise "
+ "artifacts will occur!");
}
}
- GMX_RELEASE_ASSERT(fr->bMolPBC || !mtop->bIntermolecularInteractions, "We need to use PBC within molecules with inter-molecular interactions");
+ GMX_RELEASE_ASSERT(
+ fr->bMolPBC || !mtop->bIntermolecularInteractions,
+ "We need to use PBC within molecules with inter-molecular interactions");
if (bSHAKE && fr->bMolPBC)
{
- gmx_fatal(FARGS, "SHAKE is not properly supported with intermolecular interactions. For short simulations where linked molecules remain in the same periodic image, the environment variable GMX_USE_GRAPH can be used to override this check.\n");
+ gmx_fatal(FARGS,
+ "SHAKE is not properly supported with intermolecular interactions. "
+ "For short simulations where linked molecules remain in the same "
+ "periodic image, the environment variable GMX_USE_GRAPH can be used "
+ "to override this check.\n");
}
}
}
else
{
fr->bMolPBC = dd_bonded_molpbc(cr->dd, fr->ePBC);
+
+ if (useEwaldSurfaceCorrection && !dd_moleculesAreAlwaysWhole(*cr->dd))
+ {
+ gmx_fatal(FARGS,
+ "You requested dipole correction (epsilon_surface > 0), but molecules "
+ "are broken "
+ "over periodic boundary conditions by the domain decomposition. "
+ "Run without domain decomposition instead.");
+ }
+ }
+
+ if (useEwaldSurfaceCorrection)
+ {
+ GMX_RELEASE_ASSERT((!DOMAINDECOMP(cr) && !fr->bMolPBC)
+ || (DOMAINDECOMP(cr) && dd_moleculesAreAlwaysWhole(*cr->dd)),
+ "Molecules can not be broken by PBC with epsilon_surface > 0");
}
}
fr->rc_scaling = ir->refcoord_scaling;
copy_rvec(ir->posres_com, fr->posres_com);
copy_rvec(ir->posres_comB, fr->posres_comB);
- fr->rlist = cutoff_inf(ir->rlist);
- fr->ljpme_combination_rule = ir->ljpme_combination_rule;
+ fr->rlist = cutoff_inf(ir->rlist);
+ fr->ljpme_combination_rule = ir->ljpme_combination_rule;
/* This now calculates sum for q and c6*/
bool systemHasNetCharge = set_chargesum(fp, fr, mtop);
/* fr->ic is used both by verlet and group kernels (to some extent) now */
init_interaction_const(fp, &fr->ic, ir, mtop, systemHasNetCharge);
- init_interaction_const_tables(fp, fr->ic, ir->rlist + ir->tabext);
+ init_interaction_const_tables(fp, fr->ic);
- const interaction_const_t *ic = fr->ic;
+ const interaction_const_t* ic = fr->ic;
/* TODO: Replace this Ewald table or move it into interaction_const_t */
if (ir->coulombtype == eelEWALD)
/* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
switch (ic->eeltype)
{
- case eelCUT:
- fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_COULOMB;
- break;
+ case eelCUT: fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_COULOMB; break;
case eelRF:
- case eelGRF:
- fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
- break;
-
- case eelRF_ZERO:
- fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
- GMX_RELEASE_ASSERT(ic->coulomb_modifier == eintmodEXACTCUTOFF, "With the group scheme RF-zero needs the exact cut-off modifier");
- break;
+ case eelRF_ZERO: fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD; break;
case eelSWITCH:
case eelSHIFT:
case eelPME:
case eelP3M_AD:
- case eelEWALD:
- fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD;
- break;
+ case eelEWALD: fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD; break;
default:
gmx_fatal(FARGS, "Unsupported electrostatic interaction: %s", eel_names[ic->eeltype]);
fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LENNARDJONES;
}
break;
- case evdwPME:
- fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LJEWALD;
- break;
+ case evdwPME: fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LJEWALD; break;
case evdwSWITCH:
case evdwSHIFT:
fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
break;
- default:
- gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[ic->vdwtype]);
+ default: gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[ic->vdwtype]);
}
fr->nbkernel_vdw_modifier = ic->vdw_modifier;
- if (ir->cutoff_scheme == ecutsGROUP)
- {
- fr->bvdwtab = ((ic->vdwtype != evdwCUT || !gmx_within_tol(ic->reppow, 12.0, 10*GMX_DOUBLE_EPS))
- && !EVDW_PME(ic->vdwtype));
- /* We have special kernels for standard Ewald and PME, but the pme-switch ones are tabulated above */
- fr->bcoultab = !(ic->eeltype == eelCUT ||
- ic->eeltype == eelEWALD ||
- ic->eeltype == eelPME ||
- ic->eeltype == eelP3M_AD ||
- ic->eeltype == eelRF ||
- ic->eeltype == eelRF_ZERO);
-
- /* If the user absolutely wants different switch/shift settings for coul/vdw, it is likely
- * going to be faster to tabulate the interaction than calling the generic kernel.
- * However, if generic kernels have been requested we keep things analytically.
- */
- if (fr->nbkernel_elec_modifier == eintmodPOTSWITCH &&
- fr->nbkernel_vdw_modifier == eintmodPOTSWITCH &&
- !bGenericKernelOnly)
- {
- if ((ic->rcoulomb_switch != ic->rvdw_switch) || (ic->rcoulomb != ic->rvdw))
- {
- fr->bcoultab = TRUE;
- /* Once we tabulate electrostatics, we can use the switch function for LJ,
- * which would otherwise need two tables.
- */
- }
- }
- else if ((fr->nbkernel_elec_modifier == eintmodPOTSHIFT && fr->nbkernel_vdw_modifier == eintmodPOTSHIFT) ||
- ((fr->nbkernel_elec_interaction == GMX_NBKERNEL_ELEC_REACTIONFIELD &&
- fr->nbkernel_elec_modifier == eintmodEXACTCUTOFF &&
- (fr->nbkernel_vdw_modifier == eintmodPOTSWITCH || fr->nbkernel_vdw_modifier == eintmodPOTSHIFT))))
- {
- if ((ic->rcoulomb != ic->rvdw) && (!bGenericKernelOnly))
- {
- fr->bcoultab = TRUE;
- }
- }
-
- if (fr->nbkernel_elec_modifier == eintmodFORCESWITCH)
- {
- fr->bcoultab = TRUE;
- }
- if (fr->nbkernel_vdw_modifier == eintmodFORCESWITCH)
- {
- fr->bvdwtab = TRUE;
- }
-
- if (getenv("GMX_REQUIRE_TABLES"))
- {
- fr->bvdwtab = TRUE;
- fr->bcoultab = TRUE;
- }
-
- if (fp)
- {
- fprintf(fp, "Table routines are used for coulomb: %s\n",
- gmx::boolToString(fr->bcoultab));
- fprintf(fp, "Table routines are used for vdw: %s\n",
- gmx::boolToString(fr->bvdwtab));
- }
-
- if (fr->bvdwtab)
- {
- fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
- fr->nbkernel_vdw_modifier = eintmodNONE;
- }
- if (fr->bcoultab)
- {
- fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
- fr->nbkernel_elec_modifier = eintmodNONE;
- }
- }
-
if (ir->cutoff_scheme == ecutsVERLET)
{
- if (!gmx_within_tol(ic->reppow, 12.0, 10*GMX_DOUBLE_EPS))
+ if (!gmx_within_tol(ic->reppow, 12.0, 10 * GMX_DOUBLE_EPS))
{
- gmx_fatal(FARGS, "Cut-off scheme %s only supports LJ repulsion power 12", ecutscheme_names[ir->cutoff_scheme]);
+ gmx_fatal(FARGS, "Cut-off scheme %s only supports LJ repulsion power 12",
+ ecutscheme_names[ir->cutoff_scheme]);
}
/* Older tpr files can contain Coulomb user tables with the Verlet cutoff-scheme,
* while mdrun does not (and never did) support this.
/* 1-4 interaction electrostatics */
fr->fudgeQQ = mtop->ffparams.fudgeQQ;
- /* Parameters for generalized RF */
- fr->zsquare = 0.0;
- fr->temp = 0.0;
-
- if (ic->eeltype == eelGRF)
- {
- init_generalized_rf(fp, mtop, ir, fr);
- }
-
fr->haveDirectVirialContributions =
- (EEL_FULL(ic->eeltype) || EVDW_PME(ic->vdwtype) ||
- fr->forceProviders->hasForceProvider() ||
- gmx_mtop_ftype_count(mtop, F_POSRES) > 0 ||
- gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0 ||
- ir->nwall > 0 ||
- ir->bPull ||
- ir->bRot ||
- ir->bIMD);
-
- if (fr->haveDirectVirialContributions)
- {
- fr->forceBufferForDirectVirialContributions = new std::vector<gmx::RVec>;
- }
+ (EEL_FULL(ic->eeltype) || EVDW_PME(ic->vdwtype) || fr->forceProviders->hasForceProvider()
+ || gmx_mtop_ftype_count(mtop, F_POSRES) > 0 || gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0
+ || ir->nwall > 0 || ir->bPull || ir->bRot || ir->bIMD);
- if (fr->cutoff_scheme == ecutsGROUP &&
- ncg_mtop(mtop) > fr->cg_nalloc && !DOMAINDECOMP(cr))
- {
- /* Count the total number of charge groups */
- fr->cg_nalloc = ncg_mtop(mtop);
- srenew(fr->cg_cm, fr->cg_nalloc);
- }
if (fr->shift_vec == nullptr)
{
snew(fr->shift_vec, SHIFTS);
}
- if (fr->fshift == nullptr)
- {
- snew(fr->fshift, SHIFTS);
- }
+ fr->shiftForces.resize(SHIFTS);
if (fr->nbfp == nullptr)
{
fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM);
if (EVDW_PME(ic->vdwtype))
{
- fr->ljpme_c6grid = make_ljpme_c6grid(&mtop->ffparams, fr);
+ fr->ljpme_c6grid = make_ljpme_c6grid(&mtop->ffparams, fr);
}
}
{
if (ic->rvdw_switch >= ic->rvdw)
{
- gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)",
- ic->rvdw_switch, ic->rvdw);
+ gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)", ic->rvdw_switch, ic->rvdw);
}
if (fp)
{
fprintf(fp, "Using %s Lennard-Jones, switch between %g and %g nm\n",
- (ic->eeltype == eelSWITCH) ? "switched" : "shifted",
- ic->rvdw_switch, ic->rvdw);
+ (ic->eeltype == eelSWITCH) ? "switched" : "shifted", ic->rvdw_switch, ic->rvdw);
}
}
if (fp && fr->cutoff_scheme == ecutsGROUP)
{
- fprintf(fp, "Cut-off's: NS: %g Coulomb: %g %s: %g\n",
- fr->rlist, ic->rcoulomb, fr->bBHAM ? "BHAM" : "LJ", ic->rvdw);
- }
-
- fr->eDispCorr = ir->eDispCorr;
- fr->numAtomsForDispersionCorrection = mtop->natoms;
- if (ir->eDispCorr != edispcNO)
- {
- set_avcsixtwelve(fp, fr, mtop);
+ fprintf(fp, "Cut-off's: NS: %g Coulomb: %g %s: %g\n", fr->rlist, ic->rcoulomb,
+ fr->bBHAM ? "BHAM" : "LJ", ic->rvdw);
}
if (ir->implicit_solvent)
gmx_fatal(FARGS, "Implict solvation is no longer supported.");
}
- /* Construct tables for the group scheme. A little unnecessary to
- * make both vdw and coul tables sometimes, but what the
- * heck. Note that both cutoff schemes construct Ewald tables in
- * init_interaction_const_tables. */
- needGroupSchemeTables = (ir->cutoff_scheme == ecutsGROUP &&
- (fr->bcoultab || fr->bvdwtab));
-
- negp_pp = ir->opts.ngener - ir->nwall;
- negptable = 0;
- if (!needGroupSchemeTables)
- {
- bSomeNormalNbListsAreInUse = TRUE;
- fr->nnblists = 1;
- }
- else
- {
- bSomeNormalNbListsAreInUse = FALSE;
- for (egi = 0; egi < negp_pp; egi++)
- {
- for (egj = egi; egj < negp_pp; egj++)
- {
- egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
- if (!(egp_flags & EGP_EXCL))
- {
- if (egp_flags & EGP_TABLE)
- {
- negptable++;
- }
- else
- {
- bSomeNormalNbListsAreInUse = TRUE;
- }
- }
- }
- }
- if (bSomeNormalNbListsAreInUse)
- {
- fr->nnblists = negptable + 1;
- }
- else
- {
- fr->nnblists = negptable;
- }
- if (fr->nnblists > 1)
- {
- snew(fr->gid2nblists, ir->opts.ngener*ir->opts.ngener);
- }
- }
-
- snew(fr->nblists, fr->nnblists);
/* This code automatically gives table length tabext without cut-off's,
* in that case grompp should already have checked that we do not need
*/
rtab = ir->rlist + ir->tabext;
- if (needGroupSchemeTables)
- {
- /* make tables for ordinary interactions */
- if (bSomeNormalNbListsAreInUse)
- {
- make_nbf_tables(fp, ic, rtab, tabfn, nullptr, nullptr, &fr->nblists[0]);
- m = 1;
- }
- else
- {
- m = 0;
- }
- if (negptable > 0)
- {
- /* Read the special tables for certain energy group pairs */
- nm_ind = mtop->groups.grps[egcENER].nm_ind;
- for (egi = 0; egi < negp_pp; egi++)
- {
- for (egj = egi; egj < negp_pp; egj++)
- {
- egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
- if ((egp_flags & EGP_TABLE) && !(egp_flags & EGP_EXCL))
- {
- if (fr->nnblists > 1)
- {
- fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = m;
- }
- /* Read the table file with the two energy groups names appended */
- make_nbf_tables(fp, ic, rtab, tabfn,
- *mtop->groups.grpname[nm_ind[egi]],
- *mtop->groups.grpname[nm_ind[egj]],
- &fr->nblists[m]);
- m++;
- }
- else if (fr->nnblists > 1)
- {
- fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = 0;
- }
- }
- }
- }
- }
-
- /* Tables might not be used for the potential modifier
- * interactions per se, but we still need them to evaluate
- * switch/shift dispersion corrections in this case. */
- if (fr->eDispCorr != edispcNO)
- {
- fr->dispersionCorrectionTable = makeDispersionCorrectionTable(fp, ic, rtab, tabfn);
- }
-
/* We want to use unmodified tables for 1-4 coulombic
* interactions, so we must in general have an extra set of
* tables. */
- if (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
- gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0 ||
- gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0)
+ if (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 || gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0
+ || gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0)
{
- fr->pairsTable = make_tables(fp, ic, tabpfn, rtab,
- GMX_MAKETABLES_14ONLY);
+ fr->pairsTable = make_tables(fp, ic, tabpfn, rtab, GMX_MAKETABLES_14ONLY);
}
/* Wall stuff */
// TODO Don't need to catch this here, when merging with master branch
try
{
- fcd->bondtab = make_bonded_tables(fp,
- F_TABBONDS, F_TABBONDSNC,
- mtop, tabbfnm, "b");
- fcd->angletab = make_bonded_tables(fp,
- F_TABANGLES, -1,
- mtop, tabbfnm, "a");
- fcd->dihtab = make_bonded_tables(fp,
- F_TABDIHS, -1,
- mtop, tabbfnm, "d");
+ fcd->bondtab = make_bonded_tables(fp, F_TABBONDS, F_TABBONDSNC, mtop, tabbfnm, "b");
+ fcd->angletab = make_bonded_tables(fp, F_TABANGLES, -1, mtop, tabbfnm, "a");
+ fcd->dihtab = make_bonded_tables(fp, F_TABDIHS, -1, mtop, tabbfnm, "d");
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
else
{
if (debug)
{
- fprintf(debug, "No fcdata or table file name passed, can not read table, can not do bonded interactions\n");
+ fprintf(debug,
+ "No fcdata or table file name passed, can not read table, can not do bonded "
+ "interactions\n");
}
}
// Initialize QM/MM if supported
if (GMX_QMMM)
{
- GMX_LOG(mdlog.info).asParagraph().
- appendText("Large parts of the QM/MM support is deprecated, and may be removed in a future "
- "version. Please get in touch with the developers if you find the support useful, "
- "as help is needed if the functionality is to continue to be available.");
+ GMX_LOG(mdlog.info)
+ .asParagraph()
+ .appendText(
+ "Large parts of the QM/MM support is deprecated, and may be removed in "
+ "a future "
+ "version. Please get in touch with the developers if you find the "
+ "support useful, "
+ "as help is needed if the functionality is to continue to be "
+ "available.");
fr->qr = mk_QMMMrec();
init_QMMMrec(cr, mtop, ir, fr);
}
else
{
- gmx_incons("QM/MM was requested, but is only available when GROMACS "
- "is configured with QM/MM support");
+ gmx_incons(
+ "QM/MM was requested, but is only available when GROMACS "
+ "is configured with QM/MM support");
}
}
/* Set all the static charge group info */
- fr->cginfo_mb = init_cginfo_mb(fp, mtop, fr, bNoSolvOpt,
- &bFEP_NonBonded,
- &fr->bExcl_IntraCGAll_InterCGNone);
- if (DOMAINDECOMP(cr))
- {
- fr->cginfo = nullptr;
- }
- else
+ fr->cginfo_mb = init_cginfo_mb(mtop, fr, &bFEP_NonBonded);
+ if (!DOMAINDECOMP(cr))
{
fr->cginfo = cginfo_expand(mtop->molblock.size(), fr->cginfo_mb);
}
if (!DOMAINDECOMP(cr))
{
- forcerec_set_ranges(fr, ncg_mtop(mtop), ncg_mtop(mtop),
- mtop->natoms, mtop->natoms, mtop->natoms);
+ forcerec_set_ranges(fr, mtop->natoms, mtop->natoms, mtop->natoms);
}
fr->print_force = print_force;
-
- /* coarse load balancing vars */
- fr->t_fnbf = 0.;
- fr->t_wait = 0.;
- fr->timesteps = 0;
-
- /* Initialize neighbor search */
- snew(fr->ns, 1);
- init_ns(fp, cr, fr->ns, fr, mtop);
-
- if (thisRankHasDuty(cr, DUTY_PP))
- {
- gmx_nonbonded_setup(fr, bGenericKernelOnly);
- }
-
/* Initialize the thread working data for bonded interactions */
- init_bonded_threading(fp, mtop->groups.grps[egcENER].nr,
- &fr->bondedThreading);
+ fr->bondedThreading = init_bonded_threading(
+ fp, mtop->groups.groups[SimulationAtomGroupType::EnergyOutput].size());
fr->nthread_ewc = gmx_omp_nthreads_get(emntBonded);
snew(fr->ewc_t, fr->nthread_ewc);
// We have PME+LJcutoff kernels for rcoulomb>rvdw.
if (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == eelCUT)
{
- GMX_RELEASE_ASSERT(ir->rcoulomb >= ir->rvdw, "With Verlet lists and PME we should have rcoulomb>=rvdw");
+ GMX_RELEASE_ASSERT(ir->rcoulomb >= ir->rvdw,
+ "With Verlet lists and PME we should have rcoulomb>=rvdw");
}
else
{
- GMX_RELEASE_ASSERT(ir->rcoulomb == ir->rvdw, "With Verlet lists and no PME rcoulomb and rvdw should be identical");
+ GMX_RELEASE_ASSERT(
+ ir->rcoulomb == ir->rvdw,
+ "With Verlet lists and no PME rcoulomb and rvdw should be identical");
}
- init_nb_verlet(mdlog, &fr->nbv, bFEP_NonBonded, ir, fr,
- cr, hardwareInfo, deviceInfo,
- mtop, box);
+ fr->nbv = Nbnxm::init_nb_verlet(mdlog, bFEP_NonBonded, ir, fr, cr, hardwareInfo, deviceInfo,
+ mtop, box, wcycle);
if (useGpuForBonded)
{
- auto stream = DOMAINDECOMP(cr)
- // TODO use havePPDomainDecomposition here to simplify the code.
- auto stream = (DOMAINDECOMP(cr) && (cr->nnodes - cr->npmenodes > 1)) ?
- nbnxn_gpu_get_command_stream(fr->nbv->gpu_nbv, eintNonlocal) :
- nbnxn_gpu_get_command_stream(fr->nbv->gpu_nbv, eintLocal);
++ auto stream = havePPDomainDecomposition(cr)
+ ? Nbnxm::gpu_get_command_stream(
+ fr->nbv->gpu_nbv, gmx::InteractionLocality::NonLocal)
+ : Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv,
+ gmx::InteractionLocality::Local);
// TODO the heap allocation is only needed while
// t_forcerec lacks a constructor.
- fr->gpuBonded = new gmx::GpuBonded(mtop->ffparams,
- stream);
+ fr->gpuBonded = new gmx::GpuBonded(mtop->ffparams, stream, wcycle);
}
}
+ if (ir->eDispCorr != edispcNO)
+ {
+ fr->dispersionCorrection = std::make_unique<DispersionCorrection>(
+ *mtop, *ir, fr->bBHAM, fr->ntype,
+ gmx::arrayRefFromArray(fr->nbfp, fr->ntype * fr->ntype * 2), *fr->ic, tabfn);
+ fr->dispersionCorrection->print(mdlog);
+ }
+
if (fp != nullptr)
{
/* Here we switch from using mdlog, which prints the newline before
fprintf(fp, "\n");
}
- if (ir->eDispCorr != edispcNO)
+ if (pmeOnlyRankUsesGpu && c_enableGpuPmePpComms)
{
- calc_enervirdiff(fp, ir->eDispCorr, fr);
+ fr->pmePpCommGpu = std::make_unique<gmx::PmePpCommGpu>(cr->mpi_comm_mysim, cr->dd->pme_nodeid);
}
}
+t_forcerec::t_forcerec() = default;
+
+t_forcerec::~t_forcerec() = default;
+
/* Frees GPU memory and sets a tMPI node barrier.
*
* Note that this function needs to be called even if GPUs are not used
* \todo Remove physical node barrier from this function after making sure
* that it's not needed anymore (with a shared GPU run).
*/
-void free_gpu_resources(t_forcerec *fr,
- const gmx::PhysicalNodeCommunicator &physicalNodeCommunicator)
+void free_gpu_resources(t_forcerec* fr,
+ const gmx::PhysicalNodeCommunicator& physicalNodeCommunicator,
+ const gmx_gpu_info_t& gpu_info)
{
- bool isPPrankUsingGPU = (fr != nullptr) && (fr->nbv != nullptr) && fr->nbv->bUseGPU;
+ bool isPPrankUsingGPU = (fr != nullptr) && (fr->nbv != nullptr) && fr->nbv->useGpu();
/* stop the GPU profiler (only CUDA) */
- stopGpuProfiler();
+ if (gpu_info.n_dev > 0)
+ {
+ stopGpuProfiler();
+ }
if (isPPrankUsingGPU)
{
- /* free nbnxn data in GPU memory */
- nbnxn_gpu_free(fr->nbv->gpu_nbv);
+ /* Free data in GPU memory and pinned memory before destroying the GPU context */
+ fr->nbv.reset();
+
delete fr->gpuBonded;
fr->gpuBonded = nullptr;
}
}
}
-void done_forcerec(t_forcerec *fr, int numMolBlocks, int numEnergyGroups)
+void done_forcerec(t_forcerec* fr, int numMolBlocks)
{
if (fr == nullptr)
{
}
done_cginfo_mb(fr->cginfo_mb, numMolBlocks);
sfree(fr->nbfp);
- done_interaction_const(fr->ic);
+ delete fr->ic;
sfree(fr->shift_vec);
- sfree(fr->fshift);
- sfree(fr->nblists);
- done_ns(fr->ns, numEnergyGroups);
sfree(fr->ewc_t);
tear_down_bonded_threading(fr->bondedThreading);
GMX_RELEASE_ASSERT(fr->gpuBonded == nullptr, "Should have been deleted earlier, when used");
fr->bondedThreading = nullptr;
- sfree(fr);
+ delete fr;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff