struct shakedata
{
- rvec *rij;
- real *half_of_reduced_mass;
- real *distance_squared_tolerance;
- real *constraint_distance_squared;
+ rvec* rij;
+ real* half_of_reduced_mass;
+ real* distance_squared_tolerance;
+ real* constraint_distance_squared;
int nalloc;
/* SOR stuff */
- real delta;
- real omega;
- real gamma;
- int nblocks; /* The number of SHAKE blocks */
- int *sblock; /* The SHAKE blocks */
- int sblock_nalloc; /* The allocation size of sblock */
+ real delta;
+ real omega;
+ real gamma;
+ int nblocks; /* The number of SHAKE blocks */
+ int* sblock; /* The SHAKE blocks */
+ int sblock_nalloc; /* The allocation size of sblock */
/*! \brief Scaled Lagrange multiplier for each constraint.
*
* Value is -2 * eta from p. 336 of the paper, divided by the
* constraint distance. */
- real *scaled_lagrange_multiplier;
- int lagr_nalloc; /* The allocation size of scaled_lagrange_multiplier */
+ real* scaled_lagrange_multiplier;
+ int lagr_nalloc; /* The allocation size of scaled_lagrange_multiplier */
};
-shakedata *shake_init()
+shakedata* shake_init()
{
- shakedata *d;
+ shakedata* d;
snew(d, 1);
return d;
}
-void done_shake(shakedata *d)
+void done_shake(shakedata* d)
{
sfree(d->rij);
sfree(d->half_of_reduced_mass);
sfree(d);
}
-typedef struct {
+typedef struct
+{
int iatom[3];
int blocknr;
} t_sortblock;
//! Compares sort blocks.
-static int pcomp(const void *p1, const void *p2)
+static int pcomp(const void* p1, const void* p2)
{
int db;
int min1, min2, max1, max2;
- const t_sortblock *a1 = reinterpret_cast<const t_sortblock*>(p1);
- const t_sortblock *a2 = reinterpret_cast<const t_sortblock*>(p2);
+ const t_sortblock* a1 = reinterpret_cast<const t_sortblock*>(p1);
+ const t_sortblock* a2 = reinterpret_cast<const t_sortblock*>(p2);
- db = a1->blocknr-a2->blocknr;
+ db = a1->blocknr - a2->blocknr;
if (db != 0)
{
if (min1 == min2)
{
- return max1-max2;
+ return max1 - max2;
}
else
{
- return min1-min2;
+ return min1 - min2;
}
}
//! Prints sortblocks
-static void pr_sortblock(FILE *fp, const char *title, int nsb, t_sortblock sb[])
+static void pr_sortblock(FILE* fp, const char* title, int nsb, t_sortblock sb[])
{
int i;
fprintf(fp, "%s\n", title);
for (i = 0; (i < nsb); i++)
{
- fprintf(fp, "i: %5d, iatom: (%5d %5d %5d), blocknr: %5d\n",
- i, sb[i].iatom[0], sb[i].iatom[1], sb[i].iatom[2],
- sb[i].blocknr);
+ fprintf(fp, "i: %5d, iatom: (%5d %5d %5d), blocknr: %5d\n", i, sb[i].iatom[0],
+ sb[i].iatom[1], sb[i].iatom[2], sb[i].blocknr);
}
}
//! Reallocates a vector.
-static void resizeLagrangianData(shakedata *shaked, int ncons)
+static void resizeLagrangianData(shakedata* shaked, int ncons)
{
if (ncons > shaked->lagr_nalloc)
{
}
}
-void
-make_shake_sblock_serial(shakedata *shaked,
- const t_idef *idef, const t_mdatoms &md)
+void make_shake_sblock_serial(shakedata* shaked, const t_idef* idef, const t_mdatoms& md)
{
int i, j, m, ncons;
int bstart, bnr;
t_blocka sblocks;
- t_sortblock *sb;
- t_iatom *iatom;
- int *inv_sblock;
+ t_sortblock* sb;
+ t_iatom* iatom;
+ int* inv_sblock;
/* Since we are processing the local topology,
* the F_CONSTRNC ilist has been concatenated to the F_CONSTR ilist.
*/
- ncons = idef->il[F_CONSTR].nr/3;
+ ncons = idef->il[F_CONSTR].nr / 3;
init_blocka(&sblocks);
sfree(sblocks.index); // To solve memory leak
shaked->nblocks = sblocks.nr;
if (debug)
{
- fprintf(debug, "ncons: %d, bstart: %d, nblocks: %d\n",
- ncons, bstart, shaked->nblocks);
+ fprintf(debug, "ncons: %d, bstart: %d, nblocks: %d\n", ncons, bstart, shaked->nblocks);
}
/* Calculate block number for each atom */
}
j = 0;
- snew(shaked->sblock, shaked->nblocks+1);
+ snew(shaked->sblock, shaked->nblocks + 1);
bnr = -2;
for (i = 0; (i < ncons); i++)
{
if (sb[i].blocknr != bnr)
{
bnr = sb[i].blocknr;
- shaked->sblock[j++] = 3*i;
+ shaked->sblock[j++] = 3 * i;
}
}
/* Last block... */
- shaked->sblock[j++] = 3*ncons;
+ shaked->sblock[j++] = 3 * ncons;
- if (j != (shaked->nblocks+1))
+ if (j != (shaked->nblocks + 1))
{
fprintf(stderr, "bstart: %d\n", bstart);
- fprintf(stderr, "j: %d, nblocks: %d, ncons: %d\n",
- j, shaked->nblocks, ncons);
+ fprintf(stderr, "j: %d, nblocks: %d, ncons: %d\n", j, shaked->nblocks, ncons);
for (i = 0; (i < ncons); i++)
{
fprintf(stderr, "i: %5d sb[i].blocknr: %5d\n", i, sb[i].blocknr);
{
fprintf(stderr, "sblock[%3d]=%5d\n", j, shaked->sblock[j]);
}
- gmx_fatal(FARGS, "DEATH HORROR: "
+ gmx_fatal(FARGS,
+ "DEATH HORROR: "
"sblocks does not match idef->il[F_CONSTR]");
}
sfree(sb);
}
// TODO: Check if this code is useful. It might never be called.
-void
-make_shake_sblock_dd(shakedata *shaked,
- const t_ilist *ilcon,
- const gmx_domdec_t *dd)
+void make_shake_sblock_dd(shakedata* shaked, const t_ilist* ilcon, const gmx_domdec_t* dd)
{
int ncons, c, cg;
- t_iatom *iatom;
+ t_iatom* iatom;
- if (dd->ncg_home+1 > shaked->sblock_nalloc)
+ if (dd->ncg_home + 1 > shaked->sblock_nalloc)
{
- shaked->sblock_nalloc = over_alloc_dd(dd->ncg_home+1);
+ shaked->sblock_nalloc = over_alloc_dd(dd->ncg_home + 1);
srenew(shaked->sblock, shaked->sblock_nalloc);
}
- ncons = ilcon->nr/3;
+ ncons = ilcon->nr / 3;
iatom = ilcon->iatoms;
shaked->nblocks = 0;
cg = 0;
{
if (c == 0 || iatom[1] >= cg + 1)
{
- shaked->sblock[shaked->nblocks++] = 3*c;
+ shaked->sblock[shaked->nblocks++] = 3 * c;
while (iatom[1] >= cg + 1)
{
cg++;
}
iatom += 3;
}
- shaked->sblock[shaked->nblocks] = 3*ncons;
+ shaked->sblock[shaked->nblocks] = 3 * ncons;
resizeLagrangianData(shaked, ncons);
}
* problematic constraint if the input was malformed
*
* \todo Make SHAKE use better data structures, in particular for iatom. */
-void cshake(const int iatom[], int ncon, int *nnit, int maxnit,
- const real constraint_distance_squared[], real positions[],
- const real initial_displacements[], const real half_of_reduced_mass[], real omega,
- const real invmass[], const real distance_squared_tolerance[],
- real scaled_lagrange_multiplier[], int *nerror)
+void cshake(const int iatom[],
+ int ncon,
+ int* nnit,
+ int maxnit,
+ const real constraint_distance_squared[],
+ real positions[],
+ const real initial_displacements[],
+ const real half_of_reduced_mass[],
+ real omega,
+ const real invmass[],
+ const real distance_squared_tolerance[],
+ real scaled_lagrange_multiplier[],
+ int* nerror)
{
/* default should be increased! MRS 8/4/2009 */
const real mytol = 1e-10;
- int ll, i, j, i3, j3, l3;
- int ix, iy, iz, jx, jy, jz;
- real r_dot_r_prime;
- real constraint_distance_squared_ll;
- real r_prime_squared;
- real scaled_lagrange_multiplier_ll;
- real r_prime_x, r_prime_y, r_prime_z, diff, im, jm;
- real xh, yh, zh, rijx, rijy, rijz;
- int nit, error, nconv;
- real iconvf;
+ int ll, i, j, i3, j3, l3;
+ int ix, iy, iz, jx, jy, jz;
+ real r_dot_r_prime;
+ real constraint_distance_squared_ll;
+ real r_prime_squared;
+ real scaled_lagrange_multiplier_ll;
+ real r_prime_x, r_prime_y, r_prime_z, diff, im, jm;
+ real xh, yh, zh, rijx, rijy, rijz;
+ int nit, error, nconv;
+ real iconvf;
// TODO nconv is used solely as a boolean, so we should write the
// code like that
nconv = 0;
for (ll = 0; (ll < ncon) && (error == 0); ll++)
{
- l3 = 3*ll;
- rijx = initial_displacements[l3+XX];
- rijy = initial_displacements[l3+YY];
- rijz = initial_displacements[l3+ZZ];
- i = iatom[l3+1];
- j = iatom[l3+2];
- i3 = 3*i;
- j3 = 3*j;
- ix = i3+XX;
- iy = i3+YY;
- iz = i3+ZZ;
- jx = j3+XX;
- jy = j3+YY;
- jz = j3+ZZ;
+ l3 = 3 * ll;
+ rijx = initial_displacements[l3 + XX];
+ rijy = initial_displacements[l3 + YY];
+ rijz = initial_displacements[l3 + ZZ];
+ i = iatom[l3 + 1];
+ j = iatom[l3 + 2];
+ i3 = 3 * i;
+ j3 = 3 * j;
+ ix = i3 + XX;
+ iy = i3 + YY;
+ iz = i3 + ZZ;
+ jx = j3 + XX;
+ jy = j3 + YY;
+ jz = j3 + ZZ;
/* Compute r prime between atoms i and j, which is the
displacement *before* this update stage */
- r_prime_x = positions[ix]-positions[jx];
- r_prime_y = positions[iy]-positions[jy];
- r_prime_z = positions[iz]-positions[jz];
- r_prime_squared = (r_prime_x * r_prime_x +
- r_prime_y * r_prime_y +
- r_prime_z * r_prime_z);
+ r_prime_x = positions[ix] - positions[jx];
+ r_prime_y = positions[iy] - positions[jy];
+ r_prime_z = positions[iz] - positions[jz];
+ r_prime_squared = (r_prime_x * r_prime_x + r_prime_y * r_prime_y + r_prime_z * r_prime_z);
constraint_distance_squared_ll = constraint_distance_squared[ll];
- diff = constraint_distance_squared_ll - r_prime_squared;
+ diff = constraint_distance_squared_ll - r_prime_squared;
/* iconvf is less than 1 when the error is smaller than a bound */
iconvf = fabs(diff) * distance_squared_tolerance[ll];
if (iconvf > 1.0)
{
nconv = static_cast<int>(iconvf);
- r_dot_r_prime = (rijx * r_prime_x +
- rijy * r_prime_y +
- rijz * r_prime_z);
+ r_dot_r_prime = (rijx * r_prime_x + rijy * r_prime_y + rijz * r_prime_z);
if (r_dot_r_prime < constraint_distance_squared_ll * mytol)
{
- error = ll+1;
+ error = ll + 1;
}
else
{
/* The next line solves equation 5.6 (neglecting
the term in g^2), for g */
- scaled_lagrange_multiplier_ll = omega*diff*half_of_reduced_mass[ll]/r_dot_r_prime;
+ scaled_lagrange_multiplier_ll = omega * diff * half_of_reduced_mass[ll] / r_dot_r_prime;
scaled_lagrange_multiplier[ll] += scaled_lagrange_multiplier_ll;
- xh = rijx * scaled_lagrange_multiplier_ll;
- yh = rijy * scaled_lagrange_multiplier_ll;
- zh = rijz * scaled_lagrange_multiplier_ll;
- im = invmass[i];
- jm = invmass[j];
- positions[ix] += xh*im;
- positions[iy] += yh*im;
- positions[iz] += zh*im;
- positions[jx] -= xh*jm;
- positions[jy] -= yh*jm;
- positions[jz] -= zh*jm;
+ xh = rijx * scaled_lagrange_multiplier_ll;
+ yh = rijy * scaled_lagrange_multiplier_ll;
+ zh = rijz * scaled_lagrange_multiplier_ll;
+ im = invmass[i];
+ jm = invmass[j];
+ positions[ix] += xh * im;
+ positions[iy] += yh * im;
+ positions[iz] += zh * im;
+ positions[jx] -= xh * jm;
+ positions[jy] -= yh * jm;
+ positions[jz] -= zh * jm;
}
}
}
}
//! Implements RATTLE (ie. SHAKE for velocity verlet integrators)
-static void
-crattle(const int iatom[], int ncon, int *nnit, int maxnit,
- const real constraint_distance_squared[], real vp[], const real rij[], const real m2[], real omega,
- const real invmass[], const real distance_squared_tolerance[], real scaled_lagrange_multiplier[],
- int *nerror, real invdt)
+static void crattle(const int iatom[],
+ int ncon,
+ int* nnit,
+ int maxnit,
+ const real constraint_distance_squared[],
+ real vp[],
+ const real rij[],
+ const real m2[],
+ real omega,
+ const real invmass[],
+ const real distance_squared_tolerance[],
+ real scaled_lagrange_multiplier[],
+ int* nerror,
+ real invdt)
{
/*
* r.c. van schaik and w.f. van gunsteren
* second part of rattle algorithm
*/
- int ll, i, j, i3, j3, l3;
- int ix, iy, iz, jx, jy, jz;
- real constraint_distance_squared_ll;
- real vpijd, vx, vy, vz, acor, fac, im, jm;
- real xh, yh, zh, rijx, rijy, rijz;
- int nit, error, nconv;
- real iconvf;
+ int ll, i, j, i3, j3, l3;
+ int ix, iy, iz, jx, jy, jz;
+ real constraint_distance_squared_ll;
+ real vpijd, vx, vy, vz, acor, fac, im, jm;
+ real xh, yh, zh, rijx, rijy, rijz;
+ int nit, error, nconv;
+ real iconvf;
// TODO nconv is used solely as a boolean, so we should write the
// code like that
nconv = 0;
for (ll = 0; (ll < ncon) && (error == 0); ll++)
{
- l3 = 3*ll;
- rijx = rij[l3+XX];
- rijy = rij[l3+YY];
- rijz = rij[l3+ZZ];
- i = iatom[l3+1];
- j = iatom[l3+2];
- i3 = 3*i;
- j3 = 3*j;
- ix = i3+XX;
- iy = i3+YY;
- iz = i3+ZZ;
- jx = j3+XX;
- jy = j3+YY;
- jz = j3+ZZ;
- vx = vp[ix]-vp[jx];
- vy = vp[iy]-vp[jy];
- vz = vp[iz]-vp[jz];
-
- vpijd = vx*rijx+vy*rijy+vz*rijz;
+ l3 = 3 * ll;
+ rijx = rij[l3 + XX];
+ rijy = rij[l3 + YY];
+ rijz = rij[l3 + ZZ];
+ i = iatom[l3 + 1];
+ j = iatom[l3 + 2];
+ i3 = 3 * i;
+ j3 = 3 * j;
+ ix = i3 + XX;
+ iy = i3 + YY;
+ iz = i3 + ZZ;
+ jx = j3 + XX;
+ jy = j3 + YY;
+ jz = j3 + ZZ;
+ vx = vp[ix] - vp[jx];
+ vy = vp[iy] - vp[jy];
+ vz = vp[iz] - vp[jz];
+
+ vpijd = vx * rijx + vy * rijy + vz * rijz;
constraint_distance_squared_ll = constraint_distance_squared[ll];
/* iconv is zero when the error is smaller than a bound */
- iconvf = fabs(vpijd)*(distance_squared_tolerance[ll]/invdt);
+ iconvf = fabs(vpijd) * (distance_squared_tolerance[ll] / invdt);
if (iconvf > 1)
{
- nconv = static_cast<int>(iconvf);
- fac = omega*2.0*m2[ll]/constraint_distance_squared_ll;
- acor = -fac*vpijd;
+ nconv = static_cast<int>(iconvf);
+ fac = omega * 2.0 * m2[ll] / constraint_distance_squared_ll;
+ acor = -fac * vpijd;
scaled_lagrange_multiplier[ll] += acor;
- xh = rijx*acor;
- yh = rijy*acor;
- zh = rijz*acor;
-
- im = invmass[i];
- jm = invmass[j];
-
- vp[ix] += xh*im;
- vp[iy] += yh*im;
- vp[iz] += zh*im;
- vp[jx] -= xh*jm;
- vp[jy] -= yh*jm;
- vp[jz] -= zh*jm;
+ xh = rijx * acor;
+ yh = rijy * acor;
+ zh = rijz * acor;
+
+ im = invmass[i];
+ jm = invmass[j];
+
+ vp[ix] += xh * im;
+ vp[iy] += yh * im;
+ vp[iz] += zh * im;
+ vp[jx] -= xh * jm;
+ vp[jy] -= yh * jm;
+ vp[jz] -= zh * jm;
}
}
}
}
//! Applies SHAKE
-static int vec_shakef(FILE *fplog, shakedata *shaked,
- const real invmass[], int ncon,
- t_iparams ip[], t_iatom *iatom,
- real tol, const rvec x[], rvec prime[], real omega,
- bool bFEP, real lambda, real scaled_lagrange_multiplier[],
- real invdt, rvec *v,
- bool bCalcVir, tensor vir_r_m_dr, ConstraintVariable econq)
+static int vec_shakef(FILE* fplog,
+ shakedata* shaked,
+ const real invmass[],
+ int ncon,
+ t_iparams ip[],
+ t_iatom* iatom,
+ real tol,
+ const rvec x[],
+ rvec prime[],
+ real omega,
+ bool bFEP,
+ real lambda,
+ real scaled_lagrange_multiplier[],
+ real invdt,
+ rvec* v,
+ bool bCalcVir,
+ tensor vir_r_m_dr,
+ ConstraintVariable econq)
{
- rvec *rij;
- real *half_of_reduced_mass, *distance_squared_tolerance, *constraint_distance_squared;
+ rvec* rij;
+ real * half_of_reduced_mass, *distance_squared_tolerance, *constraint_distance_squared;
int maxnit = 1000;
int nit = 0, ll, i, j, d, d2, type;
- t_iatom *ia;
+ t_iatom* ia;
real L1;
real mm = 0., tmp;
int error = 0;
srenew(shaked->distance_squared_tolerance, shaked->nalloc);
srenew(shaked->constraint_distance_squared, shaked->nalloc);
}
- rij = shaked->rij;
- half_of_reduced_mass = shaked->half_of_reduced_mass;
- distance_squared_tolerance = shaked->distance_squared_tolerance;
- constraint_distance_squared = shaked->constraint_distance_squared;
+ rij = shaked->rij;
+ half_of_reduced_mass = shaked->half_of_reduced_mass;
+ distance_squared_tolerance = shaked->distance_squared_tolerance;
+ constraint_distance_squared = shaked->constraint_distance_squared;
- L1 = 1.0-lambda;
- ia = iatom;
+ L1 = 1.0 - lambda;
+ ia = iatom;
for (ll = 0; (ll < ncon); ll++, ia += 3)
{
- type = ia[0];
- i = ia[1];
- j = ia[2];
-
- mm = 2.0*(invmass[i]+invmass[j]);
- rij[ll][XX] = x[i][XX]-x[j][XX];
- rij[ll][YY] = x[i][YY]-x[j][YY];
- rij[ll][ZZ] = x[i][ZZ]-x[j][ZZ];
- half_of_reduced_mass[ll] = 1.0/mm;
+ type = ia[0];
+ i = ia[1];
+ j = ia[2];
+
+ mm = 2.0 * (invmass[i] + invmass[j]);
+ rij[ll][XX] = x[i][XX] - x[j][XX];
+ rij[ll][YY] = x[i][YY] - x[j][YY];
+ rij[ll][ZZ] = x[i][ZZ] - x[j][ZZ];
+ half_of_reduced_mass[ll] = 1.0 / mm;
if (bFEP)
{
- constraint_distance = L1*ip[type].constr.dA + lambda*ip[type].constr.dB;
+ constraint_distance = L1 * ip[type].constr.dA + lambda * ip[type].constr.dB;
}
else
{
constraint_distance = ip[type].constr.dA;
}
- constraint_distance_squared[ll] = gmx::square(constraint_distance);
- distance_squared_tolerance[ll] = 0.5/(constraint_distance_squared[ll]*tol);
+ constraint_distance_squared[ll] = gmx::square(constraint_distance);
+ distance_squared_tolerance[ll] = 0.5 / (constraint_distance_squared[ll] * tol);
}
switch (econq)
{
case ConstraintVariable::Positions:
- cshake(iatom, ncon, &nit, maxnit, constraint_distance_squared, prime[0], rij[0], half_of_reduced_mass, omega, invmass, distance_squared_tolerance, scaled_lagrange_multiplier, &error);
+ cshake(iatom, ncon, &nit, maxnit, constraint_distance_squared, prime[0], rij[0],
+ half_of_reduced_mass, omega, invmass, distance_squared_tolerance,
+ scaled_lagrange_multiplier, &error);
break;
case ConstraintVariable::Velocities:
- crattle(iatom, ncon, &nit, maxnit, constraint_distance_squared, prime[0], rij[0], half_of_reduced_mass, omega, invmass, distance_squared_tolerance, scaled_lagrange_multiplier, &error, invdt);
+ crattle(iatom, ncon, &nit, maxnit, constraint_distance_squared, prime[0], rij[0],
+ half_of_reduced_mass, omega, invmass, distance_squared_tolerance,
+ scaled_lagrange_multiplier, &error, invdt);
break;
- default:
- gmx_incons("Unknown constraint quantity for SHAKE");
+ default: gmx_incons("Unknown constraint quantity for SHAKE");
}
if (nit >= maxnit)
{
if (fplog)
{
- fprintf(fplog, "Inner product between old and new vector <= 0.0!\n"
+ fprintf(fplog,
+ "Inner product between old and new vector <= 0.0!\n"
"constraint #%d atoms %d and %d\n",
- error-1, iatom[3*(error-1)+1]+1, iatom[3*(error-1)+2]+1);
+ error - 1, iatom[3 * (error - 1) + 1] + 1, iatom[3 * (error - 1) + 2] + 1);
}
- fprintf(stderr, "Inner product between old and new vector <= 0.0!\n"
+ fprintf(stderr,
+ "Inner product between old and new vector <= 0.0!\n"
"constraint #%d atoms %d and %d\n",
- error-1, iatom[3*(error-1)+1]+1, iatom[3*(error-1)+2]+1);
+ error - 1, iatom[3 * (error - 1) + 1] + 1, iatom[3 * (error - 1) + 2] + 1);
nit = 0;
}
for (ll = 0; (ll < ncon); ll++, ia += 3)
{
- type = ia[0];
- i = ia[1];
- j = ia[2];
+ type = ia[0];
+ i = ia[1];
+ j = ia[2];
if ((econq == ConstraintVariable::Positions) && v != nullptr)
{
/* Correct the velocities */
- mm = scaled_lagrange_multiplier[ll]*invmass[i]*invdt;
+ mm = scaled_lagrange_multiplier[ll] * invmass[i] * invdt;
for (d = 0; d < DIM; d++)
{
- v[ia[1]][d] += mm*rij[ll][d];
+ v[ia[1]][d] += mm * rij[ll][d];
}
- mm = scaled_lagrange_multiplier[ll]*invmass[j]*invdt;
+ mm = scaled_lagrange_multiplier[ll] * invmass[j] * invdt;
for (d = 0; d < DIM; d++)
{
- v[ia[2]][d] -= mm*rij[ll][d];
+ v[ia[2]][d] -= mm * rij[ll][d];
}
/* 16 flops */
}
mm = scaled_lagrange_multiplier[ll];
for (d = 0; d < DIM; d++)
{
- tmp = mm*rij[ll][d];
+ tmp = mm * rij[ll][d];
for (d2 = 0; d2 < DIM; d2++)
{
- vir_r_m_dr[d][d2] -= tmp*rij[ll][d2];
+ vir_r_m_dr[d][d2] -= tmp * rij[ll][d2];
}
}
/* 21 flops */
the reciprocal of the constraint length, so fix that */
if (bFEP)
{
- constraint_distance = L1*ip[type].constr.dA + lambda*ip[type].constr.dB;
+ constraint_distance = L1 * ip[type].constr.dA + lambda * ip[type].constr.dB;
}
else
{
}
//! Check that constraints are satisfied.
-static void check_cons(FILE *log, int nc, const rvec x[], rvec prime[], rvec v[],
- t_iparams ip[], t_iatom *iatom,
- const real invmass[], ConstraintVariable econq)
+static void check_cons(FILE* log,
+ int nc,
+ const rvec x[],
+ rvec prime[],
+ rvec v[],
+ t_iparams ip[],
+ t_iatom* iatom,
+ const real invmass[],
+ ConstraintVariable econq)
{
- t_iatom *ia;
+ t_iatom* ia;
int ai, aj;
int i;
real d, dp;
rvec dx, dv;
GMX_ASSERT(v, "Input has to be non-null");
- fprintf(log,
- " i mi j mj before after should be\n");
+ fprintf(log, " i mi j mj before after should be\n");
ia = iatom;
for (i = 0; (i < nc); i++, ia += 3)
{
case ConstraintVariable::Positions:
rvec_sub(prime[ai], prime[aj], dx);
dp = norm(dx);
- fprintf(log, "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n",
- ai+1, 1.0/invmass[ai],
- aj+1, 1.0/invmass[aj], d, dp, ip[ia[0]].constr.dA);
+ fprintf(log, "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n", ai + 1,
+ 1.0 / invmass[ai], aj + 1, 1.0 / invmass[aj], d, dp, ip[ia[0]].constr.dA);
break;
case ConstraintVariable::Velocities:
rvec_sub(v[ai], v[aj], dv);
d = iprod(dx, dv);
rvec_sub(prime[ai], prime[aj], dv);
dp = iprod(dx, dv);
- fprintf(log, "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n",
- ai+1, 1.0/invmass[ai],
- aj+1, 1.0/invmass[aj], d, dp, 0.);
+ fprintf(log, "%5d %5.2f %5d %5.2f %10.5f %10.5f %10.5f\n", ai + 1,
+ 1.0 / invmass[ai], aj + 1, 1.0 / invmass[aj], d, dp, 0.);
break;
- default:
- gmx_incons("Unknown constraint quantity for SHAKE");
+ default: gmx_incons("Unknown constraint quantity for SHAKE");
}
}
}
//! Applies SHAKE.
-static bool
-bshakef(FILE *log, shakedata *shaked,
- const real invmass[],
- const t_idef &idef, const t_inputrec &ir, const rvec x_s[], rvec prime[],
- t_nrnb *nrnb, real lambda, real *dvdlambda,
- real invdt, rvec *v, bool bCalcVir, tensor vir_r_m_dr,
- bool bDumpOnError, ConstraintVariable econq)
+static bool bshakef(FILE* log,
+ shakedata* shaked,
+ const real invmass[],
+ const t_idef& idef,
+ const t_inputrec& ir,
+ const rvec x_s[],
+ rvec prime[],
+ t_nrnb* nrnb,
+ real lambda,
+ real* dvdlambda,
+ real invdt,
+ rvec* v,
+ bool bCalcVir,
+ tensor vir_r_m_dr,
+ bool bDumpOnError,
+ ConstraintVariable econq)
{
- t_iatom *iatoms;
- real *lam, dt_2, dvdl;
+ t_iatom* iatoms;
+ real * lam, dt_2, dvdl;
int i, n0, ncon, blen, type, ll;
int tnit = 0, trij = 0;
- ncon = idef.il[F_CONSTR].nr/3;
+ ncon = idef.il[F_CONSTR].nr / 3;
for (ll = 0; ll < ncon; ll++)
{
// sblock data structure is organized differently?
iatoms = &(idef.il[F_CONSTR].iatoms[shaked->sblock[0]]);
lam = shaked->scaled_lagrange_multiplier;
- for (i = 0; (i < shaked->nblocks); )
+ for (i = 0; (i < shaked->nblocks);)
{
- blen = (shaked->sblock[i+1]-shaked->sblock[i]);
+ blen = (shaked->sblock[i + 1] - shaked->sblock[i]);
blen /= 3;
- n0 = vec_shakef(log, shaked, invmass, blen, idef.iparams,
- iatoms, ir.shake_tol, x_s, prime, shaked->omega,
- ir.efep != efepNO, lambda, lam, invdt, v, bCalcVir, vir_r_m_dr,
- econq);
+ n0 = vec_shakef(log, shaked, invmass, blen, idef.iparams, iatoms, ir.shake_tol, x_s, prime,
+ shaked->omega, ir.efep != efepNO, lambda, lam, invdt, v, bCalcVir,
+ vir_r_m_dr, econq);
if (n0 == 0)
{
}
return FALSE;
}
- tnit += n0*blen;
- trij += blen;
- iatoms += 3*blen; /* Increment pointer! */
- lam += blen;
+ tnit += n0 * blen;
+ trij += blen;
+ iatoms += 3 * blen; /* Increment pointer! */
+ lam += blen;
i++;
}
/* only for position part? */
{
real bondA, bondB;
/* TODO This should probably use invdt, so that sd integrator scaling works properly */
- dt_2 = 1/gmx::square(ir.delta_t);
+ dt_2 = 1 / gmx::square(ir.delta_t);
dvdl = 0;
for (ll = 0; ll < ncon; ll++)
{
- type = idef.il[F_CONSTR].iatoms[3*ll];
+ type = idef.il[F_CONSTR].iatoms[3 * ll];
/* Per equations in the manual, dv/dl = -2 \sum_ll lagrangian_ll * r_ll * (d_B - d_A) */
- /* The vector scaled_lagrange_multiplier[ll] contains the value -2 r_ll eta_ll (eta_ll is the
- estimate of the Langrangian, definition on page 336 of Ryckaert et al 1977),
- so the pre-factors are already present. */
+ /* The vector scaled_lagrange_multiplier[ll] contains the value -2 r_ll eta_ll
+ (eta_ll is the estimate of the Langrangian, definition on page 336 of Ryckaert et
+ al 1977), so the pre-factors are already present. */
bondA = idef.iparams[type].constr.dA;
bondB = idef.iparams[type].constr.dB;
dvdl += shaked->scaled_lagrange_multiplier[ll] * dt_2 * (bondB - bondA);
shaked->delta *= -0.5;
}
shaked->omega += shaked->delta;
- shaked->gamma = tnit;
+ shaked->gamma = tnit;
}
inc_nrnb(nrnb, eNR_SHAKE, tnit);
inc_nrnb(nrnb, eNR_SHAKE_RIJ, trij);
if (v)
{
- inc_nrnb(nrnb, eNR_CONSTR_V, trij*2);
+ inc_nrnb(nrnb, eNR_CONSTR_V, trij * 2);
}
if (bCalcVir)
{
return TRUE;
}
-bool
-constrain_shake(FILE *log,
- shakedata *shaked,
- const real invmass[],
- const t_idef &idef,
- const t_inputrec &ir,
- const rvec x_s[],
- rvec xprime[],
- rvec vprime[],
- t_nrnb *nrnb,
- real lambda,
- real *dvdlambda,
- real invdt,
- rvec *v,
- bool bCalcVir,
- tensor vir_r_m_dr,
- bool bDumpOnError,
- ConstraintVariable econq)
+bool constrain_shake(FILE* log,
+ shakedata* shaked,
+ const real invmass[],
+ const t_idef& idef,
+ const t_inputrec& ir,
+ const rvec x_s[],
+ rvec xprime[],
+ rvec vprime[],
+ t_nrnb* nrnb,
+ real lambda,
+ real* dvdlambda,
+ real invdt,
+ rvec* v,
+ bool bCalcVir,
+ tensor vir_r_m_dr,
+ bool bDumpOnError,
+ ConstraintVariable econq)
{
if (shaked->nblocks == 0)
{
switch (econq)
{
case (ConstraintVariable::Positions):
- bOK = bshakef(log, shaked,
- invmass,
- idef, ir, x_s, xprime, nrnb,
- lambda, dvdlambda,
- invdt, v, bCalcVir, vir_r_m_dr,
- bDumpOnError, econq);
+ bOK = bshakef(log, shaked, invmass, idef, ir, x_s, xprime, nrnb, lambda, dvdlambda,
+ invdt, v, bCalcVir, vir_r_m_dr, bDumpOnError, econq);
break;
case (ConstraintVariable::Velocities):
- bOK = bshakef(log, shaked,
- invmass,
- idef, ir, x_s, vprime, nrnb,
- lambda, dvdlambda,
- invdt, nullptr, bCalcVir, vir_r_m_dr,
- bDumpOnError, econq);
+ bOK = bshakef(log, shaked, invmass, idef, ir, x_s, vprime, nrnb, lambda, dvdlambda,
+ invdt, nullptr, bCalcVir, vir_r_m_dr, bDumpOnError, econq);
break;
default:
- gmx_fatal(FARGS, "Internal error, SHAKE called for constraining something else than coordinates");
+ gmx_fatal(FARGS,
+ "Internal error, SHAKE called for constraining something else than "
+ "coordinates");
}
return bOK;
}
-} // namespace gmx
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff