/* calculate the point t in [0..1] on the (convex) bezier curve
(p0,p1,p2,p3) which is tangent to q1-q0. Return -1.0 if there is no
solution in [0..1]. */
static double tangent(dpoint_t p0, dpoint_t p1, dpoint_t p2, dpoint_t p3, dpoint_t q0, dpoint_t q1) {
double A, B, C; /* (1-t)^2 A + 2(1-t)t B + t^2 C = 0 */
double a, b, c; /* a t^2 + b t + c = 0 */
double d, s, r1, r2;
A = cprod(p0, p1, q0, q1);
B = cprod(p1, p2, q0, q1);
C = cprod(p2, p3, q0, q1);
a = A - 2*B + C;
b = -2*A + 2*B;
c = A;
d = b*b - 4*a*c;
if (a==0 || d<0) {
return -1.0;
}
s = sqrt(d);
r1 = (-b + s) / (2 * a);
r2 = (-b - s) / (2 * a);
if (r1 >= 0 && r1 <= 1) {
return r1;
} else if (r2 >= 0 && r2 <= 1) {
return r2;
} else {
return -1.0;
}
}
real calc_cm(FILE *log,int natoms,real mass[],rvec x[],rvec v[],
rvec xcm,rvec vcm,rvec acm,matrix L)
{
rvec dx,a0;
real tm,m0;
int i,m;
clear_rvec(xcm);
clear_rvec(vcm);
clear_rvec(acm);
tm=0.0;
for(i=0; (i<natoms); i++) {
m0=mass[i];
tm+=m0;
cprod(x[i],v[i],a0);
for(m=0; (m<DIM); m++) {
xcm[m]+=m0*x[i][m]; /* c.o.m. position */
vcm[m]+=m0*v[i][m]; /* c.o.m. velocity */
acm[m]+=m0*a0[m]; /* rotational velocity around c.o.m. */
}
}
cprod(xcm,vcm,a0);
for(m=0; (m<DIM); m++) {
xcm[m]/=tm;
vcm[m]/=tm;
acm[m]-=a0[m]/tm;
}
#define PVEC(str,v) fprintf(log,\
"%s[X]: %10.5e %s[Y]: %10.5e %s[Z]: %10.5e\n", \
str,v[0],str,v[1],str,v[2])
#ifdef DEBUG
PVEC("xcm",xcm);
PVEC("acm",acm);
PVEC("vcm",vcm);
#endif
clear_mat(L);
for(i=0; (i<natoms); i++) {
m0=mass[i];
for(m=0; (m<DIM); m++)
dx[m]=x[i][m]-xcm[m];
L[XX][XX]+=dx[XX]*dx[XX]*m0;
L[XX][YY]+=dx[XX]*dx[YY]*m0;
L[XX][ZZ]+=dx[XX]*dx[ZZ]*m0;
L[YY][YY]+=dx[YY]*dx[YY]*m0;
L[YY][ZZ]+=dx[YY]*dx[ZZ]*m0;
L[ZZ][ZZ]+=dx[ZZ]*dx[ZZ]*m0;
}
#ifdef DEBUG
PVEC("L-x",L[XX]);
PVEC("L-y",L[YY]);
PVEC("L-z",L[ZZ]);
#endif
return tm;
}
void calc_rotmatrix(rvec principal_axis, rvec targetvec, matrix rotmatrix)
{
rvec rotvec;
real ux,uy,uz,costheta,sintheta;
costheta = cos_angle(principal_axis,targetvec);
sintheta=sqrt(1.0-costheta*costheta); /* sign is always positive since 0<theta<pi */
/* Determine rotation from cross product with target vector */
cprod(principal_axis,targetvec,rotvec);
unitv(rotvec,rotvec);
printf("Aligning %g %g %g to %g %g %g : xprod %g %g %g\n",
principal_axis[XX],principal_axis[YY],principal_axis[ZZ],targetvec[XX],targetvec[YY],targetvec[ZZ],
rotvec[XX],rotvec[YY],rotvec[ZZ]);
ux=rotvec[XX];
uy=rotvec[YY];
uz=rotvec[ZZ];
rotmatrix[0][0]=ux*ux + (1.0-ux*ux)*costheta;
rotmatrix[0][1]=ux*uy*(1-costheta)-uz*sintheta;
rotmatrix[0][2]=ux*uz*(1-costheta)+uy*sintheta;
rotmatrix[1][0]=ux*uy*(1-costheta)+uz*sintheta;
rotmatrix[1][1]=uy*uy + (1.0-uy*uy)*costheta;
rotmatrix[1][2]=uy*uz*(1-costheta)-ux*sintheta;
rotmatrix[2][0]=ux*uz*(1-costheta)-uy*sintheta;
rotmatrix[2][1]=uy*uz*(1-costheta)+ux*sintheta;
rotmatrix[2][2]=uz*uz + (1.0-uz*uz)*costheta;
printf("Rotation matrix: \n%g %g %g\n%g %g %g\n%g %g %g\n",
rotmatrix[0][0],rotmatrix[0][1],rotmatrix[0][2],
rotmatrix[1][0],rotmatrix[1][1],rotmatrix[1][2],
rotmatrix[2][0],rotmatrix[2][1],rotmatrix[2][2]);
}
/* Center of mass code for groups */
void calc_vcm_grp(int start, int homenr, t_mdatoms *md,
rvec x[], rvec v[], t_vcm *vcm)
{
int i, g, m;
real m0;
rvec j0;
if (vcm->mode != ecmNO)
{
/* Also clear a possible rest group */
for (g = 0; (g < vcm->nr+1); g++)
{
/* Reset linear momentum */
vcm->group_mass[g] = 0;
clear_rvec(vcm->group_p[g]);
if (vcm->mode == ecmANGULAR)
{
/* Reset anular momentum */
clear_rvec(vcm->group_j[g]);
clear_rvec(vcm->group_x[g]);
clear_rvec(vcm->group_w[g]);
clear_mat(vcm->group_i[g]);
}
}
g = 0;
for (i = start; (i < start+homenr); i++)
{
m0 = md->massT[i];
if (md->cVCM)
{
g = md->cVCM[i];
}
/* Calculate linear momentum */
vcm->group_mass[g] += m0;
for (m = 0; (m < DIM); m++)
{
vcm->group_p[g][m] += m0*v[i][m];
}
if (vcm->mode == ecmANGULAR)
{
/* Calculate angular momentum */
cprod(x[i], v[i], j0);
for (m = 0; (m < DIM); m++)
{
vcm->group_j[g][m] += m0*j0[m];
vcm->group_x[g][m] += m0*x[i][m];
}
/* Update inertia tensor */
update_tensor(x[i], m0, vcm->group_i[g]);
}
}
}
}
static void calculate_normal(atom_id index[],rvec x[],rvec result,rvec center)
{
rvec c1,c2;
int i;
/* calculate centroid of triangle spanned by the three points */
for(i=0;i<3;i++)
center[i] = (x[index[0]][i] + x[index[1]][i] + x[index[2]][i])/3;
/* use P1P2 x P1P3 to calculate normal, given three points P1-P3 */
rvec_sub(x[index[1]],x[index[0]],c1); /* find two vectors */
rvec_sub(x[index[2]],x[index[0]],c2);
cprod(c1,c2,result); /* take crossproduct between these */
}
void do_stopcm_grp(FILE *fp,int start,int homenr,unsigned short *group_id,
rvec x[],rvec v[],t_vcm *vcm)
{
int i,g,m;
real tm,tm_1;
rvec dv,dx;
if (vcm->mode != ecmNO) {
/* Subtract linear momentum */
g = 0;
switch (vcm->ndim) {
case 1:
for(i=start; (i<start+homenr); i++) {
if (group_id)
g = group_id[i];
v[i][XX] -= vcm->group_v[g][XX];
}
break;
case 2:
for(i=start; (i<start+homenr); i++) {
if (group_id)
g = group_id[i];
v[i][XX] -= vcm->group_v[g][XX];
v[i][YY] -= vcm->group_v[g][YY];
}
break;
case 3:
for(i=start; (i<start+homenr); i++) {
if (group_id)
g = group_id[i];
rvec_dec(v[i],vcm->group_v[g]);
}
break;
}
if (vcm->mode == ecmANGULAR) {
/* Subtract angular momentum */
for(i=start; (i<start+homenr); i++) {
if (group_id)
g = group_id[i];
/* Compute the correction to the velocity for each atom */
rvec_sub(x[i],vcm->group_x[g],dx);
cprod(vcm->group_w[g],dx,dv);
rvec_dec(v[i],dv);
}
}
}
}
//! Helper method to calculate a vector from two or three positions.
static void
calc_vec(int natoms, rvec x[], t_pbc *pbc, rvec xout, rvec cout)
{
switch (natoms)
{
case 2:
if (pbc)
{
pbc_dx(pbc, x[1], x[0], xout);
}
else
{
rvec_sub(x[1], x[0], xout);
}
svmul(0.5, xout, cout);
rvec_add(x[0], cout, cout);
break;
case 3:
{
rvec v1, v2;
if (pbc)
{
pbc_dx(pbc, x[1], x[0], v1);
pbc_dx(pbc, x[2], x[0], v2);
}
else
{
rvec_sub(x[1], x[0], v1);
rvec_sub(x[2], x[0], v2);
}
cprod(v1, v2, xout);
rvec_add(x[0], x[1], cout);
rvec_add(cout, x[2], cout);
svmul(1.0/3.0, cout, cout);
break;
}
default:
GMX_RELEASE_ASSERT(false, "Incorrectly initialized number of atoms");
}
}
static void
calc_vec(int natoms, rvec x[], t_pbc *pbc, rvec xout, rvec cout)
{
switch (natoms)
{
case 2:
if (pbc)
{
pbc_dx(pbc, x[1], x[0], xout);
}
else
{
rvec_sub(x[1], x[0], xout);
}
svmul(0.5, xout, cout);
rvec_add(x[0], cout, cout);
break;
case 3: {
rvec v1, v2;
if (pbc)
{
pbc_dx(pbc, x[1], x[0], v1);
pbc_dx(pbc, x[2], x[0], v2);
}
else
{
rvec_sub(x[1], x[0], v1);
rvec_sub(x[2], x[0], v2);
}
cprod(v1, v2, xout);
rvec_add(x[0], x[1], cout);
rvec_add(cout, x[2], cout);
svmul(1.0/3.0, cout, cout);
break;
}
}
}
int gmx_helixorient(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] calculates the coordinates and direction of the average",
"axis inside an alpha helix, and the direction/vectors of both the",
"C[GRK]alpha[grk] and (optionally) a sidechain atom relative to the axis.[PAR]",
"As input, you need to specify an index group with C[GRK]alpha[grk] atoms",
"corresponding to an [GRK]alpha[grk]-helix of continuous residues. Sidechain",
"directions require a second index group of the same size, containing",
"the heavy atom in each residue that should represent the sidechain.[PAR]",
"[BB]Note[bb] that this program does not do any fitting of structures.[PAR]",
"We need four C[GRK]alpha[grk] coordinates to define the local direction of the helix",
"axis.[PAR]",
"The tilt/rotation is calculated from Euler rotations, where we define",
"the helix axis as the local [IT]x[it]-axis, the residues/C[GRK]alpha[grk] vector as [IT]y[it], and the",
"[IT]z[it]-axis from their cross product. We use the Euler Y-Z-X rotation, meaning",
"we first tilt the helix axis (1) around and (2) orthogonal to the residues",
"vector, and finally apply the (3) rotation around it. For debugging or other",
"purposes, we also write out the actual Euler rotation angles as [TT]theta[1-3].xvg[tt]"
};
t_topology *top = NULL;
real t;
rvec *x = NULL;
matrix box;
t_trxstatus *status;
int natoms;
real theta1, theta2, theta3;
int i, j, teller = 0;
int iCA, iSC;
int *ind_CA;
int *ind_SC;
char *gn_CA;
char *gn_SC;
rvec v1, v2;
rvec *x_CA, *x_SC;
rvec *r12;
rvec *r23;
rvec *r34;
rvec *diff13;
rvec *diff24;
rvec *helixaxis;
rvec *residuehelixaxis;
rvec *residueorigin;
rvec *residuevector;
rvec *sidechainvector;
rvec *residuehelixaxis_t0;
rvec *residuevector_t0;
rvec *axis3_t0;
rvec *residuehelixaxis_tlast;
rvec *residuevector_tlast;
rvec *axis3_tlast;
rvec refaxes[3], newaxes[3];
rvec unitaxes[3];
rvec rot_refaxes[3], rot_newaxes[3];
real tilt, rotation;
rvec *axis3;
real *twist, *residuetwist;
real *radius, *residueradius;
real *rise, *residuerise;
real *residuebending;
real tmp;
real weight[3];
t_pbc pbc;
matrix A;
FILE *fpaxis, *fpcenter, *fptilt, *fprotation;
FILE *fpradius, *fprise, *fptwist;
FILE *fptheta1, *fptheta2, *fptheta3;
FILE *fpbending;
int ePBC;
gmx_output_env_t *oenv;
gmx_rmpbc_t gpbc = NULL;
static gmx_bool bSC = FALSE;
static gmx_bool bIncremental = FALSE;
static t_pargs pa[] = {
{ "-sidechain", FALSE, etBOOL, {&bSC},
"Calculate sidechain directions relative to helix axis too." },
{ "-incremental", FALSE, etBOOL, {&bIncremental},
"Calculate incremental rather than total rotation/tilt." },
};
#define NPA asize(pa)
t_filenm fnm[] = {
{ efTPR, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efDAT, "-oaxis", "helixaxis", ffWRITE },
{ efDAT, "-ocenter", "center", ffWRITE },
{ efXVG, "-orise", "rise", ffWRITE },
{ efXVG, "-oradius", "radius", ffWRITE },
{ efXVG, "-otwist", "twist", ffWRITE },
{ efXVG, "-obending", "bending", ffWRITE },
{ efXVG, "-otilt", "tilt", ffWRITE },
{ efXVG, "-orot", "rotation", ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
for (i = 0; i < 3; i++)
{
weight[i] = 1.0;
}
/* read index files */
printf("Select a group of Calpha atoms corresponding to a single continuous helix:\n");
get_index(&(top->atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &iCA, &ind_CA, &gn_CA);
snew(x_CA, iCA);
snew(x_SC, iCA); /* sic! */
snew(r12, iCA-3);
snew(r23, iCA-3);
snew(r34, iCA-3);
snew(diff13, iCA-3);
snew(diff24, iCA-3);
snew(helixaxis, iCA-3);
snew(twist, iCA);
snew(residuetwist, iCA);
snew(radius, iCA);
snew(residueradius, iCA);
snew(rise, iCA);
snew(residuerise, iCA);
snew(residueorigin, iCA);
snew(residuehelixaxis, iCA);
snew(residuevector, iCA);
snew(sidechainvector, iCA);
snew(residuebending, iCA);
snew(residuehelixaxis_t0, iCA);
snew(residuevector_t0, iCA);
snew(axis3_t0, iCA);
snew(residuehelixaxis_tlast, iCA);
snew(residuevector_tlast, iCA);
snew(axis3_tlast, iCA);
snew(axis3, iCA);
if (bSC)
{
printf("Select a group of atoms defining the sidechain direction (1/residue):\n");
get_index(&(top->atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &iSC, &ind_SC, &gn_SC);
if (iSC != iCA)
{
gmx_fatal(FARGS, "Number of sidechain atoms (%d) != number of CA atoms (%d)", iSC, iCA);
}
}
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
fpaxis = gmx_ffopen(opt2fn("-oaxis", NFILE, fnm), "w");
fpcenter = gmx_ffopen(opt2fn("-ocenter", NFILE, fnm), "w");
fprise = gmx_ffopen(opt2fn("-orise", NFILE, fnm), "w");
fpradius = gmx_ffopen(opt2fn("-oradius", NFILE, fnm), "w");
fptwist = gmx_ffopen(opt2fn("-otwist", NFILE, fnm), "w");
fpbending = gmx_ffopen(opt2fn("-obending", NFILE, fnm), "w");
fptheta1 = gmx_ffopen("theta1.xvg", "w");
fptheta2 = gmx_ffopen("theta2.xvg", "w");
fptheta3 = gmx_ffopen("theta3.xvg", "w");
if (bIncremental)
{
fptilt = xvgropen(opt2fn("-otilt", NFILE, fnm),
"Incremental local helix tilt", "Time(ps)", "Tilt (degrees)",
oenv);
fprotation = xvgropen(opt2fn("-orot", NFILE, fnm),
"Incremental local helix rotation", "Time(ps)",
"Rotation (degrees)", oenv);
}
else
{
fptilt = xvgropen(opt2fn("-otilt", NFILE, fnm),
"Cumulative local helix tilt", "Time(ps)", "Tilt (degrees)", oenv);
fprotation = xvgropen(opt2fn("-orot", NFILE, fnm),
"Cumulative local helix rotation", "Time(ps)",
"Rotation (degrees)", oenv);
}
clear_rvecs(3, unitaxes);
unitaxes[0][0] = 1;
unitaxes[1][1] = 1;
unitaxes[2][2] = 1;
gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
do
{
/* initialisation for correct distance calculations */
set_pbc(&pbc, ePBC, box);
/* make molecules whole again */
gmx_rmpbc(gpbc, natoms, box, x);
/* copy coords to our smaller arrays */
for (i = 0; i < iCA; i++)
{
copy_rvec(x[ind_CA[i]], x_CA[i]);
if (bSC)
{
copy_rvec(x[ind_SC[i]], x_SC[i]);
}
}
for (i = 0; i < iCA-3; i++)
{
rvec_sub(x_CA[i+1], x_CA[i], r12[i]);
rvec_sub(x_CA[i+2], x_CA[i+1], r23[i]);
rvec_sub(x_CA[i+3], x_CA[i+2], r34[i]);
rvec_sub(r12[i], r23[i], diff13[i]);
rvec_sub(r23[i], r34[i], diff24[i]);
/* calculate helix axis */
cprod(diff13[i], diff24[i], helixaxis[i]);
svmul(1.0/norm(helixaxis[i]), helixaxis[i], helixaxis[i]);
tmp = cos_angle(diff13[i], diff24[i]);
twist[i] = 180.0/M_PI * std::acos( tmp );
radius[i] = std::sqrt( norm(diff13[i])*norm(diff24[i]) ) / (2.0* (1.0-tmp) );
rise[i] = std::abs(iprod(r23[i], helixaxis[i]));
svmul(radius[i]/norm(diff13[i]), diff13[i], v1);
svmul(radius[i]/norm(diff24[i]), diff24[i], v2);
rvec_sub(x_CA[i+1], v1, residueorigin[i+1]);
rvec_sub(x_CA[i+2], v2, residueorigin[i+2]);
}
residueradius[0] = residuetwist[0] = residuerise[0] = 0;
residueradius[1] = radius[0];
residuetwist[1] = twist[0];
residuerise[1] = rise[0];
residuebending[0] = residuebending[1] = 0;
for (i = 2; i < iCA-2; i++)
{
residueradius[i] = 0.5*(radius[i-2]+radius[i-1]);
residuetwist[i] = 0.5*(twist[i-2]+twist[i-1]);
residuerise[i] = 0.5*(rise[i-2]+rise[i-1]);
residuebending[i] = 180.0/M_PI*std::acos( cos_angle(helixaxis[i-2], helixaxis[i-1]) );
}
residueradius[iCA-2] = radius[iCA-4];
residuetwist[iCA-2] = twist[iCA-4];
residuerise[iCA-2] = rise[iCA-4];
residueradius[iCA-1] = residuetwist[iCA-1] = residuerise[iCA-1] = 0;
residuebending[iCA-2] = residuebending[iCA-1] = 0;
clear_rvec(residueorigin[0]);
clear_rvec(residueorigin[iCA-1]);
/* average helix axes to define them on the residues.
* Just extrapolate second first/list atom.
*/
copy_rvec(helixaxis[0], residuehelixaxis[0]);
copy_rvec(helixaxis[0], residuehelixaxis[1]);
for (i = 2; i < iCA-2; i++)
{
rvec_add(helixaxis[i-2], helixaxis[i-1], residuehelixaxis[i]);
svmul(0.5, residuehelixaxis[i], residuehelixaxis[i]);
}
copy_rvec(helixaxis[iCA-4], residuehelixaxis[iCA-2]);
copy_rvec(helixaxis[iCA-4], residuehelixaxis[iCA-1]);
/* Normalize the axis */
for (i = 0; i < iCA; i++)
{
svmul(1.0/norm(residuehelixaxis[i]), residuehelixaxis[i], residuehelixaxis[i]);
}
/* calculate vector from origin to residue CA */
fprintf(fpaxis, "%15.12g ", t);
fprintf(fpcenter, "%15.12g ", t);
fprintf(fprise, "%15.12g ", t);
fprintf(fpradius, "%15.12g ", t);
fprintf(fptwist, "%15.12g ", t);
fprintf(fpbending, "%15.12g ", t);
for (i = 0; i < iCA; i++)
{
if (i == 0 || i == iCA-1)
{
fprintf(fpaxis, "%15.12g %15.12g %15.12g ", 0.0, 0.0, 0.0);
fprintf(fpcenter, "%15.12g %15.12g %15.12g ", 0.0, 0.0, 0.0);
fprintf(fprise, "%15.12g ", 0.0);
fprintf(fpradius, "%15.12g ", 0.0);
fprintf(fptwist, "%15.12g ", 0.0);
fprintf(fpbending, "%15.12g ", 0.0);
}
else
{
rvec_sub( bSC ? x_SC[i] : x_CA[i], residueorigin[i], residuevector[i]);
svmul(1.0/norm(residuevector[i]), residuevector[i], residuevector[i]);
cprod(residuehelixaxis[i], residuevector[i], axis3[i]);
fprintf(fpaxis, "%15.12g %15.12g %15.12g ", residuehelixaxis[i][0], residuehelixaxis[i][1], residuehelixaxis[i][2]);
fprintf(fpcenter, "%15.12g %15.12g %15.12g ", residueorigin[i][0], residueorigin[i][1], residueorigin[i][2]);
fprintf(fprise, "%15.12g ", residuerise[i]);
fprintf(fpradius, "%15.12g ", residueradius[i]);
fprintf(fptwist, "%15.12g ", residuetwist[i]);
fprintf(fpbending, "%15.12g ", residuebending[i]);
}
}
fprintf(fprise, "\n");
fprintf(fpradius, "\n");
fprintf(fpaxis, "\n");
fprintf(fpcenter, "\n");
fprintf(fptwist, "\n");
fprintf(fpbending, "\n");
if (teller == 0)
{
for (i = 0; i < iCA; i++)
{
copy_rvec(residuehelixaxis[i], residuehelixaxis_t0[i]);
copy_rvec(residuevector[i], residuevector_t0[i]);
copy_rvec(axis3[i], axis3_t0[i]);
}
}
else
{
fprintf(fptilt, "%15.12g ", t);
fprintf(fprotation, "%15.12g ", t);
fprintf(fptheta1, "%15.12g ", t);
fprintf(fptheta2, "%15.12g ", t);
fprintf(fptheta3, "%15.12g ", t);
for (i = 0; i < iCA; i++)
{
if (i == 0 || i == iCA-1)
{
tilt = rotation = 0;
}
else
{
if (!bIncremental)
{
/* Total rotation & tilt */
copy_rvec(residuehelixaxis_t0[i], refaxes[0]);
copy_rvec(residuevector_t0[i], refaxes[1]);
copy_rvec(axis3_t0[i], refaxes[2]);
}
else
{
/* Rotation/tilt since last step */
copy_rvec(residuehelixaxis_tlast[i], refaxes[0]);
copy_rvec(residuevector_tlast[i], refaxes[1]);
copy_rvec(axis3_tlast[i], refaxes[2]);
}
copy_rvec(residuehelixaxis[i], newaxes[0]);
copy_rvec(residuevector[i], newaxes[1]);
copy_rvec(axis3[i], newaxes[2]);
/* rotate reference frame onto unit axes */
calc_fit_R(3, 3, weight, unitaxes, refaxes, A);
for (j = 0; j < 3; j++)
{
mvmul(A, refaxes[j], rot_refaxes[j]);
mvmul(A, newaxes[j], rot_newaxes[j]);
}
/* Determine local rotation matrix A */
calc_fit_R(3, 3, weight, rot_newaxes, rot_refaxes, A);
/* Calculate euler angles, from rotation order y-z-x, where
* x is helixaxis, y residuevector, and z axis3.
*
* A contains rotation column vectors.
*/
theta1 = 180.0/M_PI*std::atan2(A[0][2], A[0][0]);
theta2 = 180.0/M_PI*std::asin(-A[0][1]);
theta3 = 180.0/M_PI*std::atan2(A[2][1], A[1][1]);
tilt = std::sqrt(theta1*theta1+theta2*theta2);
rotation = theta3;
fprintf(fptheta1, "%15.12g ", theta1);
fprintf(fptheta2, "%15.12g ", theta2);
fprintf(fptheta3, "%15.12g ", theta3);
}
fprintf(fptilt, "%15.12g ", tilt);
fprintf(fprotation, "%15.12g ", rotation);
}
fprintf(fptilt, "\n");
fprintf(fprotation, "\n");
fprintf(fptheta1, "\n");
fprintf(fptheta2, "\n");
fprintf(fptheta3, "\n");
}
for (i = 0; i < iCA; i++)
{
copy_rvec(residuehelixaxis[i], residuehelixaxis_tlast[i]);
copy_rvec(residuevector[i], residuevector_tlast[i]);
copy_rvec(axis3[i], axis3_tlast[i]);
}
teller++;
}
while (read_next_x(oenv, status, &t, x, box));
gmx_rmpbc_done(gpbc);
gmx_ffclose(fpaxis);
gmx_ffclose(fpcenter);
xvgrclose(fptilt);
xvgrclose(fprotation);
gmx_ffclose(fprise);
gmx_ffclose(fpradius);
gmx_ffclose(fptwist);
gmx_ffclose(fpbending);
gmx_ffclose(fptheta1);
gmx_ffclose(fptheta2);
gmx_ffclose(fptheta3);
close_trj(status);
return 0;
}
int gmx_bundle(int argc,char *argv[])
{
const char *desc[] = {
"g_bundle analyzes bundles of axes. The axes can be for instance",
"helix axes. The program reads two index groups and divides both",
"of them in [TT]-na[tt] parts. The centers of mass of these parts",
"define the tops and bottoms of the axes.",
"Several quantities are written to file:",
"the axis length, the distance and the z-shift of the axis mid-points",
"with respect to the average center of all axes, the total tilt,",
"the radial tilt and the lateral tilt with respect to the average axis.",
"[PAR]",
"With options [TT]-ok[tt], [TT]-okr[tt] and [TT]-okl[tt] the total,",
"radial and lateral kinks of the axes are plotted. An extra index",
"group of kink atoms is required, which is also divided into [TT]-na[tt]",
"parts. The kink angle is defined as the angle between the kink-top and",
"the bottom-kink vectors.",
"[PAR]",
"With option [TT]-oa[tt] the top, mid (or kink when [TT]-ok[tt] is set)",
"and bottom points of each axis",
"are written to a pdb file each frame. The residue numbers correspond",
"to the axis numbers. When viewing this file with [TT]rasmol[tt], use the",
"command line option [TT]-nmrpdb[tt], and type [TT]set axis true[tt] to",
"display the reference axis."
};
static int n=0;
static gmx_bool bZ=FALSE;
t_pargs pa[] = {
{ "-na", FALSE, etINT, {&n},
"Number of axes" },
{ "-z", FALSE, etBOOL, {&bZ},
"Use the Z-axis as reference iso the average axis" }
};
FILE *out,*flen,*fdist,*fz,*ftilt,*ftiltr,*ftiltl;
FILE *fkink=NULL,*fkinkr=NULL,*fkinkl=NULL;
t_trxstatus *status;
t_trxstatus *fpdb;
t_topology top;
int ePBC;
rvec *xtop;
matrix box;
t_trxframe fr;
t_atoms outatoms;
real t,comp;
int natoms;
char *grpname[MAX_ENDS],title[256];
/* FIXME: The constness should not be cast away */
char *anm=(char *)"CA",*rnm=(char *)"GLY";
int i,j,gnx[MAX_ENDS];
atom_id *index[MAX_ENDS];
t_bundle bun;
gmx_bool bKink;
rvec va,vb,vc,vr,vl;
output_env_t oenv;
gmx_rmpbc_t gpbc=NULL;
#define NLEG asize(leg)
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-ol", "bun_len", ffWRITE },
{ efXVG, "-od", "bun_dist", ffWRITE },
{ efXVG, "-oz", "bun_z", ffWRITE },
{ efXVG, "-ot", "bun_tilt", ffWRITE },
{ efXVG, "-otr", "bun_tiltr", ffWRITE },
{ efXVG, "-otl", "bun_tiltl", ffWRITE },
{ efXVG, "-ok", "bun_kink", ffOPTWR },
{ efXVG, "-okr", "bun_kinkr", ffOPTWR },
{ efXVG, "-okl", "bun_kinkl", ffOPTWR },
{ efPDB, "-oa", "axes", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,box,TRUE);
bKink = opt2bSet("-ok",NFILE,fnm) || opt2bSet("-okr",NFILE,fnm)
|| opt2bSet("-okl",NFILE,fnm);
if (bKink)
bun.nend = 3;
else
bun.nend = 2;
fprintf(stderr,"Select a group of top and a group of bottom ");
if (bKink)
fprintf(stderr,"and a group of kink ");
fprintf(stderr,"atoms\n");
get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),bun.nend,
gnx,index,grpname);
if (n<=0 || gnx[0] % n || gnx[1] % n || (bKink && gnx[2] % n))
gmx_fatal(FARGS,
"The size of one of your index groups is not a multiple of n");
bun.n = n;
snew(bun.end[0],n);
snew(bun.end[1],n);
if (bKink)
snew(bun.end[2],n);
snew(bun.mid,n);
snew(bun.dir,n);
snew(bun.len,n);
flen = xvgropen(opt2fn("-ol",NFILE,fnm),"Axis lengths",
output_env_get_xvgr_tlabel(oenv),"(nm)",oenv);
fdist = xvgropen(opt2fn("-od",NFILE,fnm),"Distance of axis centers",
output_env_get_xvgr_tlabel(oenv),"(nm)",oenv);
fz = xvgropen(opt2fn("-oz",NFILE,fnm),"Z-shift of axis centers",
output_env_get_xvgr_tlabel(oenv),"(nm)",oenv);
ftilt = xvgropen(opt2fn("-ot",NFILE,fnm),"Axis tilts",
output_env_get_xvgr_tlabel(oenv),"(degrees)",oenv);
ftiltr = xvgropen(opt2fn("-otr",NFILE,fnm),"Radial axis tilts",
output_env_get_xvgr_tlabel(oenv),"(degrees)",oenv);
ftiltl = xvgropen(opt2fn("-otl",NFILE,fnm),"Lateral axis tilts",
output_env_get_xvgr_tlabel(oenv),"(degrees)",oenv);
if (bKink) {
fkink = xvgropen(opt2fn("-ok",NFILE,fnm),"Kink angles",
output_env_get_xvgr_tlabel(oenv),"(degrees)",oenv);
fkinkr = xvgropen(opt2fn("-okr",NFILE,fnm),"Radial kink angles",
output_env_get_xvgr_tlabel(oenv),"(degrees)",oenv);
if (output_env_get_print_xvgr_codes(oenv))
fprintf(fkinkr,"@ subtitle \"+ = ) ( - = ( )\"\n");
fkinkl = xvgropen(opt2fn("-okl",NFILE,fnm),"Lateral kink angles",
output_env_get_xvgr_tlabel(oenv),"(degrees)",oenv);
}
if (opt2bSet("-oa",NFILE,fnm)) {
init_t_atoms(&outatoms,3*n,FALSE);
outatoms.nr = 3*n;
for(i=0; i<3*n; i++) {
outatoms.atomname[i] = &anm;
outatoms.atom[i].resind = i/3;
outatoms.resinfo[i/3].name = &rnm;
outatoms.resinfo[i/3].nr = i/3 + 1;
outatoms.resinfo[i/3].ic = ' ';
}
fpdb = open_trx(opt2fn("-oa",NFILE,fnm),"w");
} else
fpdb = NULL;
read_first_frame(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&fr,TRX_NEED_X);
gpbc = gmx_rmpbc_init(&top.idef,ePBC,fr.natoms,fr.box);
do {
gmx_rmpbc_trxfr(gpbc,&fr);
calc_axes(fr.x,top.atoms.atom,gnx,index,!bZ,&bun);
t = output_env_conv_time(oenv,fr.time);
fprintf(flen," %10g",t);
fprintf(fdist," %10g",t);
fprintf(fz," %10g",t);
fprintf(ftilt," %10g",t);
fprintf(ftiltr," %10g",t);
fprintf(ftiltl," %10g",t);
if (bKink) {
fprintf(fkink," %10g",t);
fprintf(fkinkr," %10g",t);
fprintf(fkinkl," %10g",t);
}
for(i=0; i<bun.n; i++) {
fprintf(flen," %6g",bun.len[i]);
fprintf(fdist," %6g",norm(bun.mid[i]));
fprintf(fz," %6g",bun.mid[i][ZZ]);
fprintf(ftilt," %6g",RAD2DEG*acos(bun.dir[i][ZZ]));
comp = bun.mid[i][XX]*bun.dir[i][XX]+bun.mid[i][YY]*bun.dir[i][YY];
fprintf(ftiltr," %6g",RAD2DEG*
asin(comp/sqrt(sqr(comp)+sqr(bun.dir[i][ZZ]))));
comp = bun.mid[i][YY]*bun.dir[i][XX]-bun.mid[i][XX]*bun.dir[i][YY];
fprintf(ftiltl," %6g",RAD2DEG*
asin(comp/sqrt(sqr(comp)+sqr(bun.dir[i][ZZ]))));
if (bKink) {
rvec_sub(bun.end[0][i],bun.end[2][i],va);
rvec_sub(bun.end[2][i],bun.end[1][i],vb);
unitv_no_table(va,va);
unitv_no_table(vb,vb);
fprintf(fkink," %6g",RAD2DEG*acos(iprod(va,vb)));
cprod(va,vb,vc);
copy_rvec(bun.mid[i],vr);
vr[ZZ] = 0;
unitv_no_table(vr,vr);
fprintf(fkinkr," %6g",RAD2DEG*asin(iprod(vc,vr)));
vl[XX] = vr[YY];
vl[YY] = -vr[XX];
vl[ZZ] = 0;
fprintf(fkinkl," %6g",RAD2DEG*asin(iprod(vc,vl)));
}
}
fprintf(flen,"\n");
fprintf(fdist,"\n");
fprintf(fz,"\n");
fprintf(ftilt,"\n");
fprintf(ftiltr,"\n");
fprintf(ftiltl,"\n");
if (bKink) {
fprintf(fkink,"\n");
fprintf(fkinkr,"\n");
fprintf(fkinkl,"\n");
}
if (fpdb )
dump_axes(fpdb,&fr,&outatoms,&bun);
} while(read_next_frame(oenv,status,&fr));
gmx_rmpbc_done(gpbc);
close_trx(status);
if (fpdb )
close_trx(fpdb);
ffclose(flen);
ffclose(fdist);
ffclose(fz);
ffclose(ftilt);
ffclose(ftiltr);
ffclose(ftiltl);
if (bKink) {
ffclose(fkink);
ffclose(fkinkr);
ffclose(fkinkl);
}
thanx(stderr);
return 0;
}
static void set_tric_dir(ivec *dd_nc, gmx_ddbox_t *ddbox, matrix box)
{
int npbcdim, d, i, j;
rvec *v, *normal;
real dep, inv_skew_fac2;
npbcdim = ddbox->npbcdim;
normal = ddbox->normal;
for (d = 0; d < DIM; d++)
{
ddbox->tric_dir[d] = 0;
for (j = d+1; j < npbcdim; j++)
{
if (box[j][d] != 0)
{
ddbox->tric_dir[d] = 1;
if (dd_nc != NULL && (*dd_nc)[j] > 1 && (*dd_nc)[d] == 1)
{
gmx_fatal(FARGS, "Domain decomposition has not been implemented for box vectors that have non-zero components in directions that do not use domain decomposition: ncells = %d %d %d, box vector[%d] = %f %f %f",
dd_nc[XX], dd_nc[YY], dd_nc[ZZ],
j+1, box[j][XX], box[j][YY], box[j][ZZ]);
}
}
}
/* Convert box vectors to orthogonal vectors for this dimension,
* for use in distance calculations.
* Set the trilinic skewing factor that translates
* the thickness of a slab perpendicular to this dimension
* into the real thickness of the slab.
*/
if (ddbox->tric_dir[d])
{
inv_skew_fac2 = 1;
v = ddbox->v[d];
if (d == XX || d == YY)
{
/* Normalize such that the "diagonal" is 1 */
svmul(1/box[d+1][d+1], box[d+1], v[d+1]);
for (i = 0; i < d; i++)
{
v[d+1][i] = 0;
}
inv_skew_fac2 += sqr(v[d+1][d]);
if (d == XX)
{
/* Normalize such that the "diagonal" is 1 */
svmul(1/box[d+2][d+2], box[d+2], v[d+2]);
for (i = 0; i < d; i++)
{
v[d+2][i] = 0;
}
/* Make vector [d+2] perpendicular to vector [d+1],
* this does not affect the normalization.
*/
dep = iprod(v[d+1], v[d+2])/norm2(v[d+1]);
for (i = 0; i < DIM; i++)
{
v[d+2][i] -= dep*v[d+1][i];
}
inv_skew_fac2 += sqr(v[d+2][d]);
cprod(v[d+1], v[d+2], normal[d]);
}
else
{
/* cross product with (1,0,0) */
normal[d][XX] = 0;
normal[d][YY] = v[d+1][ZZ];
normal[d][ZZ] = -v[d+1][YY];
}
if (debug)
{
fprintf(debug, "box[%d] %.3f %.3f %.3f\n",
d, box[d][XX], box[d][YY], box[d][ZZ]);
for (i = d+1; i < DIM; i++)
{
fprintf(debug, " v[%d] %.3f %.3f %.3f\n",
i, v[i][XX], v[i][YY], v[i][ZZ]);
}
}
}
ddbox->skew_fac[d] = 1.0/sqrt(inv_skew_fac2);
/* Set the normal vector length to skew_fac */
dep = ddbox->skew_fac[d]/norm(normal[d]);
svmul(dep, normal[d], normal[d]);
if (debug)
{
fprintf(debug, "skew_fac[%d] = %f\n", d, ddbox->skew_fac[d]);
fprintf(debug, "normal[%d] %.3f %.3f %.3f\n",
d, normal[d][XX], normal[d][YY], normal[d][ZZ]);
}
}
else
{
ddbox->skew_fac[d] = 1;
for (i = 0; i < DIM; i++)
{
clear_rvec(ddbox->v[d][i]);
ddbox->v[d][i][i] = 1;
}
clear_rvec(normal[d]);
normal[d][d] = 1;
}
}
}
static void do_sdf(char *fnNDX,char *fnTPS,char *fnTRX, char *fnSDF,
char *fnREF, bool bRef, rvec cutoff, real binwidth,
int mode, rvec triangle, rvec dtri)
{
FILE *fp;
int status;
int ng,natoms,i,j,k,l,X,Y,Z,lc,dest;
ivec nbin;
int ***count;
/* real ***sdf; */
real sdf,min_sdf=1e10,max_sdf=0;
char **grpname;
int *isize;
int isize_cg=0;
int isize_ref=3;
int ref_resind[3];
int nrefmol=0,refc=0;
atom_id **index;
atom_id *index_cg=NULL;
atom_id *index_ref=NULL;
real t,boxmin,hbox,normfac;
real invbinw;
rvec tri_upper,tri_lower;
rvec *x,xcog,dx,*x_i1,xi,*x_refmol;
matrix box;
matrix rot; /* rotation matrix := unit vectors for the molecule frame */
rvec k_mol,i1_mol,i2_mol,dx_mol;
real delta;
atom_id ix,jx;
t_topology top;
int ePBC=-1;
t_pbc pbc;
bool bTop=FALSE,bRefDone=FALSE,bInGroup=FALSE;
char title[STRLEN];
/* Read Topology */
if (fnTPS) {
bTop=read_tps_conf(fnTPS,title,&top,&ePBC,&x,NULL,box,TRUE);
}
if ( !bTop ) {
fprintf(stderr,"\nNeed tpr-file to make a reference structure.\n");
fprintf(stderr,"Option -r will be ignored!\n");
bRef = FALSE;
}
/* Allocate memory for 4 groups, 3 dummy groups and a group for the ref
structure if needed */
ng = 4;
snew(grpname,ng);
/* the dummy groups are used to dynamically store triples of atoms */
/* for molecular coordinate systems */
if ( bRef )
{
snew(isize,ng+4);
snew(index,ng+4);
}
else
{
snew(isize,ng+3);
snew(index,ng+3);
}
/* Read the index groups */
fprintf(stderr,"\nSelect the 3 reference groups and the SDF group:\n");
if (fnTPS)
get_index(&top.atoms,fnNDX,ng,isize,index,grpname);
else
rd_index(fnNDX,ng,isize,index,grpname);
isize[NDX_REF1]=isize[G_REF1];
for (i=NDX_REF1; i<=NDX_REF3; i++)
snew(index[i],isize[NDX_REF1]);
/* Read first frame and check it */
natoms=read_first_x(&status,fnTRX,&t,&x,box);
if ( !natoms )
gmx_fatal(FARGS,"Could not read coordinates from statusfile!\n");
/* check with topology */
if (fnTPS)
if ( natoms > top.atoms.nr )
gmx_fatal(FARGS,"Trajectory (%d atoms) does not match topology (%d atoms)!\n",
natoms,top.atoms.nr);
/* check with index groups */
for (i=0; i<ng; i++)
for (j=0; j<isize[i]; j++)
if ( index[i][j] >= natoms )
gmx_fatal(FARGS,"Atom index (%d) in index group %s (%d atoms) larger "
"than number of atoms in trajectory (%d atoms)!\n",
index[i][j],grpname[i],isize[i],natoms);
/* check reference groups */
if ( mode == 1 )
{
if ( isize[G_REF1] != isize[G_REF2] || isize[G_REF1] != isize[G_REF3] ||
isize[G_REF2] != isize[G_REF3] )
gmx_fatal(FARGS,"For single particle SDF, all reference groups"
"must have the same size.\n");
/* for single particle SDF dynamic triples are not needed */
/* so we build them right here */
/* copy all triples from G_REFx to NDX_REFx */
for (i=0; i<isize[G_REF1]; i++)
{
/* check if all three atoms come from the same molecule */
for (j=G_REF1; j<=G_REF3; j++)
ref_resind[j] = top.atoms.atom[index[j][i]].resind;
if ( ref_resind[G_REF1] != ref_resind[G_REF2] ||
ref_resind[G_REF2] != ref_resind[G_REF3] ||
ref_resind[G_REF3] != ref_resind[G_REF1] )
{
fprintf(stderr,"\nWarning: reference triple (%d) will be skipped.\n",i);
fprintf(stderr, " resnr[1]: %d, resnr[2]: %d, resnr[3]: %d\n",
ref_resind[G_REF1],ref_resind[G_REF2], ref_resind[G_REF3]);
isize[NDX_REF1]--;
for (j=NDX_REF1; j<=NDX_REF3; j++)
srenew(index[j],isize[NDX_REF1]);
continue;
}
else
/* check if all entries are unique*/
if ( index[G_REF1][i] == index[G_REF2][i] ||
index[G_REF2][i] == index[G_REF3][i] ||
index[G_REF3][i] == index[G_REF1][i] )
{
fprintf(stderr,"Warning: reference triple (%d) will be skipped.\n",i);
fprintf(stderr, " index[1]: %d, index[2]: %d, index[3]: %d\n",
index[G_REF1][i],index[G_REF2][i],index[G_REF3][i]);
isize[NDX_REF1]--;
for (j=NDX_REF1; j<=NDX_REF3; j++)
srenew(index[j],isize[NDX_REF1]);
continue;
}
else /* everythings fine, copy that one */
for (j=G_REF1; j<=G_REF3; j++)
index[j+4][i] = index[j][i];
}
}
else if ( mode == 2 )
{
if ( isize[G_REF1] != isize[G_REF2] )
gmx_fatal(FARGS,"For two particle SDF, reference groups 1 and 2"
"must have the same size.\n");
for (i=0; i<isize[G_REF1]; i++)
{
/* check consistency for atoms 1 and 2 */
for (j=G_REF1; j<=G_REF2; j++)
ref_resind[j] = top.atoms.atom[index[j][i]].resind;
if ( ref_resind[G_REF1] != ref_resind[G_REF2] ||
index[G_REF1][i] == index[G_REF2][i] )
{
if ( ref_resind[G_REF1] != ref_resind[G_REF2] )
{
fprintf(stderr,"\nWarning: bond (%d) not from one molecule."
"Will not be used for SDF.\n",i);
fprintf(stderr, " resnr[1]: %d, resnr[2]: %d\n",
ref_resind[G_REF1],ref_resind[G_REF2]);
}
else
{
fprintf(stderr,"\nWarning: atom1 and atom2 are identical."
"Bond (%d) will not be used for SDF.\n",i);
fprintf(stderr, " index[1]: %d, index[2]: %d\n",
index[G_REF1][i],index[G_REF2][i]);
}
for (j=NDX_REF1; j<=NDX_REF2; j++)
{
for (k=i; k<isize[G_REF1]-1; k++)
index[j][k]=index[j][k+1];
isize[j]--;
srenew(index[j],isize[j]);
}
}
}
}
/* Read Atoms for refmol group */
if ( bRef )
{
snew(index[G_REFMOL],1);
for (i=G_REF1; i<=G_REF3; i++)
ref_resind[i] = top.atoms.atom[index[i][0]].resind;
for (i=0; i<natoms; i++)
{
if ( ref_resind[G_REF1] == top.atoms.atom[i].resind ||
ref_resind[G_REF2] == top.atoms.atom[i].resind ||
ref_resind[G_REF3] == top.atoms.atom[i].resind )
nrefmol++;
}
srenew(index[G_REFMOL],nrefmol);
isize[G_REFMOL] = nrefmol;
nrefmol = 0;
for (i=0; i<natoms; i++)
{
if ( ref_resind[G_REF1] == top.atoms.atom[i].resind ||
ref_resind[G_REF2] == top.atoms.atom[i].resind ||
ref_resind[G_REF3] == top.atoms.atom[i].resind )
{
index[G_REFMOL][nrefmol] = i;
nrefmol++;
}
}
}
/* initialize some stuff */
boxmin = min( norm(box[XX]), min( norm(box[YY]), norm(box[ZZ]) ) );
hbox = boxmin / 2.0;
for (i=0; i<DIM; i++)
{
cutoff[i] = cutoff[i] / 2;
nbin[i] = (int)(2 * cutoff[i] / binwidth) + 1;
invbinw = 1.0 / binwidth;
tri_upper[i] = triangle[i] + dtri[i];
tri_upper[i] = sqr(tri_upper[i]);
tri_lower[i] = triangle[i] - dtri[i];
tri_lower[i] = sqr(tri_lower[i]);
}
/* Allocate the array's for sdf */
snew(count,nbin[0]+1);
for(i=0; i<nbin[0]+1; i++)
{
snew(count[i],nbin[1]+1);
for (j=0; j<nbin[1]+1; j++)
snew(count[i][j],nbin[2]+1);
}
/* Allocate space for the coordinates */
snew(x_i1,isize[G_SDF]);
snew(x_refmol,isize[G_REFMOL]);
for (i=0; i<isize[G_REFMOL]; i++)
for (j=XX; j<=ZZ; j++)
x_refmol[i][j] = 0;
normfac = 0;
do {
/* Must init pbc every step because of pressure coupling */
set_pbc(&pbc,ePBC,box);
rm_pbc(&top.idef,ePBC,natoms,box,x,x);
/* Dynamically build the ref tripels */
if ( mode == 2 )
{
isize[NDX_REF1]=0;
for (j=NDX_REF1; j<=NDX_REF3; j++)
srenew(index[j],isize[NDX_REF1]+1);
/* consistancy of G_REF[1,2] has already been check */
/* hence we can look for the third atom right away */
for (i=0; i<isize[G_REF1]; i++)
{
for (j=0; j<isize[G_REF3]; j++)
{
/* Avoid expensive stuff if possible */
if ( top.atoms.atom[index[G_REF1][i]].resind !=
top.atoms.atom[index[G_REF3][j]].resind &&
index[G_REF1][i] != index[G_REF3][j] &&
index[G_REF2][i] != index[G_REF3][j] )
{
pbc_dx(&pbc,x[index[G_REF1][i]],x[index[G_REF3][j]],dx);
delta = norm2(dx);
if ( delta < tri_upper[G_REF1] &&
delta > tri_lower[G_REF1] )
{
pbc_dx(&pbc,x[index[G_REF2][i]],x[index[G_REF3][j]],dx);
delta = norm2(dx);
if ( delta < tri_upper[G_REF2] &&
delta > tri_lower[G_REF2] )
{
/* found triple */
index[NDX_REF1][isize[NDX_REF1]]=index[G_REF1][i];
index[NDX_REF2][isize[NDX_REF1]]=index[G_REF2][i];
index[NDX_REF3][isize[NDX_REF1]]=index[G_REF3][j];
/* resize groups */
isize[NDX_REF1]++;
for (k=NDX_REF1; k<=NDX_REF3; k++)
srenew(index[k],isize[NDX_REF1]+1);
}
}
}
}
}
}
else if ( mode ==3 )
{
isize[NDX_REF1]=0;
for (j=NDX_REF1; j<=NDX_REF3; j++)
srenew(index[j],isize[NDX_REF1]+1);
/* consistancy will be checked while searching */
for (i=0; i<isize[G_REF1]; i++)
{
for (j=0; j<isize[G_REF2]; j++)
{
/* Avoid expensive stuff if possible */
if ( top.atoms.atom[index[G_REF1][i]].resind !=
top.atoms.atom[index[G_REF2][j]].resind &&
index[G_REF1][i] != index[G_REF2][j] )
{
pbc_dx(&pbc,x[index[G_REF1][i]],x[index[G_REF2][j]],dx);
delta = norm2(dx);
if ( delta < tri_upper[G_REF3] &&
delta > tri_lower[G_REF3] )
{
for (k=0; k<isize[G_REF3]; k++)
{
if ( top.atoms.atom[index[G_REF1][i]].resind !=
top.atoms.atom[index[G_REF3][k]].resind &&
top.atoms.atom[index[G_REF2][j]].resind !=
top.atoms.atom[index[G_REF3][k]].resind &&
index[G_REF1][i] != index[G_REF3][k] &&
index[G_REF2][j] != index[G_REF3][k])
{
pbc_dx(&pbc,x[index[G_REF1][i]],x[index[G_REF3][k]],dx);
delta = norm2(dx);
if ( delta < tri_upper[G_REF1] &&
delta > tri_lower[G_REF1] )
{
pbc_dx(&pbc,x[index[G_REF2][j]],x[index[G_REF3][k]],dx);
delta = norm2(dx);
if ( delta < tri_upper[G_REF2] &&
delta > tri_lower[G_REF2] )
{
/* found triple */
index[NDX_REF1][isize[NDX_REF1]]=index[G_REF1][i];
index[NDX_REF2][isize[NDX_REF1]]=index[G_REF2][j];
index[NDX_REF3][isize[NDX_REF1]]=index[G_REF3][k];
/* resize groups */
isize[NDX_REF1]++;
for (l=NDX_REF1; l<=NDX_REF3; l++)
srenew(index[l],isize[NDX_REF1]+1);
}
}
}
}
}
}
}
}
}
for (i=0; i<isize[NDX_REF1]; i++)
{
/* setup the molecular coordinate system (i',j',k') */
/* because the coodinate system of the box forms a unit matrix */
/* (i',j',k') is identical with the rotation matrix */
clear_mat(rot);
/* k' = unitv(r(atom0) - r(atom1)) */
pbc_dx(&pbc,x[index[NDX_REF1][i]],x[index[NDX_REF2][i]],k_mol);
unitv(k_mol,rot[2]);
/* i' = unitv(k' x (r(atom2) - r(atom1))) */
pbc_dx(&pbc,x[index[NDX_REF3][i]],x[index[NDX_REF2][i]],i1_mol);
cprod(i1_mol,rot[2],i2_mol);
unitv(i2_mol,rot[0]);
/* j' = k' x i' */
cprod(rot[2],rot[0],rot[1]);
/* set the point of reference */
if ( mode == 2 )
copy_rvec(x[index[NDX_REF3][i]],xi);
else
copy_rvec(x[index[NDX_REF1][i]],xi);
/* make the reference */
if ( bRef )
{
for (j=0; j<isize[G_REFMOL]; j++)
{
pbc_dx(&pbc,xi,x[index[G_REFMOL][j]],dx);
mvmul(rot,dx,dx_mol);
rvec_inc(x_refmol[j],dx_mol);
for(k=XX; k<=ZZ; k++)
x_refmol[j][k] = x_refmol[j][k] / 2;
}
}
/* Copy the indexed coordinates to a continuous array */
for(j=0; j<isize[G_SDF]; j++)
copy_rvec(x[index[G_SDF][j]],x_i1[j]);
/* count the SDF */
for(j=0; j<isize[G_SDF]; j++)
{
/* Exclude peaks from the reference set */
bInGroup=FALSE;
for (k=NDX_REF1; k<=NDX_REF3; k++)
if ( index[G_SDF][j] == index[k][i] )
bInGroup=TRUE;
if ( !bInGroup )
{
pbc_dx(&pbc,xi,x_i1[j],dx);
/* transfer dx to the molecular coordinate system */
mvmul(rot,dx,dx_mol);
/* check cutoff's and count */
if ( dx_mol[XX] > -cutoff[XX] && dx_mol[XX] < cutoff[XX] )
if ( dx_mol[YY] > -cutoff[YY] && dx_mol[YY] < cutoff[YY] )
if ( dx_mol[ZZ] > -cutoff[ZZ] && dx_mol[ZZ] < cutoff[ZZ] )
{
X = (int)(floor(dx_mol[XX]*invbinw)) + (nbin[XX]-1)/2
+1;
Y = (int)(floor(dx_mol[YY]*invbinw)) + (nbin[YY]-1)/2
+1;
Z = (int)(floor(dx_mol[ZZ]*invbinw)) + (nbin[ZZ]-1)/2
+1;
count[X][Y][Z]++;
normfac++;
}
}
}
}
} while (read_next_x(status,&t,natoms,x,box));
fprintf(stderr,"\n");
close_trj(status);
sfree(x);
/* write the reference strcture*/
if ( bRef )
{
fp=ffopen(fnREF,"w");
fprintf(fp,"%s\n",title);
fprintf(fp," %d\n",isize[G_REFMOL]);
for (i=0; i<isize[G_REFMOL]; i++)
fprintf(fp,"%5d%5s%5s%5d%8.3f%8.3f%8.3f\n",
top.atoms.resinfo[top.atoms.atom[index[G_REFMOL][i]].resind].nr,
*(top.atoms.resinfo[top.atoms.atom[index[G_REFMOL][i]].resind].name),
*(top.atoms.atomname[index[G_REFMOL][i]]),i+1,
-1*x_refmol[i][XX],-1*x_refmol[i][YY],-1*x_refmol[i][ZZ]);
/* Inserted -1* on the line above three times */
fprintf(fp," 10.00000 10.00000 10.00000\n");
ffclose(fp);
fprintf(stderr,"\nWrote reference structure. (%d Atoms)\n",isize[G_REFMOL]);
}
/* Calculate the mean probability density */
fprintf(stderr,"\nNumber of configuations used for SDF: %d\n",(int)normfac);
normfac = nbin[0]*nbin[1]*nbin[2] / normfac;
fprintf(stderr,"\nMean probability density: %f\n",1/normfac);
/* normalize the SDF and write output */
/* see http://www.csc.fi/gopenmol/index.phtml for documentation */
fp=ffopen(fnSDF,"wb");
/* rank */
i_write(fp,3);
/* Type of surface */
i_write(fp,42);
/* Zdim, Ydim, Xdim */
for (i=ZZ; i>=XX; i--)
i_write(fp,nbin[i]);
/* [Z,Y,X][min,max] (box corners in Angstroem)*/
for (i=ZZ; i>=XX; i--)
{
f_write(fp,-cutoff[i]*10);
f_write(fp,cutoff[i]*10);
}
/* Original Code
for (i=1; i<nbin[2]+1; i++)
for (j=1; j<nbin[1]+1; j++)
for (k=1; k<nbin[0]+1; k++)
{
sdf = normfac * count[k][j][i];
if ( sdf < min_sdf ) min_sdf = sdf;
if ( sdf > max_sdf ) max_sdf = sdf;
f_write(fp,sdf);
}*/
/* Changed Code to Mirror SDF to correct coordinates */
for (i=nbin[2]; i>0; i--)
for (j=nbin[1]; j>0; j--)
for (k=nbin[0]; k>0; k--)
{
sdf = normfac * count[k][j][i];
if ( sdf < min_sdf ) min_sdf = sdf;
if ( sdf > max_sdf ) max_sdf = sdf;
f_write(fp,sdf);
}
fprintf(stderr,"\nMin: %f Max: %f\n",min_sdf,max_sdf);
ffclose(fp);
/* Give back the mem */
for(i=0; i<nbin[0]+1; i++)
{
for (j=0; j<nbin[1]+1; j++)
{
sfree(count[i][j]);
}
sfree(count[i]);
}
sfree(count);
}
int gmx_sorient(int argc, char *argv[])
{
t_topology top;
int ePBC = -1;
t_trxstatus *status;
int natoms;
real t;
rvec *xtop, *x;
matrix box;
FILE *fp;
int i, p, sa0, sa1, sa2, n, ntot, nf, m, *hist1, *hist2, *histn, nbin1, nbin2, nrbin;
real *histi1, *histi2, invbw, invrbw;
double sum1, sum2;
int *isize, nrefgrp, nrefat;
int **index;
char **grpname;
real inp, outp, nav, normfac, rmin2, rmax2, rcut, rcut2, r2, r;
real c1, c2;
char str[STRLEN];
gmx_bool bTPS;
rvec xref, dx, dxh1, dxh2, outer;
gmx_rmpbc_t gpbc = NULL;
t_pbc pbc;
const char *legr[] = {
"<cos(\\8q\\4\\s1\\N)>",
"<3cos\\S2\\N(\\8q\\4\\s2\\N)-1>"
};
const char *legc[] = {
"cos(\\8q\\4\\s1\\N)",
"3cos\\S2\\N(\\8q\\4\\s2\\N)-1"
};
const char *desc[] = {
"[THISMODULE] analyzes solvent orientation around solutes.",
"It calculates two angles between the vector from one or more",
"reference positions to the first atom of each solvent molecule:",
"",
" * [GRK]theta[grk][SUB]1[sub]: the angle with the vector from the first atom of the solvent",
" molecule to the midpoint between atoms 2 and 3.",
" * [GRK]theta[grk][SUB]2[sub]: the angle with the normal of the solvent plane, defined by the",
" same three atoms, or, when the option [TT]-v23[tt] is set, ",
" the angle with the vector between atoms 2 and 3.",
"",
"The reference can be a set of atoms or",
"the center of mass of a set of atoms. The group of solvent atoms should",
"consist of 3 atoms per solvent molecule.",
"Only solvent molecules between [TT]-rmin[tt] and [TT]-rmax[tt] are",
"considered for [TT]-o[tt] and [TT]-no[tt] each frame.[PAR]",
"[TT]-o[tt]: distribtion of [MATH][COS][GRK]theta[grk][SUB]1[sub][cos][math] for rmin<=r<=rmax.[PAR]",
"[TT]-no[tt]: distribution of [MATH][COS][GRK]theta[grk][SUB]2[sub][cos][math] for rmin<=r<=rmax.[PAR]",
"[TT]-ro[tt]: [MATH][CHEVRON][COS][GRK]theta[grk][SUB]1[sub][cos][chevron][math] and [MATH][CHEVRON]3[COS]^2[GRK]theta[grk][SUB]2[sub][cos]-1[chevron][math] as a function of the",
"distance.[PAR]",
"[TT]-co[tt]: the sum over all solvent molecules within distance r",
"of [MATH][COS][GRK]theta[grk][SUB]1[sub][cos][math] and [MATH]3[COS]^2([GRK]theta[grk][SUB]2[sub])-1[cos][math] as a function of r.[PAR]",
"[TT]-rc[tt]: the distribution of the solvent molecules as a function of r"
};
gmx_output_env_t *oenv;
static gmx_bool bCom = FALSE, bVec23 = FALSE, bPBC = FALSE;
static real rmin = 0.0, rmax = 0.5, binwidth = 0.02, rbinw = 0.02;
t_pargs pa[] = {
{ "-com", FALSE, etBOOL, {&bCom},
"Use the center of mass as the reference postion"
},
{ "-v23", FALSE, etBOOL, {&bVec23},
"Use the vector between atoms 2 and 3"
},
{ "-rmin", FALSE, etREAL, {&rmin}, "Minimum distance (nm)" },
{ "-rmax", FALSE, etREAL, {&rmax}, "Maximum distance (nm)" },
{ "-cbin", FALSE, etREAL, {&binwidth}, "Binwidth for the cosine" },
{ "-rbin", FALSE, etREAL, {&rbinw}, "Binwidth for r (nm)" },
{ "-pbc", FALSE, etBOOL, {&bPBC}, "Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules." }
};
t_filenm fnm[] = {
{ efTRX, NULL, NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, NULL, "sori", ffWRITE },
{ efXVG, "-no", "snor", ffWRITE },
{ efXVG, "-ro", "sord", ffWRITE },
{ efXVG, "-co", "scum", ffWRITE },
{ efXVG, "-rc", "scount", ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
bTPS = (opt2bSet("-s", NFILE, fnm) || !opt2bSet("-n", NFILE, fnm) || bCom);
if (bTPS)
{
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, NULL, box,
bCom);
}
/* get index groups */
printf("Select a group of reference particles and a solvent group:\n");
snew(grpname, 2);
snew(index, 2);
snew(isize, 2);
if (bTPS)
{
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 2, isize, index, grpname);
}
else
{
get_index(NULL, ftp2fn(efNDX, NFILE, fnm), 2, isize, index, grpname);
}
if (bCom)
{
nrefgrp = 1;
nrefat = isize[0];
}
else
{
nrefgrp = isize[0];
nrefat = 1;
}
if (isize[1] % 3)
{
gmx_fatal(FARGS, "The number of solvent atoms (%d) is not a multiple of 3",
isize[1]);
}
/* initialize reading trajectory: */
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
rmin2 = sqr(rmin);
rmax2 = sqr(rmax);
rcut = 0.99*std::sqrt(max_cutoff2(guess_ePBC(box), box));
if (rcut == 0)
{
rcut = 10*rmax;
}
rcut2 = sqr(rcut);
invbw = 1/binwidth;
nbin1 = 1+static_cast<int>(2*invbw + 0.5);
nbin2 = 1+static_cast<int>(invbw + 0.5);
invrbw = 1/rbinw;
snew(hist1, nbin1);
snew(hist2, nbin2);
nrbin = 1+static_cast<int>(rcut/rbinw);
if (nrbin == 0)
{
nrbin = 1;
}
snew(histi1, nrbin);
snew(histi2, nrbin);
snew(histn, nrbin);
ntot = 0;
nf = 0;
sum1 = 0;
sum2 = 0;
if (bTPS)
{
/* make molecules whole again */
gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
}
/* start analysis of trajectory */
do
{
if (bTPS)
{
/* make molecules whole again */
gmx_rmpbc(gpbc, natoms, box, x);
}
set_pbc(&pbc, ePBC, box);
n = 0;
inp = 0;
for (p = 0; (p < nrefgrp); p++)
{
if (bCom)
{
calc_com_pbc(nrefat, &top, x, &pbc, index[0], xref, bPBC);
}
else
{
copy_rvec(x[index[0][p]], xref);
}
for (m = 0; m < isize[1]; m += 3)
{
sa0 = index[1][m];
sa1 = index[1][m+1];
sa2 = index[1][m+2];
range_check(sa0, 0, natoms);
range_check(sa1, 0, natoms);
range_check(sa2, 0, natoms);
pbc_dx(&pbc, x[sa0], xref, dx);
r2 = norm2(dx);
if (r2 < rcut2)
{
r = std::sqrt(r2);
if (!bVec23)
{
/* Determine the normal to the plain */
rvec_sub(x[sa1], x[sa0], dxh1);
rvec_sub(x[sa2], x[sa0], dxh2);
rvec_inc(dxh1, dxh2);
svmul(1/r, dx, dx);
unitv(dxh1, dxh1);
inp = iprod(dx, dxh1);
cprod(dxh1, dxh2, outer);
unitv(outer, outer);
outp = iprod(dx, outer);
}
else
{
/* Use the vector between the 2nd and 3rd atom */
rvec_sub(x[sa2], x[sa1], dxh2);
unitv(dxh2, dxh2);
outp = iprod(dx, dxh2)/r;
}
{
int ii = static_cast<int>(invrbw*r);
range_check(ii, 0, nrbin);
histi1[ii] += inp;
histi2[ii] += 3*sqr(outp) - 1;
histn[ii]++;
}
if ((r2 >= rmin2) && (r2 < rmax2))
{
int ii1 = static_cast<int>(invbw*(inp + 1));
int ii2 = static_cast<int>(invbw*std::abs(outp));
range_check(ii1, 0, nbin1);
range_check(ii2, 0, nbin2);
hist1[ii1]++;
hist2[ii2]++;
sum1 += inp;
sum2 += outp;
n++;
}
}
}
}
ntot += n;
nf++;
}
while (read_next_x(oenv, status, &t, x, box));
/* clean up */
sfree(x);
close_trj(status);
gmx_rmpbc_done(gpbc);
/* Add the bin for the exact maximum to the previous bin */
hist1[nbin1-1] += hist1[nbin1];
hist2[nbin2-1] += hist2[nbin2];
nav = static_cast<real>(ntot)/(nrefgrp*nf);
normfac = invbw/ntot;
fprintf(stderr, "Average nr of molecules between %g and %g nm: %.1f\n",
rmin, rmax, nav);
if (ntot > 0)
{
sum1 /= ntot;
sum2 /= ntot;
fprintf(stderr, "Average cos(theta1) between %g and %g nm: %6.3f\n",
rmin, rmax, sum1);
fprintf(stderr, "Average 3cos2(theta2)-1 between %g and %g nm: %6.3f\n",
rmin, rmax, sum2);
}
sprintf(str, "Solvent orientation between %g and %g nm", rmin, rmax);
fp = xvgropen(opt2fn("-o", NFILE, fnm), str, "cos(\\8q\\4\\s1\\N)", "", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"average shell size %.1f molecules\"\n", nav);
}
for (i = 0; i < nbin1; i++)
{
fprintf(fp, "%g %g\n", (i+0.5)*binwidth-1, 2*normfac*hist1[i]);
}
xvgrclose(fp);
sprintf(str, "Solvent normal orientation between %g and %g nm", rmin, rmax);
fp = xvgropen(opt2fn("-no", NFILE, fnm), str, "cos(\\8q\\4\\s2\\N)", "", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"average shell size %.1f molecules\"\n", nav);
}
for (i = 0; i < nbin2; i++)
{
fprintf(fp, "%g %g\n", (i+0.5)*binwidth, normfac*hist2[i]);
}
xvgrclose(fp);
sprintf(str, "Solvent orientation");
fp = xvgropen(opt2fn("-ro", NFILE, fnm), str, "r (nm)", "", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"as a function of distance\"\n");
}
xvgr_legend(fp, 2, legr, oenv);
for (i = 0; i < nrbin; i++)
{
fprintf(fp, "%g %g %g\n", (i+0.5)*rbinw,
histn[i] ? histi1[i]/histn[i] : 0,
histn[i] ? histi2[i]/histn[i] : 0);
}
xvgrclose(fp);
sprintf(str, "Cumulative solvent orientation");
fp = xvgropen(opt2fn("-co", NFILE, fnm), str, "r (nm)", "", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"as a function of distance\"\n");
}
xvgr_legend(fp, 2, legc, oenv);
normfac = 1.0/(nrefgrp*nf);
c1 = 0;
c2 = 0;
fprintf(fp, "%g %g %g\n", 0.0, c1, c2);
for (i = 0; i < nrbin; i++)
{
c1 += histi1[i]*normfac;
c2 += histi2[i]*normfac;
fprintf(fp, "%g %g %g\n", (i+1)*rbinw, c1, c2);
}
xvgrclose(fp);
sprintf(str, "Solvent distribution");
fp = xvgropen(opt2fn("-rc", NFILE, fnm), str, "r (nm)", "molecules/nm", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"as a function of distance\"\n");
}
normfac = 1.0/(rbinw*nf);
for (i = 0; i < nrbin; i++)
{
fprintf(fp, "%g %g\n", (i+0.5)*rbinw, histn[i]*normfac);
}
xvgrclose(fp);
do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
do_view(oenv, opt2fn("-no", NFILE, fnm), NULL);
do_view(oenv, opt2fn("-ro", NFILE, fnm), "-nxy");
do_view(oenv, opt2fn("-co", NFILE, fnm), "-nxy");
return 0;
}
static void list_trn(char *fn)
{
static real mass[5] = { 15.9994, 1.008, 1.008, 0.0, 0.0 };
int i,j=0,m,fpread,fpwrite,nframe;
rvec *x,*v,*f,fmol[2],xcm[2],torque[j],dx;
real mmm,len;
matrix box;
t_trnheader trn;
gmx_bool bOK;
printf("Going to open %s\n",fn);
fpread = open_trn(fn,"r");
fpwrite = open_tpx(NULL,"w");
gmx_fio_setdebug(fpwrite,TRUE);
mmm=mass[0]+2*mass[1];
for(i=0; (i<5); i++)
mass[i] /= mmm;
nframe = 0;
while (fread_trnheader(fpread,&trn,&bOK)) {
snew(x,trn.natoms);
snew(v,trn.natoms);
snew(f,trn.natoms);
if (fread_htrn(fpread,&trn,
trn.box_size ? box : NULL,
trn.x_size ? x : NULL,
trn.v_size ? v : NULL,
trn.f_size ? f : NULL)) {
if (trn.x_size && trn.f_size) {
printf("There are %d atoms\n",trn.natoms);
for(j=0; (j<2); j++) {
clear_rvec(xcm[j]);
clear_rvec(fmol[j]);
clear_rvec(torque[j]);
for(i=5*j; (i<5*j+5); i++) {
rvec_inc(fmol[j],f[i]);
for(m=0; (m<DIM); m++)
xcm[j][m] += mass[i%5]*x[i][m];
}
for(i=5*j; (i<5*j+5); i++) {
rvec_dec(x[i],xcm[j]);
cprod(x[i],f[i],dx);
rvec_inc(torque[j],dx);
rvec_inc(x[i],xcm[j]);
}
}
pr_rvecs(stdout,0,"FMOL ",fmol,2);
pr_rvecs(stdout,0,"TORQUE",torque,2);
printf("Distance matrix Water1-Water2\n%5s","");
for(j=0; (j<5); j++)
printf(" %10s",nm[j]);
printf("\n");
for(j=0; (j<5); j++) {
printf("%5s",nm[j]);
for(i=5; (i<10); i++) {
rvec_sub(x[i],x[j],dx);
len = sqrt(iprod(dx,dx));
printf(" %10.7f",len);
}
printf("\n");
}
}
}
sfree(x);
sfree(v);
sfree(f);
nframe++;
}
if (!bOK)
fprintf(stderr,"\nWARNING: Incomplete frame header: nr %d, t=%g\n",
nframe,trn.t);
close_tpx(fpwrite);
close_trn(fpread);
}
void calc_order(const char *fn, atom_id *index, atom_id *a, rvec **order,
real ***slOrder, real *slWidth, int nslices, gmx_bool bSliced,
gmx_bool bUnsat, t_topology *top, int ePBC, int ngrps, int axis,
gmx_bool permolecule, gmx_bool radial, gmx_bool distcalc, const char *radfn,
real ***distvals,
const gmx_output_env_t *oenv)
{
/* if permolecule = TRUE, order parameters will be calculed per molecule
* and stored in slOrder with #slices = # molecules */
rvec *x0, /* coordinates with pbc */
*x1, /* coordinates without pbc */
dist; /* vector between two atoms */
matrix box; /* box (3x3) */
t_trxstatus *status;
rvec cossum, /* sum of vector angles for three axes */
Sx, Sy, Sz, /* the three molecular axes */
tmp1, tmp2, /* temp. rvecs for calculating dot products */
frameorder; /* order parameters for one frame */
real *slFrameorder; /* order parameter for one frame, per slice */
real length, /* total distance between two atoms */
t, /* time from trajectory */
z_ave, z1, z2; /* average z, used to det. which slice atom is in */
int natoms, /* nr. atoms in trj */
nr_tails, /* nr tails, to check if index file is correct */
size = 0, /* nr. of atoms in group. same as nr_tails */
i, j, m, k, teller = 0,
slice, /* current slice number */
nr_frames = 0;
int *slCount; /* nr. of atoms in one slice */
real sdbangle = 0; /* sum of these angles */
gmx_bool use_unitvector = FALSE; /* use a specified unit vector instead of axis to specify unit normal*/
rvec direction, com, dref, dvec;
int comsize, distsize;
atom_id *comidx = NULL, *distidx = NULL;
char *grpname = NULL;
t_pbc pbc;
real arcdist, tmpdist;
gmx_rmpbc_t gpbc = NULL;
/* PBC added for center-of-mass vector*/
/* Initiate the pbc structure */
std::memset(&pbc, 0, sizeof(pbc));
if ((natoms = read_first_x(oenv, &status, fn, &t, &x0, box)) == 0)
{
gmx_fatal(FARGS, "Could not read coordinates from statusfile\n");
}
nr_tails = index[1] - index[0];
fprintf(stderr, "Number of elements in first group: %d\n", nr_tails);
/* take first group as standard. Not rocksolid, but might catch error in index*/
if (permolecule)
{
nslices = nr_tails;
bSliced = FALSE; /*force slices off */
fprintf(stderr, "Calculating order parameters for each of %d molecules\n",
nslices);
}
if (radial)
{
use_unitvector = TRUE;
fprintf(stderr, "Select an index group to calculate the radial membrane normal\n");
get_index(&top->atoms, radfn, 1, &comsize, &comidx, &grpname);
}
if (distcalc)
{
if (grpname != NULL)
{
sfree(grpname);
}
fprintf(stderr, "Select an index group to use as distance reference\n");
get_index(&top->atoms, radfn, 1, &distsize, &distidx, &grpname);
bSliced = FALSE; /*force slices off*/
}
if (use_unitvector && bSliced)
{
fprintf(stderr, "Warning: slicing and specified unit vectors are not currently compatible\n");
}
snew(slCount, nslices);
snew(*slOrder, nslices);
for (i = 0; i < nslices; i++)
{
snew((*slOrder)[i], ngrps);
}
if (distcalc)
{
snew(*distvals, nslices);
for (i = 0; i < nslices; i++)
{
snew((*distvals)[i], ngrps);
}
}
snew(*order, ngrps);
snew(slFrameorder, nslices);
snew(x1, natoms);
if (bSliced)
{
*slWidth = box[axis][axis]/nslices;
fprintf(stderr, "Box divided in %d slices. Initial width of slice: %f\n",
nslices, *slWidth);
}
#if 0
nr_tails = index[1] - index[0];
fprintf(stderr, "Number of elements in first group: %d\n", nr_tails);
/* take first group as standard. Not rocksolid, but might catch error
in index*/
#endif
teller = 0;
gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
/*********** Start processing trajectory ***********/
do
{
if (bSliced)
{
*slWidth = box[axis][axis]/nslices;
}
teller++;
set_pbc(&pbc, ePBC, box);
gmx_rmpbc_copy(gpbc, natoms, box, x0, x1);
/* Now loop over all groups. There are ngrps groups, the order parameter can
be calculated for grp 1 to grp ngrps - 1. For each group, loop over all
atoms in group, which is index[i] to (index[i+1] - 1) See block.h. Of
course, in this case index[i+1] -index[i] has to be the same for all
groups, namely the number of tails. i just runs over all atoms in a tail,
so for DPPC ngrps = 16 and i runs from 1 to 14, including 14
*/
if (radial)
{
/*center-of-mass determination*/
com[XX] = 0.0; com[YY] = 0.0; com[ZZ] = 0.0;
for (j = 0; j < comsize; j++)
{
rvec_inc(com, x1[comidx[j]]);
}
svmul(1.0/comsize, com, com);
}
if (distcalc)
{
dref[XX] = 0.0; dref[YY] = 0.0; dref[ZZ] = 0.0;
for (j = 0; j < distsize; j++)
{
rvec_inc(dist, x1[distidx[j]]);
}
svmul(1.0/distsize, dref, dref);
if (radial)
{
pbc_dx(&pbc, dref, com, dvec);
unitv(dvec, dvec);
}
}
for (i = 1; i < ngrps - 1; i++)
{
clear_rvec(frameorder);
size = index[i+1] - index[i];
if (size != nr_tails)
{
gmx_fatal(FARGS, "grp %d does not have same number of"
" elements as grp 1\n", i);
}
for (j = 0; j < size; j++)
{
if (radial)
/*create unit vector*/
{
pbc_dx(&pbc, x1[a[index[i]+j]], com, direction);
unitv(direction, direction);
/*DEBUG*/
/*if (j==0)
fprintf(stderr,"X %f %f %f\tcom %f %f %f\tdirection %f %f %f\n",x1[a[index[i]+j]][0],x1[a[index[i]+j]][1],x1[a[index[i]+j]][2],com[0],com[1],com[2],
direction[0],direction[1],direction[2]);*/
}
if (bUnsat)
{
/* Using convention for unsaturated carbons */
/* first get Sz, the vector from Cn to Cn+1 */
rvec_sub(x1[a[index[i+1]+j]], x1[a[index[i]+j]], dist);
length = norm(dist);
check_length(length, a[index[i]+j], a[index[i+1]+j]);
svmul(1.0/length, dist, Sz);
/* this is actually the cosine of the angle between the double bond
and axis, because Sz is normalized and the two other components of
the axis on the bilayer are zero */
if (use_unitvector)
{
sdbangle += gmx_angle(direction, Sz); /*this can probably be optimized*/
}
else
{
sdbangle += std::acos(Sz[axis]);
}
}
else
{
/* get vector dist(Cn-1,Cn+1) for tail atoms */
rvec_sub(x1[a[index[i+1]+j]], x1[a[index[i-1]+j]], dist);
length = norm(dist); /* determine distance between two atoms */
check_length(length, a[index[i-1]+j], a[index[i+1]+j]);
svmul(1.0/length, dist, Sz);
/* Sz is now the molecular axis Sz, normalized and all that */
}
/* now get Sx. Sx is normal to the plane of Cn-1, Cn and Cn+1 so
we can use the outer product of Cn-1->Cn and Cn+1->Cn, I hope */
rvec_sub(x1[a[index[i+1]+j]], x1[a[index[i]+j]], tmp1);
rvec_sub(x1[a[index[i-1]+j]], x1[a[index[i]+j]], tmp2);
cprod(tmp1, tmp2, Sx);
svmul(1.0/norm(Sx), Sx, Sx);
/* now we can get Sy from the outer product of Sx and Sz */
cprod(Sz, Sx, Sy);
svmul(1.0/norm(Sy), Sy, Sy);
/* the square of cosine of the angle between dist and the axis.
Using the innerproduct, but two of the three elements are zero
Determine the sum of the orderparameter of all atoms in group
*/
if (use_unitvector)
{
cossum[XX] = sqr(iprod(Sx, direction)); /* this is allowed, since Sa is normalized */
cossum[YY] = sqr(iprod(Sy, direction));
cossum[ZZ] = sqr(iprod(Sz, direction));
}
else
{
cossum[XX] = sqr(Sx[axis]); /* this is allowed, since Sa is normalized */
cossum[YY] = sqr(Sy[axis]);
cossum[ZZ] = sqr(Sz[axis]);
}
for (m = 0; m < DIM; m++)
{
frameorder[m] += 0.5 * (3.0 * cossum[m] - 1.0);
}
if (bSliced)
{
/* get average coordinate in box length for slicing,
determine which slice atom is in, increase count for that
slice. slFrameorder and slOrder are reals, not
rvecs. Only the component [axis] of the order tensor is
kept, until I find it necessary to know the others too
*/
z1 = x1[a[index[i-1]+j]][axis];
z2 = x1[a[index[i+1]+j]][axis];
z_ave = 0.5 * (z1 + z2);
if (z_ave < 0)
{
z_ave += box[axis][axis];
}
if (z_ave > box[axis][axis])
{
z_ave -= box[axis][axis];
}
slice = static_cast<int>((0.5 + (z_ave / (*slWidth))) - 1);
slCount[slice]++; /* determine slice, increase count */
slFrameorder[slice] += 0.5 * (3 * cossum[axis] - 1);
}
else if (permolecule)
{
/* store per-molecule order parameter
* To just track single-axis order: (*slOrder)[j][i] += 0.5 * (3 * iprod(cossum,direction) - 1);
* following is for Scd order: */
(*slOrder)[j][i] += -1* (1.0/3.0 * (3 * cossum[XX] - 1) + 1.0/3.0 * 0.5 * (3.0 * cossum[YY] - 1));
}
if (distcalc)
{
if (radial)
{
/* bin order parameter by arc distance from reference group*/
arcdist = gmx_angle(dvec, direction);
(*distvals)[j][i] += arcdist;
}
else if (i == 1)
{
/* Want minimum lateral distance to first group calculated */
tmpdist = trace(box); /* should be max value */
for (k = 0; k < distsize; k++)
{
pbc_dx(&pbc, x1[distidx[k]], x1[a[index[i]+j]], dvec);
/* at the moment, just remove dvec[axis] */
dvec[axis] = 0;
tmpdist = std::min(tmpdist, norm2(dvec));
}
//fprintf(stderr, "Min dist %f; trace %f\n", tmpdist, trace(box));
(*distvals)[j][i] += std::sqrt(tmpdist);
}
}
} /* end loop j, over all atoms in group */
for (m = 0; m < DIM; m++)
{
(*order)[i][m] += (frameorder[m]/size);
}
if (!permolecule)
{ /*Skip following if doing per-molecule*/
for (k = 0; k < nslices; k++)
{
if (slCount[k]) /* if no elements, nothing has to be added */
{
(*slOrder)[k][i] += slFrameorder[k]/slCount[k];
slFrameorder[k] = 0; slCount[k] = 0;
}
}
} /* end loop i, over all groups in indexfile */
}
nr_frames++;
}
while (read_next_x(oenv, status, &t, x0, box));
/*********** done with status file **********/
fprintf(stderr, "\nRead trajectory. Printing parameters to file\n");
gmx_rmpbc_done(gpbc);
/* average over frames */
for (i = 1; i < ngrps - 1; i++)
{
svmul(1.0/nr_frames, (*order)[i], (*order)[i]);
fprintf(stderr, "Atom %d Tensor: x=%g , y=%g, z=%g\n", i, (*order)[i][XX],
(*order)[i][YY], (*order)[i][ZZ]);
if (bSliced || permolecule)
{
for (k = 0; k < nslices; k++)
{
(*slOrder)[k][i] /= nr_frames;
}
}
if (distcalc)
{
for (k = 0; k < nslices; k++)
{
(*distvals)[k][i] /= nr_frames;
}
}
}
if (bUnsat)
{
fprintf(stderr, "Average angle between double bond and normal: %f\n",
180*sdbangle/(nr_frames * size*M_PI));
}
sfree(x0); /* free memory used by coordinate arrays */
sfree(x1);
if (comidx != NULL)
{
sfree(comidx);
}
if (distidx != NULL)
{
sfree(distidx);
}
if (grpname != NULL)
{
sfree(grpname);
}
}
void
Angle::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
TrajectoryAnalysisModuleData *pdata)
{
AnalysisDataHandle *dh = pdata->dataHandle("angle");
std::vector<Selection *> sel1 = pdata->parallelSelections(_sel1);
std::vector<Selection *> sel2 = pdata->parallelSelections(_sel2);
checkSelections(sel1, sel2);
rvec v1, v2;
rvec c1, c2;
switch (_g2type[0])
{
case 'z':
clear_rvec(v2);
v2[ZZ] = 1.0;
clear_rvec(c2);
break;
case 's':
copy_rvec(_sel2[0]->x(0), c2);
break;
}
dh->startFrame(frnr, fr.time);
int incr1 = _bSplit1 ? 1 : _natoms1;
int incr2 = _bSplit2 ? 1 : _natoms2;
int ngrps = _bMulti ? _sel1.size() : 1;
for (int g = 0; g < ngrps; ++g)
{
real ave = 0.0;
int n = 0;
int i, j;
for (i = j = 0; i < sel1[g]->posCount(); i += incr1)
{
rvec x[4];
real angle;
copy_pos(sel1, _bSplit1, _natoms1, g, i, x);
switch (_g1type[0])
{
case 'a':
if (pbc)
{
pbc_dx(pbc, x[0], x[1], v1);
pbc_dx(pbc, x[2], x[1], v2);
}
else
{
rvec_sub(x[0], x[1], v1);
rvec_sub(x[2], x[1], v2);
}
angle = gmx_angle(v1, v2);
break;
case 'd': {
rvec dx[3];
if (pbc)
{
pbc_dx(pbc, x[0], x[1], dx[0]);
pbc_dx(pbc, x[2], x[1], dx[1]);
pbc_dx(pbc, x[2], x[3], dx[2]);
}
else
{
rvec_sub(x[0], x[1], dx[0]);
rvec_sub(x[2], x[1], dx[1]);
rvec_sub(x[2], x[3], dx[2]);
}
cprod(dx[0], dx[1], v1);
cprod(dx[1], dx[2], v2);
angle = gmx_angle(v1, v2);
real ipr = iprod(dx[0], v2);
if (ipr < 0)
{
angle = -angle;
}
break;
}
case 'v':
case 'p':
calc_vec(_natoms1, x, pbc, v1, c1);
switch (_g2type[0])
{
case 'v':
case 'p':
copy_pos(sel2, _bSplit2, _natoms2, 0, j, x);
calc_vec(_natoms2, x, pbc, v2, c2);
j += incr2;
break;
case 't':
// FIXME: This is not parallelizable.
if (frnr == 0)
{
copy_rvec(v1, _vt0[n]);
}
copy_rvec(_vt0[n], v2);
break;
case 'z':
c1[XX] = c1[YY] = 0.0;
break;
case 's':
if (pbc)
{
pbc_dx(pbc, c1, c2, v2);
}
else
{
rvec_sub(c1, c2, v2);
}
break;
default:
GMX_THROW(InternalError("invalid -g2 value"));
}
angle = gmx_angle(v1, v2);
break;
default:
GMX_THROW(InternalError("invalid -g1 value"));
}
angle *= RAD2DEG;
real dist = 0.0;
if (_bDumpDist)
{
if (pbc)
{
rvec dx;
pbc_dx(pbc, c2, c1, dx);
dist = norm(dx);
}
else
{
dist = sqrt(distance2(c1, c2));
}
}
if (_bAll)
{
dh->addPoint(n + 1, angle);
}
ave += angle;
++n;
}
if (n > 0)
{
ave /= n;
}
dh->addPoint(g, ave);
}
dh->finishFrame();
}
int gmx_rotacf(int argc,char *argv[])
{
static char *desc[] = {
"g_rotacf calculates the rotational correlation function",
"for molecules. Three atoms (i,j,k) must be given in the index",
"file, defining two vectors ij and jk. The rotational acf",
"is calculated as the autocorrelation function of the vector",
"n = ij x jk, i.e. the cross product of the two vectors.",
"Since three atoms span a plane, the order of the three atoms",
"does not matter. Optionally, controlled by the -d switch, you can",
"calculate the rotational correlation function for linear molecules",
"by specifying two atoms (i,j) in the index file.",
"[PAR]",
"EXAMPLES[PAR]",
"g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1",
"-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0[PAR]",
"This will calculate the rotational correlation function using a first",
"order Legendre polynomial of the angle of a vector defined by the index",
"file. The correlation function will be fitted from 2.5 ps till 20.0 ps",
"to a two parameter exponential",
""
};
static bool bVec = FALSE,bAver=TRUE;
t_pargs pa[] = {
{ "-d", FALSE, etBOOL, {&bVec},
"Use index doublets (vectors) for correlation function instead of triplets (planes)" },
{ "-aver",FALSE, etBOOL, {&bAver},
"Average over molecules" }
};
int status,isize;
atom_id *index;
char *grpname;
rvec *x,*x_s;
matrix box;
real **c1;
rvec xij,xjk,n;
int i,m,teller,n_alloc,natoms,nvec,ai,aj,ak;
unsigned long mode;
real t,t0,t1,dt;
t_topology *top;
int ePBC;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPX, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffREAD },
{ efXVG, "-o", "rotacf", ffWRITE }
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
CopyRight(stderr,argv[0]);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL);
rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
if (bVec)
nvec = isize/2;
else
nvec = isize/3;
if (((isize % 3) != 0) && !bVec)
gmx_fatal(FARGS,"number of index elements not multiple of 3, "
"these can not be atom triplets\n");
if (((isize % 2) != 0) && bVec)
gmx_fatal(FARGS,"number of index elements not multiple of 2, "
"these can not be atom doublets\n");
top=read_top(ftp2fn(efTPX,NFILE,fnm),&ePBC);
snew(c1,nvec);
for (i=0; (i<nvec); i++)
c1[i]=NULL;
n_alloc=0;
natoms=read_first_x(&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
snew(x_s,natoms);
/* Start the loop over frames */
t1 = t0 = t;
teller = 0;
do {
if (teller >= n_alloc) {
n_alloc+=100;
for (i=0; (i<nvec); i++)
srenew(c1[i],DIM*n_alloc);
}
t1 = t;
/* Remove periodicity */
rm_pbc(&(top->idef),ePBC,natoms,box,x,x_s);
/* Compute crossproducts for all vectors, if triplets.
* else, just get the vectors in case of doublets.
*/
if (bVec == FALSE) {
for (i=0; (i<nvec); i++) {
ai=index[3*i];
aj=index[3*i+1];
ak=index[3*i+2];
rvec_sub(x_s[ai],x_s[aj],xij);
rvec_sub(x_s[aj],x_s[ak],xjk);
cprod(xij,xjk,n);
for(m=0; (m<DIM); m++)
c1[i][DIM*teller+m]=n[m];
}
}
else {
for (i=0; (i<nvec); i++) {
ai=index[2*i];
aj=index[2*i+1];
rvec_sub(x_s[ai],x_s[aj],n);
for(m=0; (m<DIM); m++)
c1[i][DIM*teller+m]=n[m];
}
}
/* Increment loop counter */
teller++;
} while (read_next_x(status,&t,natoms,x,box));
close_trj(status);
fprintf(stderr,"\nDone with trajectory\n");
/* Autocorrelation function */
if (teller < 2)
fprintf(stderr,"Not enough frames for correlation function\n");
else {
dt=(t1 - t0)/(teller-1);
mode = eacVector;
do_autocorr(ftp2fn(efXVG,NFILE,fnm),"Rotational Correlation Function",
teller,nvec,c1,dt,mode,bAver);
}
do_view(ftp2fn(efXVG,NFILE,fnm),NULL);
thanx(stderr);
return 0;
}
static void do_ac_core(int nframes,int nout,
real corr[],real c1[],int nrestart,
unsigned long mode)
{
int j,k,j3,jk3,m,n;
real ccc,cth;
rvec xj,xk,rr;
if (nrestart < 1) {
printf("WARNING: setting number of restarts to 1\n");
nrestart = 1;
}
if (debug)
fprintf(debug,
"Starting do_ac_core: nframes=%d, nout=%d, nrestart=%d,mode=%lu\n",
nframes,nout,nrestart,mode);
for(j=0; (j<nout); j++)
corr[j]=0;
/* Loop over starting points. */
for(j=0; (j<nframes); j+=nrestart) {
j3 = DIM*j;
/* Loop over the correlation length for this starting point */
for(k=0; (k<nout) && (j+k < nframes); k++) {
jk3 = DIM*(j+k);
/* Switch over possible ACF types.
* It might be more efficient to put the loops inside the switch,
* but this is more clear, and save development time!
*/
if (MODE(eacNormal)) {
corr[k] += c1[j]*c1[j+k];
}
else if (MODE(eacCos)) {
/* Compute the cos (phi(t)-phi(t+dt)) */
corr[k] += cos(c1[j]-c1[j+k]);
}
else if (MODE(eacIden)) {
/* Check equality (phi(t)==phi(t+dt)) */
corr[k] += (c1[j]==c1[j+k])? 1 : 0;
}
else if (MODE(eacP1) || MODE(eacP2) || MODE(eacP3)) {
for(m=0; (m<DIM); m++) {
xj[m] = c1[j3+m];
xk[m] = c1[jk3+m];
}
cth=cos_angle(xj,xk);
if (cth-1.0 > 1.0e-15) {
printf("j: %d, k: %d, xj:(%g,%g,%g), xk:(%g,%g,%g)\n",
j,k,xj[XX],xj[YY],xj[ZZ],xk[XX],xk[YY],xk[ZZ]);
}
corr[k] += LegendreP(cth,mode); /* 1.5*cth*cth-0.5; */
}
else if (MODE(eacRcross)) {
for(m=0; (m<DIM); m++) {
xj[m] = c1[j3+m];
xk[m] = c1[jk3+m];
}
cprod(xj,xk,rr);
corr[k] += iprod(rr,rr);
}
else if (MODE(eacVector)) {
for(m=0; (m<DIM); m++) {
xj[m] = c1[j3+m];
xk[m] = c1[jk3+m];
}
ccc = iprod(xj,xk);
corr[k] += ccc;
}
else
gmx_fatal(FARGS,"\nInvalid mode (%d) in do_ac_core",mode);
}
}
/* Correct for the number of points and copy results to the data array */
for(j=0; (j<nout); j++) {
n = (nframes-j+(nrestart-1))/nrestart;
c1[j] = corr[j]/n;
}
}
void check_cm_grp(FILE *fp, t_vcm *vcm, t_inputrec *ir, real Temp_Max)
{
int m, g;
real ekcm, ekrot, tm, tm_1, Temp_cm;
rvec jcm;
tensor Icm;
/* First analyse the total results */
if (vcm->mode != ecmNO)
{
for (g = 0; (g < vcm->nr); g++)
{
tm = vcm->group_mass[g];
if (tm != 0)
{
tm_1 = 1.0/tm;
svmul(tm_1, vcm->group_p[g], vcm->group_v[g]);
}
/* Else it's zero anyway! */
}
if (vcm->mode == ecmANGULAR)
{
for (g = 0; (g < vcm->nr); g++)
{
tm = vcm->group_mass[g];
if (tm != 0)
{
tm_1 = 1.0/tm;
/* Compute center of mass for this group */
for (m = 0; (m < DIM); m++)
{
vcm->group_x[g][m] *= tm_1;
}
/* Subtract the center of mass contribution to the
* angular momentum
*/
cprod(vcm->group_x[g], vcm->group_v[g], jcm);
for (m = 0; (m < DIM); m++)
{
vcm->group_j[g][m] -= tm*jcm[m];
}
/* Subtract the center of mass contribution from the inertia
* tensor (this is not as trivial as it seems, but due to
* some cancellation we can still do it, even in parallel).
*/
clear_mat(Icm);
update_tensor(vcm->group_x[g], tm, Icm);
m_sub(vcm->group_i[g], Icm, vcm->group_i[g]);
/* Compute angular velocity, using matrix operation
* Since J = I w
* we have
* w = I^-1 J
*/
get_minv(vcm->group_i[g], Icm);
mvmul(Icm, vcm->group_j[g], vcm->group_w[g]);
}
/* Else it's zero anyway! */
}
}
}
for (g = 0; (g < vcm->nr); g++)
{
ekcm = 0;
if (vcm->group_mass[g] != 0 && vcm->group_ndf[g] > 0)
{
for (m = 0; m < vcm->ndim; m++)
{
ekcm += sqr(vcm->group_v[g][m]);
}
ekcm *= 0.5*vcm->group_mass[g];
Temp_cm = 2*ekcm/vcm->group_ndf[g];
if ((Temp_cm > Temp_Max) && fp)
{
fprintf(fp, "Large VCM(group %s): %12.5f, %12.5f, %12.5f, Temp-cm: %12.5e\n",
vcm->group_name[g], vcm->group_v[g][XX],
vcm->group_v[g][YY], vcm->group_v[g][ZZ], Temp_cm);
}
if (vcm->mode == ecmANGULAR)
{
ekrot = 0.5*iprod(vcm->group_j[g], vcm->group_w[g]);
if ((ekrot > 1) && fp && !EI_RANDOM(ir->eI))
{
/* if we have an integrator that may not conserve momenta, skip */
tm = vcm->group_mass[g];
fprintf(fp, "Group %s with mass %12.5e, Ekrot %12.5e Det(I) = %12.5e\n",
vcm->group_name[g], tm, ekrot, det(vcm->group_i[g]));
fprintf(fp, " COM: %12.5f %12.5f %12.5f\n",
vcm->group_x[g][XX], vcm->group_x[g][YY], vcm->group_x[g][ZZ]);
fprintf(fp, " P: %12.5f %12.5f %12.5f\n",
vcm->group_p[g][XX], vcm->group_p[g][YY], vcm->group_p[g][ZZ]);
fprintf(fp, " V: %12.5f %12.5f %12.5f\n",
vcm->group_v[g][XX], vcm->group_v[g][YY], vcm->group_v[g][ZZ]);
fprintf(fp, " J: %12.5f %12.5f %12.5f\n",
vcm->group_j[g][XX], vcm->group_j[g][YY], vcm->group_j[g][ZZ]);
fprintf(fp, " w: %12.5f %12.5f %12.5f\n",
vcm->group_w[g][XX], vcm->group_w[g][YY], vcm->group_w[g][ZZ]);
pr_rvecs(fp, 0, "Inertia tensor", vcm->group_i[g], DIM);
}
}
}
}
}
void
Angle::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
TrajectoryAnalysisModuleData *pdata)
{
AnalysisDataHandle dh = pdata->dataHandle(angles_);
const SelectionList &sel1 = pdata->parallelSelections(sel1_);
const SelectionList &sel2 = pdata->parallelSelections(sel2_);
checkSelections(sel1, sel2);
dh.startFrame(frnr, fr.time);
for (size_t g = 0; g < sel1_.size(); ++g)
{
rvec v1, v2;
rvec c1, c2;
switch (g2type_[0])
{
case 'z':
clear_rvec(v2);
v2[ZZ] = 1.0;
clear_rvec(c2);
break;
case 's':
copy_rvec(sel2_[g].position(0).x(), c2);
break;
}
for (int i = 0, j = 0, n = 0;
i < sel1[g].posCount();
i += natoms1_, j += natoms2_, ++n)
{
rvec x[4];
real angle;
copy_pos(sel1, natoms1_, g, i, x);
switch (g1type_[0])
{
case 'a':
if (pbc)
{
pbc_dx(pbc, x[0], x[1], v1);
pbc_dx(pbc, x[2], x[1], v2);
}
else
{
rvec_sub(x[0], x[1], v1);
rvec_sub(x[2], x[1], v2);
}
angle = gmx_angle(v1, v2);
break;
case 'd':
{
rvec dx[3];
if (pbc)
{
pbc_dx(pbc, x[0], x[1], dx[0]);
pbc_dx(pbc, x[2], x[1], dx[1]);
pbc_dx(pbc, x[2], x[3], dx[2]);
}
else
{
rvec_sub(x[0], x[1], dx[0]);
rvec_sub(x[2], x[1], dx[1]);
rvec_sub(x[2], x[3], dx[2]);
}
cprod(dx[0], dx[1], v1);
cprod(dx[1], dx[2], v2);
angle = gmx_angle(v1, v2);
real ipr = iprod(dx[0], v2);
if (ipr < 0)
{
angle = -angle;
}
break;
}
case 'v':
case 'p':
calc_vec(natoms1_, x, pbc, v1, c1);
switch (g2type_[0])
{
case 'v':
case 'p':
copy_pos(sel2, natoms2_, 0, j, x);
calc_vec(natoms2_, x, pbc, v2, c2);
break;
case 't':
// FIXME: This is not parallelizable.
if (frnr == 0)
{
copy_rvec(v1, vt0_[g][n]);
}
copy_rvec(vt0_[g][n], v2);
break;
case 'z':
c1[XX] = c1[YY] = 0.0;
break;
case 's':
if (pbc)
{
pbc_dx(pbc, c1, c2, v2);
}
else
{
rvec_sub(c1, c2, v2);
}
break;
default:
GMX_THROW(InternalError("invalid -g2 value"));
}
angle = gmx_angle(v1, v2);
break;
default:
GMX_THROW(InternalError("invalid -g1 value"));
}
/* TODO: Should we also calculate distances like g_sgangle?
* Could be better to leave that for a separate tool.
real dist = 0.0;
if (bDumpDist_)
{
if (pbc)
{
rvec dx;
pbc_dx(pbc, c2, c1, dx);
dist = norm(dx);
}
else
{
dist = sqrt(distance2(c1, c2));
}
}
*/
dh.setPoint(n, angle * RAD2DEG);
}
}
dh.finishFrame();
}
/* calculate best fit from i+.5 to j+.5. Assume i<j (cyclically).
Return 0 and set badness and parameters (alpha, beta), if
possible. Return 1 if impossible. */
static int opti_penalty(privpath_t *pp, int i, int j, opti_t *res, double opttolerance, int *convc, double *areac) {
int m = pp->curve.n;
int k, k1, k2, conv, i1;
double area, alpha, d, d1, d2;
dpoint_t p0, p1, p2, p3, pt;
double A, R, A1, A2, A3, A4;
double s, t;
/* check convexity, corner-freeness, and maximum bend < 179 degrees */
if (i==j) { /* sanity - a full loop can never be an opticurve */
return 1;
}
k = i;
i1 = mod(i+1, m);
k1 = mod(k+1, m);
conv = convc[k1];
if (conv == 0) {
return 1;
}
d = ddist(pp->curve.vertex[i], pp->curve.vertex[i1]);
for (k=k1; k!=j; k=k1) {
k1 = mod(k+1, m);
k2 = mod(k+2, m);
if (convc[k1] != conv) {
return 1;
}
if (sign(cprod(pp->curve.vertex[i], pp->curve.vertex[i1], pp->curve.vertex[k1], pp->curve.vertex[k2])) != conv) {
return 1;
}
if (iprod1(pp->curve.vertex[i], pp->curve.vertex[i1], pp->curve.vertex[k1], pp->curve.vertex[k2]) < d * ddist(pp->curve.vertex[k1], pp->curve.vertex[k2]) * COS179) {
return 1;
}
}
/* the curve we're working in: */
p0 = pp->curve.c[mod(i,m)][2];
p1 = pp->curve.vertex[mod(i+1,m)];
p2 = pp->curve.vertex[mod(j,m)];
p3 = pp->curve.c[mod(j,m)][2];
/* determine its area */
area = areac[j] - areac[i];
area -= dpara(pp->curve.vertex[0], pp->curve.c[i][2], pp->curve.c[j][2])/2;
if (i>=j) {
area += areac[m];
}
/* find intersection o of p0p1 and p2p3. Let t,s such that o =
interval(t,p0,p1) = interval(s,p3,p2). Let A be the area of the
triangle (p0,o,p3). */
A1 = dpara(p0, p1, p2);
A2 = dpara(p0, p1, p3);
A3 = dpara(p0, p2, p3);
/* A4 = dpara(p1, p2, p3); */
A4 = A1+A3-A2;
if (A2 == A1) { /* this should never happen */
return 1;
}
t = A3/(A3-A4);
s = A2/(A2-A1);
A = A2 * t / 2.0;
if (A == 0.0) { /* this should never happen */
return 1;
}
R = area / A; /* relative area */
alpha = 2 - sqrt(4 - R / 0.3); /* overall alpha for p0-o-p3 curve */
res->c[0] = interval(t * alpha, p0, p1);
res->c[1] = interval(s * alpha, p3, p2);
res->alpha = alpha;
res->t = t;
res->s = s;
p1 = res->c[0];
p2 = res->c[1]; /* the proposed curve is now (p0,p1,p2,p3) */
res->pen = 0;
/* calculate penalty */
/* check tangency with edges */
for (k=mod(i+1,m); k!=j; k=k1) {
k1 = mod(k+1,m);
t = tangent(p0, p1, p2, p3, pp->curve.vertex[k], pp->curve.vertex[k1]);
if (t<-.5) {
return 1;
}
pt = bezier(t, p0, p1, p2, p3);
d = ddist(pp->curve.vertex[k], pp->curve.vertex[k1]);
if (d == 0.0) { /* this should never happen */
return 1;
}
d1 = dpara(pp->curve.vertex[k], pp->curve.vertex[k1], pt) / d;
if (fabs(d1) > opttolerance) {
return 1;
}
if (iprod(pp->curve.vertex[k], pp->curve.vertex[k1], pt) < 0 || iprod(pp->curve.vertex[k1], pp->curve.vertex[k], pt) < 0) {
return 1;
}
res->pen += sq(d1);
}
/* check corners */
for (k=i; k!=j; k=k1) {
k1 = mod(k+1,m);
t = tangent(p0, p1, p2, p3, pp->curve.c[k][2], pp->curve.c[k1][2]);
if (t<-.5) {
return 1;
}
pt = bezier(t, p0, p1, p2, p3);
d = ddist(pp->curve.c[k][2], pp->curve.c[k1][2]);
if (d == 0.0) { /* this should never happen */
return 1;
}
d1 = dpara(pp->curve.c[k][2], pp->curve.c[k1][2], pt) / d;
d2 = dpara(pp->curve.c[k][2], pp->curve.c[k1][2], pp->curve.vertex[k1]) / d;
d2 *= 0.75 * pp->curve.alpha[k1];
if (d2 < 0) {
d1 = -d1;
d2 = -d2;
}
if (d1 < d2 - opttolerance) {
return 1;
}
if (d1 < d2) {
res->pen += sq(d1 - d2);
}
}
return 0;
}
static real ekrot(rvec x[], rvec v[], real mass[], int isize, int index[])
{
static real **TCM = NULL, **L;
double tm, m0, lxx, lxy, lxz, lyy, lyz, lzz, ekrot;
rvec a0, ocm;
dvec dx, b0;
dvec xcm, vcm, acm;
int i, j, m, n;
if (TCM == NULL)
{
snew(TCM, DIM);
for (i = 0; i < DIM; i++)
{
snew(TCM[i], DIM);
}
snew(L, DIM);
for (i = 0; i < DIM; i++)
{
snew(L[i], DIM);
}
}
clear_dvec(xcm);
clear_dvec(vcm);
clear_dvec(acm);
tm = 0.0;
for (i = 0; i < isize; i++)
{
j = index[i];
m0 = mass[j];
tm += m0;
cprod(x[j], v[j], a0);
for (m = 0; (m < DIM); m++)
{
xcm[m] += m0*x[j][m]; /* c.o.m. position */
vcm[m] += m0*v[j][m]; /* c.o.m. velocity */
acm[m] += m0*a0[m]; /* rotational velocity around c.o.m. */
}
}
dcprod(xcm, vcm, b0);
for (m = 0; (m < DIM); m++)
{
xcm[m] /= tm;
vcm[m] /= tm;
acm[m] -= b0[m]/tm;
}
lxx = lxy = lxz = lyy = lyz = lzz = 0.0;
for (i = 0; i < isize; i++)
{
j = index[i];
m0 = mass[j];
for (m = 0; m < DIM; m++)
{
dx[m] = x[j][m] - xcm[m];
}
lxx += dx[XX]*dx[XX]*m0;
lxy += dx[XX]*dx[YY]*m0;
lxz += dx[XX]*dx[ZZ]*m0;
lyy += dx[YY]*dx[YY]*m0;
lyz += dx[YY]*dx[ZZ]*m0;
lzz += dx[ZZ]*dx[ZZ]*m0;
}
L[XX][XX] = lyy + lzz;
L[YY][XX] = -lxy;
L[ZZ][XX] = -lxz;
L[XX][YY] = -lxy;
L[YY][YY] = lxx + lzz;
L[ZZ][YY] = -lyz;
L[XX][ZZ] = -lxz;
L[YY][ZZ] = -lyz;
L[ZZ][ZZ] = lxx + lyy;
m_inv_gen(L, DIM, TCM);
/* Compute omega (hoeksnelheid) */
clear_rvec(ocm);
ekrot = 0;
for (m = 0; m < DIM; m++)
{
for (n = 0; n < DIM; n++)
{
ocm[m] += TCM[m][n]*acm[n];
}
ekrot += 0.5*ocm[m]*acm[m];
}
return ekrot;
}
void calc_h_pos(int nht, rvec xa[], rvec xh[])
{
#define alfaH (acos(-1/3.0)) /* 109.47 degrees */
#define alfaHpl (2*M_PI/3) /* 120 degrees */
#define distH 0.1
#define alfaCOM (DEG2RAD*117)
#define alfaCO (DEG2RAD*121)
#define alfaCOA (DEG2RAD*115)
#define distO 0.123
#define distOA 0.125
#define distOM 0.136
rvec sa,sb,sij;
real s6,rij,ra,rb,xd;
int d;
s6=0.5*sqrt(3.e0);
/* common work for constructing one, two or three dihedral hydrogens */
switch (nht) {
case 2:
case 3:
case 4:
case 8:
case 9:
rij = 0.e0;
for(d=0; (d<DIM); d++) {
xd = xAJ[d];
sij[d] = xAI[d]-xd;
sb[d] = xd-xAK[d];
rij += sqr(sij[d]);
}
rij = sqrt(rij);
sa[XX] = sij[YY]*sb[ZZ]-sij[ZZ]*sb[YY];
sa[YY] = sij[ZZ]*sb[XX]-sij[XX]*sb[ZZ];
sa[ZZ] = sij[XX]*sb[YY]-sij[YY]*sb[XX];
ra = 0.e0;
for(d=0; (d<DIM); d++) {
sij[d] = sij[d]/rij;
ra += sqr(sa[d]);
}
ra = sqrt(ra);
for(d=0; (d<DIM); d++)
sa[d] = sa[d]/ra;
sb[XX] = sa[YY]*sij[ZZ]-sa[ZZ]*sij[YY];
sb[YY] = sa[ZZ]*sij[XX]-sa[XX]*sij[ZZ];
sb[ZZ] = sa[XX]*sij[YY]-sa[YY]*sij[XX];
break;
}/* end switch */
switch (nht) {
case 1: /* construct one planar hydrogen (peptide,rings) */
rij = 0.e0;
rb = 0.e0;
for(d=0; (d<DIM); d++) {
sij[d] = xAI[d]-xAJ[d];
sb[d] = xAI[d]-xAK[d];
rij += sqr(sij[d]);
rb += sqr(sb[d]);
}
rij = sqrt(rij);
rb = sqrt(rb);
ra = 0.e0;
for(d=0; (d<DIM); d++) {
sa[d] = sij[d]/rij+sb[d]/rb;
ra += sqr(sa[d]);
}
ra = sqrt(ra);
for(d=0; (d<DIM); d++)
xH1[d] = xAI[d]+distH*sa[d]/ra;
break;
case 2: /* one single hydrogen, e.g. hydroxyl */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]+distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
}
break;
case 3: /* two planar hydrogens, e.g. -NH2 */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]-distH*sin(alfaHpl)*sb[d]-distH*cos(alfaHpl)*sij[d];
xH2[d] = xAI[d]+distH*sin(alfaHpl)*sb[d]-distH*cos(alfaHpl)*sij[d];
}
break;
case 4: /* two or three tetrahedral hydrogens, e.g. -CH3 */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]+distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
xH2[d] = ( xAI[d]
- distH*sin(alfaH)*0.5*sb[d]
+ distH*sin(alfaH)*s6*sa[d]
- distH*cos(alfaH)*sij[d] );
if ( xH3[XX]!=NOTSET && xH3[YY]!=NOTSET && xH3[ZZ]!=NOTSET )
xH3[d] = ( xAI[d]
- distH*sin(alfaH)*0.5*sb[d]
- distH*sin(alfaH)*s6*sa[d]
- distH*cos(alfaH)*sij[d] );
}
break;
case 5: { /* one tetrahedral hydrogen, e.g. C3CH */
real center;
rvec dxc;
for(d=0; (d<DIM); d++) {
center=(xAJ[d]+xAK[d]+xAL[d])/3.0;
dxc[d]=xAI[d]-center;
}
center=norm(dxc);
for(d=0; (d<DIM); d++)
xH1[d]=xAI[d]+dxc[d]*distH/center;
break;
}
case 6: { /* two tetrahedral hydrogens, e.g. C-CH2-C */
rvec rBB,rCC1,rCC2,rNN;
real bb,nn;
for(d=0; (d<DIM); d++)
rBB[d]=xAI[d]-0.5*(xAJ[d]+xAK[d]);
bb=norm(rBB);
rvec_sub(xAI,xAJ,rCC1);
rvec_sub(xAI,xAK,rCC2);
cprod(rCC1,rCC2,rNN);
nn=norm(rNN);
for(d=0; (d<DIM); d++) {
xH1[d]=xAI[d]+distH*(cos(alfaH/2.0)*rBB[d]/bb+
sin(alfaH/2.0)*rNN[d]/nn);
xH2[d]=xAI[d]+distH*(cos(alfaH/2.0)*rBB[d]/bb-
sin(alfaH/2.0)*rNN[d]/nn);
}
break;
}
case 7: /* two water hydrogens */
gen_waterhydrogen(2, xa, xh);
break;
case 10: /* three water hydrogens */
gen_waterhydrogen(3, xa, xh);
break;
case 11: /* four water hydrogens */
gen_waterhydrogen(4, xa, xh);
break;
case 8: /* two carboxyl oxygens, -COO- */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]-distOM*sin(alfaCOM)*sb[d]-distOM*cos(alfaCOM)*sij[d];
xH2[d] = xAI[d]+distOM*sin(alfaCOM)*sb[d]-distOM*cos(alfaCOM)*sij[d];
}
break;
case 9: { /* carboxyl oxygens and hydrogen, -COOH */
rvec xa2[4]; /* i,j,k,l */
/* first add two oxygens */
for(d=0; (d<DIM); d++) {
xH1[d] = xAI[d]-distO *sin(alfaCO )*sb[d]-distO *cos(alfaCO )*sij[d];
xH2[d] = xAI[d]+distOA*sin(alfaCOA)*sb[d]-distOA*cos(alfaCOA)*sij[d];
}
/* now use rule 2 to add hydrogen to 2nd oxygen */
copy_rvec(xH2, xa2[0]); /* new i = n' */
copy_rvec(xAI, xa2[1]); /* new j = i */
copy_rvec(xAJ, xa2[2]); /* new k = j */
copy_rvec(xAK, xa2[3]); /* new l = k, not used */
calc_h_pos(2, xa2, (xh+2));
break;
}
default:
gmx_fatal(FARGS,"Invalid argument (%d) for nht in routine genh\n",nht);
} /* end switch */
}
void calc_fit_R(int ndim,int natoms,real *w_rls,rvec *xp,rvec *x,matrix R)
{
int c,r,n,j,m,i,irot,s;
double **omega,**om;
double d[2*DIM],xnr,xpc;
matrix vh,vk,u;
real mn;
int index;
real max_d;
if (ndim != 3 && ndim != 2)
gmx_fatal(FARGS,"calc_fit_R called with ndim=%d instead of 3 or 2",ndim);
snew(omega,2*ndim);
snew(om,2*ndim);
for(i=0; i<2*ndim; i++) {
snew(omega[i],2*ndim);
snew(om[i],2*ndim);
}
for(i=0; i<2*ndim; i++) {
d[i]=0;
for(j=0; j<2*ndim; j++) {
omega[i][j]=0;
om[i][j]=0;
}
}
/*calculate the matrix U*/
clear_mat(u);
for(n=0;(n<natoms);n++)
if ((mn = w_rls[n]) != 0.0)
for(c=0; (c<ndim); c++) {
xpc=xp[n][c];
for(r=0; (r<ndim); r++) {
xnr=x[n][r];
u[c][r]+=mn*xnr*xpc;
}
}
/*construct omega*/
/*omega is symmetric -> omega==omega' */
for(r=0; r<2*ndim; r++)
for(c=0; c<=r; c++)
if (r>=ndim && c<ndim) {
omega[r][c]=u[r-ndim][c];
omega[c][r]=u[r-ndim][c];
} else {
omega[r][c]=0;
omega[c][r]=0;
}
/*determine h and k*/
jacobi(omega,2*ndim,d,om,&irot);
/*real **omega = input matrix a[0..n-1][0..n-1] must be symmetric
*int natoms = number of rows and columns
*real NULL = d[0]..d[n-1] are the eigenvalues of a[][]
*real **v = v[0..n-1][0..n-1] contains the vectors in columns
*int *irot = number of jacobi rotations
*/
if (debug && irot==0) fprintf(debug,"IROT=0\n");
index=0; /* For the compiler only */
/* Copy only the first ndim-1 eigenvectors */
for(j=0; j<ndim-1; j++) {
max_d=-1000;
for(i=0; i<2*ndim; i++)
if (d[i]>max_d) {
max_d=d[i];
index=i;
}
d[index]=-10000;
for(i=0; i<ndim; i++) {
vh[j][i]=M_SQRT2*om[i][index];
vk[j][i]=M_SQRT2*om[i+ndim][index];
}
}
if (ndim == 3) {
/* Calculate the last eigenvector as the outer-product of the first two.
* This insures that the conformation is not mirrored and
* prevents problems with completely flat reference structures.
*/
cprod(vh[0],vh[1],vh[2]);
cprod(vk[0],vk[1],vk[2]);
} else if (ndim == 2) {
/* Calculate the last eigenvector from the first one */
vh[1][XX] = -vh[0][YY];
vh[1][YY] = vh[0][XX];
vk[1][XX] = -vk[0][YY];
vk[1][YY] = vk[0][XX];
}
/* determine R */
clear_mat(R);
for(r=0; r<ndim; r++)
for(c=0; c<ndim; c++)
for(s=0; s<ndim; s++)
R[r][c] += vk[s][r]*vh[s][c];
for(r=ndim; r<DIM; r++)
R[r][r] = 1;
for(i=0; i<2*ndim; i++) {
sfree(omega[i]);
sfree(om[i]);
}
sfree(omega);
sfree(om);
}