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42 #include "gromacs/commandline/pargs.h"
43 #include "gromacs/commandline/viewit.h"
44 #include "gromacs/fileio/tpxio.h"
45 #include "gromacs/fileio/trxio.h"
46 #include "gromacs/fileio/xvgr.h"
47 #include "gromacs/gmxana/gmx_ana.h"
48 #include "gromacs/gmxana/gstat.h"
49 #include "gromacs/math/functions.h"
50 #include "gromacs/math/units.h"
51 #include "gromacs/math/vec.h"
52 #include "gromacs/mdtypes/inputrec.h"
53 #include "gromacs/pbcutil/pbc.h"
54 #include "gromacs/pbcutil/rmpbc.h"
55 #include "gromacs/topology/index.h"
56 #include "gromacs/topology/topology.h"
57 #include "gromacs/utility/arraysize.h"
58 #include "gromacs/utility/cstringutil.h"
59 #include "gromacs/utility/fatalerror.h"
60 #include "gromacs/utility/smalloc.h"
62 static void calc_com_pbc(int nrefat, const t_topology* top, rvec x[], t_pbc* pbc, const int index[], rvec xref, int ePBC)
64 const real tol = 1e-4;
70 /* First simple calculation */
73 for (m = 0; (m < nrefat); m++)
76 mass = top->atoms.atom[ai].m;
77 for (j = 0; (j < DIM); j++)
79 xref[j] += mass * x[ai][j];
83 svmul(1 / mtot, xref, xref);
84 /* Now check if any atom is more than half the box from the COM */
91 for (m = 0; (m < nrefat); m++)
94 mass = top->atoms.atom[ai].m / mtot;
95 pbc_dx(pbc, x[ai], xref, dx);
96 rvec_add(xref, dx, xtest);
97 for (j = 0; (j < DIM); j++)
99 if (std::abs(xtest[j] - x[ai][j]) > tol)
101 /* Here we have used the wrong image for contributing to the COM */
102 xref[j] += mass * (xtest[j] - x[ai][j]);
110 printf("COM: %8.3f %8.3f %8.3f iter = %d\n", xref[XX], xref[YY], xref[ZZ], iter);
117 static void spol_atom2molindex(int* n, int* index, const t_block* mols)
126 while (m < mols->nr && index[i] != mols->index[m])
132 gmx_fatal(FARGS, "index[%d]=%d does not correspond to the first atom of a molecule",
133 i + 1, index[i] + 1);
135 for (j = mols->index[m]; j < mols->index[m + 1]; j++)
137 if (i >= *n || index[i] != j)
139 gmx_fatal(FARGS, "The index group is not a set of whole molecules");
143 /* Modify the index in place */
146 printf("There are %d molecules in the selection\n", nmol);
151 int gmx_spol(int argc, char* argv[])
156 int nrefat, natoms, nf, ntot;
158 rvec * x, xref, trial, dx = { 0 }, dip, dir;
162 int * isize, nrefgrp;
163 int ** index, *molindex;
165 real rmin2, rmax2, rcut, rcut2, rdx2 = 0, rtry2, qav, q, dip2, invbw;
166 int nbin, i, m, mol, a0, a1, a, d;
167 double sdip, sdip2, sinp, sdinp, nmol;
170 gmx_rmpbc_t gpbc = nullptr;
173 const char* desc[] = {
174 "[THISMODULE] analyzes dipoles around a solute; it is especially useful",
175 "for polarizable water. A group of reference atoms, or a center",
176 "of mass reference (option [TT]-com[tt]) and a group of solvent",
177 "atoms is required. The program splits the group of solvent atoms",
178 "into molecules. For each solvent molecule the distance to the",
179 "closest atom in reference group or to the COM is determined.",
180 "A cumulative distribution of these distances is plotted.",
181 "For each distance between [TT]-rmin[tt] and [TT]-rmax[tt]",
182 "the inner product of the distance vector",
183 "and the dipole of the solvent molecule is determined.",
184 "For solvent molecules with net charge (ions), the net charge of the ion",
185 "is subtracted evenly from all atoms in the selection of each ion.",
186 "The average of these dipole components is printed.",
187 "The same is done for the polarization, where the average dipole is",
188 "subtracted from the instantaneous dipole. The magnitude of the average",
189 "dipole is set with the option [TT]-dip[tt], the direction is defined",
190 "by the vector from the first atom in the selected solvent group",
191 "to the midpoint between the second and the third atom."
194 gmx_output_env_t* oenv;
195 static gmx_bool bCom = FALSE;
196 static int srefat = 1;
197 static real rmin = 0.0, rmax = 0.32, refdip = 0, bw = 0.01;
199 { "-com", FALSE, etBOOL, { &bCom }, "Use the center of mass as the reference position" },
200 { "-refat", FALSE, etINT, { &srefat }, "The reference atom of the solvent molecule" },
201 { "-rmin", FALSE, etREAL, { &rmin }, "Maximum distance (nm)" },
202 { "-rmax", FALSE, etREAL, { &rmax }, "Maximum distance (nm)" },
203 { "-dip", FALSE, etREAL, { &refdip }, "The average dipole (D)" },
204 { "-bw", FALSE, etREAL, { &bw }, "The bin width" }
207 t_filenm fnm[] = { { efTRX, nullptr, nullptr, ffREAD },
208 { efTPR, nullptr, nullptr, ffREAD },
209 { efNDX, nullptr, nullptr, ffOPTRD },
210 { efXVG, nullptr, "scdist", ffWRITE } };
211 #define NFILE asize(fnm)
213 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW, NFILE, fnm, asize(pa), pa,
214 asize(desc), desc, 0, nullptr, &oenv))
220 // TODO: Only ePBC is used, not the full inputrec.
221 t_inputrec irInstance;
222 t_inputrec* ir = &irInstance;
223 read_tpx_top(ftp2fn(efTPR, NFILE, fnm), ir, box, &natoms, nullptr, nullptr, top);
225 /* get index groups */
226 printf("Select a group of reference particles and a solvent group:\n");
230 get_index(&top->atoms, ftp2fn_null(efNDX, NFILE, fnm), 2, isize, index, grpname);
243 spol_atom2molindex(&(isize[1]), index[1], &(top->mols));
246 /* initialize reading trajectory: */
247 natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
249 rcut = 0.99 * std::sqrt(max_cutoff2(ir->ePBC, box));
254 rcut2 = gmx::square(rcut);
256 nbin = static_cast<int>(rcut * invbw) + 2;
259 rmin2 = gmx::square(rmin);
260 rmax2 = gmx::square(rmax);
269 molindex = top->mols.index;
270 atom = top->atoms.atom;
272 gpbc = gmx_rmpbc_init(&top->idef, ir->ePBC, natoms);
274 /* start analysis of trajectory */
277 /* make molecules whole again */
278 gmx_rmpbc(gpbc, natoms, box, x);
280 set_pbc(&pbc, ir->ePBC, box);
283 calc_com_pbc(nrefat, top, x, &pbc, index[0], xref, ir->ePBC);
286 for (m = 0; m < isize[1]; m++)
290 a1 = molindex[mol + 1];
291 for (i = 0; i < nrefgrp; i++)
293 pbc_dx(&pbc, x[a0 + srefat], bCom ? xref : x[index[0][i]], trial);
294 rtry2 = norm2(trial);
295 if (i == 0 || rtry2 < rdx2)
297 copy_rvec(trial, dx);
303 hist[static_cast<int>(std::sqrt(rdx2) * invbw) + 1]++;
305 if (rdx2 >= rmin2 && rdx2 < rmax2)
310 for (a = a0; a < a1; a++)
315 for (a = a0; a < a1; a++)
318 for (d = 0; d < DIM; d++)
320 dip[d] += q * x[a][d];
323 for (d = 0; d < DIM; d++)
327 for (a = a0 + 1; a < a0 + 3; a++)
329 for (d = 0; d < DIM; d++)
331 dir[d] += 0.5 * x[a][d];
336 svmul(ENM2DEBYE, dip, dip);
338 sdip += std::sqrt(dip2);
340 for (d = 0; d < DIM; d++)
342 sinp += dx[d] * dip[d];
343 sdinp += dx[d] * (dip[d] - refdip * dir[d]);
351 } while (read_next_x(oenv, status, &t, x, box));
353 gmx_rmpbc_done(gpbc);
359 fprintf(stderr, "Average number of molecules within %g nm is %.1f\n", rmax,
360 static_cast<real>(ntot) / nf);
367 fprintf(stderr, "Average dipole: %f (D), std.dev. %f\n", sdip,
368 std::sqrt(sdip2 - gmx::square(sdip)));
369 fprintf(stderr, "Average radial component of the dipole: %f (D)\n", sinp);
370 fprintf(stderr, "Average radial component of the polarization: %f (D)\n", sdinp);
373 fp = xvgropen(opt2fn("-o", NFILE, fnm), "Cumulative solvent distribution", "r (nm)", "molecules", oenv);
375 for (i = 0; i <= nbin; i++)
378 fprintf(fp, "%g %g\n", i * bw, nmol / nf);
382 do_view(oenv, opt2fn("-o", NFILE, fnm), nullptr);