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45 #include "gromacs/commandline/pargs.h"
47 #include "gromacs/utility/smalloc.h"
49 #include "gromacs/utility/fatalerror.h"
50 #include "gromacs/math/vec.h"
51 #include "gromacs/utility/futil.h"
55 #include "gromacs/fileio/xvgr.h"
56 #include "gromacs/math/units.h"
57 #include "gromacs/fileio/pdbio.h"
58 #include "gromacs/fileio/matio.h"
62 static int index2(int *ibox
, int x
, int y
)
67 static int index3(int *ibox
, int x
, int y
, int z
)
69 return (ibox
[2]*(ibox
[1]*x
+y
)+z
);
72 static gmx_int64_t
indexn(int ndim
, const int *ibox
, const int *nxyz
)
77 /* Compute index in 1-D array */
79 for (k
= 0; (k
< ndim
); k
++)
82 for (kk
= k
+1; (kk
< ndim
); kk
++)
92 int Nx
; /* x grid points in unit cell */
93 int Ny
; /* y grid points in unit cell */
94 int Nz
; /* z grid points in unit cell */
95 int dmin
[3]; /* starting point x,y,z*/
96 int dmax
[3]; /* ending point x,y,z */
97 real cell
[6]; /* usual cell parameters */
101 static void lo_write_xplor(XplorMap
* map
, const char * file
)
106 fp
= gmx_ffopen(file
, "w");
107 /* The REMARKS part is the worst part of the XPLOR format
108 * and may cause problems with some programs
110 fprintf(fp
, "\n 2 !NTITLE\n");
111 fprintf(fp
, " REMARKS Energy Landscape from GROMACS\n");
112 fprintf(fp
, " REMARKS DATE: 2004-12-21 \n");
113 fprintf(fp
, " %7d %7d %7d %7d %7d %7d %7d %7d %7d\n",
114 map
->Nx
, map
->dmin
[0], map
->dmax
[0],
115 map
->Ny
, map
->dmin
[1], map
->dmax
[1],
116 map
->Nz
, map
->dmin
[2], map
->dmax
[2]);
117 fprintf(fp
, "%12.5E%12.5E%12.5E%12.5E%12.5E%12.5E\n",
118 map
->cell
[0], map
->cell
[1], map
->cell
[2],
119 map
->cell
[3], map
->cell
[4], map
->cell
[5]);
120 fprintf(fp
, "ZYX\n");
123 for (n
= 0; n
< map
->Nz
; n
++, z
++)
125 fprintf(fp
, "%8d\n", z
);
126 for (i
= 0; i
< map
->Nx
*map
->Ny
; i
+= 6)
128 for (j
= 0; j
< 6; j
++)
130 if (i
+j
< map
->Nx
*map
->Ny
)
132 fprintf(fp
, "%12.5E", map
->ed
[n
*map
->Nx
*map
->Ny
+i
+j
]);
138 fprintf(fp
, " -9999\n");
142 static void write_xplor(const char *file
, real
*data
, int *ibox
, real dmin
[], real dmax
[])
151 snew(xm
->ed
, xm
->Nx
*xm
->Ny
*xm
->Nz
);
153 for (k
= 0; (k
< xm
->Nz
); k
++)
155 for (j
= 0; (j
< xm
->Ny
); j
++)
157 for (i
= 0; (i
< xm
->Nx
); i
++)
159 xm
->ed
[n
++] = data
[index3(ibox
, i
, j
, k
)];
163 xm
->cell
[0] = dmax
[XX
]-dmin
[XX
];
164 xm
->cell
[1] = dmax
[YY
]-dmin
[YY
];
165 xm
->cell
[2] = dmax
[ZZ
]-dmin
[ZZ
];
166 xm
->cell
[3] = xm
->cell
[4] = xm
->cell
[5] = 90;
168 clear_ivec(xm
->dmin
);
169 xm
->dmax
[XX
] = ibox
[XX
]-1;
170 xm
->dmax
[YY
] = ibox
[YY
]-1;
171 xm
->dmax
[ZZ
] = ibox
[ZZ
]-1;
173 lo_write_xplor(xm
, file
);
179 static void normalize_p_e(int len
, double *P
, int *nbin
, real
*E
, real pmin
)
184 for (i
= 0; (i
< len
); i
++)
192 printf("Ptot = %g\n", Ptot
);
193 for (i
= 0; (i
< len
); i
++)
196 /* Have to check for pmin after normalizing to prevent "stretching"
211 static int comp_minima(const void *a
, const void *b
)
213 t_minimum
*ma
= (t_minimum
*) a
;
214 t_minimum
*mb
= (t_minimum
*) b
;
216 if (ma
->ener
< mb
->ener
)
220 else if (ma
->ener
> mb
->ener
)
231 void print_minimum(FILE *fp
, int num
, const t_minimum
*min
)
234 "Minimum %d at index " "%"GMX_PRId64
" energy %10.3f\n",
235 num
, min
->index
, min
->ener
);
239 void add_minimum(FILE *fp
, int num
, const t_minimum
*min
, t_minimum
*mm
)
241 print_minimum(fp
, num
, min
);
242 mm
[num
].index
= min
->index
;
243 mm
[num
].ener
= min
->ener
;
247 gmx_bool
is_local_minimum_from_below(const t_minimum
*this_min
,
253 return ((dimension_index
== dimension_min
) ||
254 ((dimension_index
> dimension_min
) &&
255 (this_min
->ener
< W
[neighbour_index
])));
256 /* Note over/underflow within W cannot occur. */
260 gmx_bool
is_local_minimum_from_above(const t_minimum
*this_min
,
266 return ((dimension_index
== dimension_max
) ||
267 ((dimension_index
< dimension_max
) &&
268 (this_min
->ener
< W
[neighbour_index
])));
269 /* Note over/underflow within W cannot occur. */
272 static void pick_minima(const char *logfile
, int *ibox
, int ndim
, int len
, real W
[])
276 t_minimum
*mm
, this_min
;
278 int loopmax
, loopcounter
;
282 fp
= gmx_ffopen(logfile
, "w");
283 /* Loop over each element in the array of dimenion ndim seeking
284 * minima with respect to every dimension. Specialized loops for
285 * speed with ndim == 2 and ndim == 3. */
289 /* This is probably impossible to reach anyway. */
292 for (i
= 0; (i
< ibox
[0]); i
++)
294 for (j
= 0; (j
< ibox
[1]); j
++)
296 /* Get the index of this point in the flat array */
297 this_min
.index
= index2(ibox
, i
, j
);
298 this_min
.ener
= W
[this_min
.index
];
299 if (is_local_minimum_from_below(&this_min
, i
, 0, index2(ibox
, i
-1, j
), W
) &&
300 is_local_minimum_from_above(&this_min
, i
, ibox
[0]-1, index2(ibox
, i
+1, j
), W
) &&
301 is_local_minimum_from_below(&this_min
, j
, 0, index2(ibox
, i
, j
-1), W
) &&
302 is_local_minimum_from_above(&this_min
, j
, ibox
[1]-1, index2(ibox
, i
, j
+1), W
))
304 add_minimum(fp
, nmin
, &this_min
, mm
);
311 for (i
= 0; (i
< ibox
[0]); i
++)
313 for (j
= 0; (j
< ibox
[1]); j
++)
315 for (k
= 0; (k
< ibox
[2]); k
++)
317 /* Get the index of this point in the flat array */
318 this_min
.index
= index3(ibox
, i
, j
, k
);
319 this_min
.ener
= W
[this_min
.index
];
320 if (is_local_minimum_from_below(&this_min
, i
, 0, index3(ibox
, i
-1, j
, k
), W
) &&
321 is_local_minimum_from_above(&this_min
, i
, ibox
[0]-1, index3(ibox
, i
+1, j
, k
), W
) &&
322 is_local_minimum_from_below(&this_min
, j
, 0, index3(ibox
, i
, j
-1, k
), W
) &&
323 is_local_minimum_from_above(&this_min
, j
, ibox
[1]-1, index3(ibox
, i
, j
+1, k
), W
) &&
324 is_local_minimum_from_below(&this_min
, k
, 0, index3(ibox
, i
, j
, k
-1), W
) &&
325 is_local_minimum_from_above(&this_min
, k
, ibox
[2]-1, index3(ibox
, i
, j
, k
+1), W
))
327 add_minimum(fp
, nmin
, &this_min
, mm
);
335 /* Note this treats ndim == 1 and ndim > 3 */
337 /* Set up an ndim-dimensional vector to loop over the points
338 * on the grid. (0,0,0, ... 0) is an acceptable place to
340 snew(this_point
, ndim
);
342 /* Determine the number of points of the ndim-dimensional
345 for (i
= 1; i
< ndim
; i
++)
351 while (loopmax
> loopcounter
)
353 gmx_bool bMin
= TRUE
;
355 /* Get the index of this_point in the flat array */
356 this_min
.index
= indexn(ndim
, ibox
, this_point
);
357 this_min
.ener
= W
[this_min
.index
];
359 /* Is this_point a minimum from above and below in each
361 for (i
= 0; bMin
&& (i
< ndim
); i
++)
363 /* Save the index of this_point within the curent
364 * dimension so we can change that index in the
365 * this_point array for use with indexn(). */
366 int index
= this_point
[i
];
369 is_local_minimum_from_below(&this_min
, index
, 0, indexn(ndim
, ibox
, this_point
), W
);
372 is_local_minimum_from_above(&this_min
, index
, ibox
[i
]-1, indexn(ndim
, ibox
, this_point
), W
);
377 add_minimum(fp
, nmin
, &this_min
, mm
);
381 /* update global loop counter */
384 /* Avoid underflow of this_point[i] */
385 if (loopmax
> loopcounter
)
387 /* update this_point non-recursively */
390 while (ibox
[i
] == this_point
[i
])
394 /* this_point[i] cannot underflow because
395 * loopmax > loopcounter. */
404 qsort(mm
, nmin
, sizeof(mm
[0]), comp_minima
);
405 fprintf(fp
, "Minima sorted after energy\n");
406 for (i
= 0; (i
< nmin
); i
++)
408 print_minimum(fp
, i
, &mm
[i
]);
414 static void do_sham(const char *fn
, const char *ndx
,
415 const char *xpmP
, const char *xpm
, const char *xpm2
,
416 const char *xpm3
, const char *xpm4
, const char *pdb
,
418 int n
, int neig
, real
**eig
,
419 gmx_bool bGE
, int nenerT
, real
**enerT
,
420 int nmap
, real
*mapindex
, real
**map
,
422 real pmax
, real gmax
,
423 real
*emin
, real
*emax
, int nlevels
, real pmin
,
424 const char *mname
, int *idim
, int *ibox
,
425 gmx_bool bXmin
, real
*xmin
, gmx_bool bXmax
, real
*xmax
)
428 real
*min_eig
, *max_eig
;
429 real
*axis_x
, *axis_y
, *axis_z
, *axis
= NULL
;
431 real
**PP
, *W
, *E
, **WW
, **EE
, *S
, **SS
, *M
, **MM
, *bE
;
434 double *bfac
, efac
, bref
, Pmax
, Wmin
, Wmax
, Winf
, Emin
, Emax
, Einf
, Smin
, Smax
, Sinf
, Mmin
, Mmax
, Minf
;
436 int i
, j
, k
, imin
, len
, index
, d
, *nbin
, *bindex
, bi
;
441 t_rgb rlo
= { 0, 0, 0 };
442 t_rgb rhi
= { 1, 1, 1 };
444 /* Determine extremes for the eigenvectors */
451 for (i
= 0; (i
< neig
); i
++)
453 /* Check for input constraints */
454 min_eig
[i
] = max_eig
[i
] = eig
[i
][0];
455 for (j
= 0; (j
< n
); j
++)
457 min_eig
[i
] = min(min_eig
[i
], eig
[i
][j
]);
458 max_eig
[i
] = max(max_eig
[i
], eig
[i
][j
]);
459 delta
[i
] = (max_eig
[i
]-min_eig
[i
])/(2.0*ibox
[i
]);
461 /* Add some extra space, half a bin on each side, unless the
462 * user has set the limits.
466 if (max_eig
[i
] > xmax
[i
])
468 gmx_warning("Your xmax[%d] value %f is smaller than the largest data point %f", i
, xmax
[i
], max_eig
[i
]);
470 max_eig
[i
] = xmax
[i
];
474 max_eig
[i
] += delta
[i
];
479 if (min_eig
[i
] < xmin
[i
])
481 gmx_warning("Your xmin[%d] value %f is larger than the smallest data point %f", i
, xmin
[i
], min_eig
[i
]);
483 min_eig
[i
] = xmin
[i
];
487 min_eig
[i
] -= delta
[i
];
489 bfac
[i
] = ibox
[i
]/(max_eig
[i
]-min_eig
[i
]);
492 bref
= 1/(BOLTZ
*Tref
);
494 if (bGE
|| nenerT
== 2)
497 for (j
= 0; (j
< n
); j
++)
501 bE
[j
] = bref
*enerT
[0][j
];
505 bE
[j
] = (bref
- 1/(BOLTZ
*enerT
[1][j
]))*enerT
[0][j
];
507 Emin
= min(Emin
, bE
[j
]);
515 for (i
= 0; (i
< neig
); i
++)
519 printf("There are %d bins in the %d-dimensional histogram. Beta-Emin = %g\n",
530 /* Loop over projections */
531 for (j
= 0; (j
< n
); j
++)
533 /* Loop over dimensions */
535 for (i
= 0; (i
< neig
); i
++)
537 nxyz
[i
] = bfac
[i
]*(eig
[i
][j
]-min_eig
[i
]);
538 if (nxyz
[i
] < 0 || nxyz
[i
] >= ibox
[i
])
545 index
= indexn(neig
, ibox
, nxyz
);
546 range_check(index
, 0, len
);
547 /* Compute the exponential factor */
550 efac
= exp(-bE
[j
]+Emin
);
556 /* Apply the bin volume correction for a multi-dimensional distance */
557 for (i
= 0; i
< neig
; i
++)
563 else if (idim
[i
] == 3)
565 efac
/= sqr(eig
[i
][j
]);
567 else if (idim
[i
] == -1)
569 efac
/= sin(DEG2RAD
*eig
[i
][j
]);
572 /* Update the probability */
574 /* Update the energy */
577 E
[index
] += enerT
[0][j
];
579 /* Statistics: which "structure" in which bin */
584 /* Normalize probability */
585 normalize_p_e(len
, P
, nbin
, E
, pmin
);
587 /* Compute boundaries for the Free energy */
591 /* Recompute Emin: it may have changed due to averaging */
594 for (i
= 0; (i
< len
); i
++)
598 Pmax
= max(P
[i
], Pmax
);
599 W
[i
] = -BOLTZ
*Tref
*log(P
[i
]);
605 Emin
= min(E
[i
], Emin
);
606 Emax
= max(E
[i
], Emax
);
607 Wmax
= max(W
[i
], Wmax
);
627 /* Write out the free energy as a function of bin index */
628 fp
= gmx_ffopen(fn
, "w");
629 for (i
= 0; (i
< len
); i
++)
634 S
[i
] = E
[i
]-W
[i
]-Smin
;
635 fprintf(fp
, "%5d %10.5e %10.5e %10.5e\n", i
, W
[i
], E
[i
], S
[i
]);
645 /* Organize the structures in the bins */
647 snew(b
->index
, len
+1);
650 for (i
= 0; (i
< len
); i
++)
652 b
->index
[i
+1] = b
->index
[i
]+nbin
[i
];
655 for (i
= 0; (i
< n
); i
++)
658 b
->a
[b
->index
[bi
]+nbin
[bi
]] = i
;
661 /* Consistency check */
662 /* This no longer applies when we allow the plot to be smaller
663 than the sampled space.
664 for(i=0; (i<len); i++) {
665 if (nbin[i] != (b->index[i+1] - b->index[i]))
666 gmx_fatal(FARGS,"nbin[%d] = %d, should be %d",i,nbin[i],
667 b->index[i+1] - b->index[i]);
670 /* Write the index file */
671 fp
= gmx_ffopen(ndx
, "w");
672 for (i
= 0; (i
< len
); i
++)
676 fprintf(fp
, "[ %d ]\n", i
);
677 for (j
= b
->index
[i
]; (j
< b
->index
[i
+1]); j
++)
679 fprintf(fp
, "%d\n", b
->a
[j
]+1);
684 snew(axis_x
, ibox
[0]+1);
685 snew(axis_y
, ibox
[1]+1);
686 snew(axis_z
, ibox
[2]+1);
687 maxbox
= max(ibox
[0], max(ibox
[1], ibox
[2]));
688 snew(PP
, maxbox
*maxbox
);
689 snew(WW
, maxbox
*maxbox
);
690 snew(EE
, maxbox
*maxbox
);
691 snew(SS
, maxbox
*maxbox
);
692 for (i
= 0; (i
< min(neig
, 3)); i
++)
696 case 0: axis
= axis_x
; break;
697 case 1: axis
= axis_y
; break;
698 case 2: axis
= axis_z
; break;
701 for (j
= 0; j
<= ibox
[i
]; j
++)
703 axis
[j
] = min_eig
[i
] + j
/bfac
[i
];
709 snew(MM
, maxbox
*maxbox
);
710 for (i
= 0; (i
< ibox
[0]); i
++)
712 MM
[i
] = &(M
[i
*ibox
[1]]);
716 for (i
= 0; (i
< nmap
); i
++)
718 Mmin
= min(Mmin
, map
[0][i
]);
719 Mmax
= max(Mmax
, map
[0][i
]);
722 for (i
= 0; (i
< len
); i
++)
726 for (i
= 0; (i
< nmap
); i
++)
728 index
= gmx_nint(mapindex
[i
]);
731 gmx_fatal(FARGS
, "Number of bins in file from -mdata option does not correspond to current analysis");
736 M
[index
] = map
[0][i
];
745 pick_minima(logf
, ibox
, neig
, len
, W
);
750 flags
= MAT_SPATIAL_X
| MAT_SPATIAL_Y
;
753 /* Dump to XPM file */
755 for (i
= 0; (i
< ibox
[0]); i
++)
757 snew(PP
[i
], ibox
[1]);
758 for (j
= 0; j
< ibox
[1]; j
++)
760 PP
[i
][j
] = P
[i
*ibox
[1]+j
];
762 WW
[i
] = &(W
[i
*ibox
[1]]);
763 EE
[i
] = &(E
[i
*ibox
[1]]);
764 SS
[i
] = &(S
[i
*ibox
[1]]);
766 fp
= gmx_ffopen(xpmP
, "w");
767 write_xpm(fp
, flags
, "Probability Distribution", "", "PC1", "PC2",
768 ibox
[0], ibox
[1], axis_x
, axis_y
, PP
, 0, Pmax
, rlo
, rhi
, &nlevels
);
770 fp
= gmx_ffopen(xpm
, "w");
771 write_xpm(fp
, flags
, "Gibbs Energy Landscape", "G (kJ/mol)", "PC1", "PC2",
772 ibox
[0], ibox
[1], axis_x
, axis_y
, WW
, 0, gmax
, rlo
, rhi
, &nlevels
);
774 fp
= gmx_ffopen(xpm2
, "w");
775 write_xpm(fp
, flags
, "Enthalpy Landscape", "H (kJ/mol)", "PC1", "PC2",
776 ibox
[0], ibox
[1], axis_x
, axis_y
, EE
,
777 emin
? *emin
: Emin
, emax
? *emax
: Einf
, rlo
, rhi
, &nlevels
);
779 fp
= gmx_ffopen(xpm3
, "w");
780 write_xpm(fp
, flags
, "Entropy Landscape", "TDS (kJ/mol)", "PC1", "PC2",
781 ibox
[0], ibox
[1], axis_x
, axis_y
, SS
, 0, Sinf
, rlo
, rhi
, &nlevels
);
785 fp
= gmx_ffopen(xpm4
, "w");
786 write_xpm(fp
, flags
, "Custom Landscape", mname
, "PC1", "PC2",
787 ibox
[0], ibox
[1], axis_x
, axis_y
, MM
, 0, Minf
, rlo
, rhi
, &nlevels
);
793 /* Dump to PDB file */
794 fp
= gmx_ffopen(pdb
, "w");
795 for (i
= 0; (i
< ibox
[0]); i
++)
797 xxx
[XX
] = 3*(i
+0.5-ibox
[0]/2);
798 for (j
= 0; (j
< ibox
[1]); j
++)
800 xxx
[YY
] = 3*(j
+0.5-ibox
[1]/2);
801 for (k
= 0; (k
< ibox
[2]); k
++)
803 xxx
[ZZ
] = 3*(k
+0.5-ibox
[2]/2);
804 index
= index3(ibox
, i
, j
, k
);
807 fprintf(fp
, "%-6s%5u %-4.4s%3.3s %4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
808 "ATOM", (index
+1) %10000, "H", "H", (index
+1)%10000,
809 xxx
[XX
], xxx
[YY
], xxx
[ZZ
], 1.0, W
[index
]);
815 write_xplor("out.xplor", W
, ibox
, min_eig
, max_eig
);
818 write_xplor("user.xplor", M
, ibox
, min_eig
, max_eig
);
820 nxyz
[XX
] = imin
/(ibox
[1]*ibox
[2]);
821 nxyz
[YY
] = (imin
-nxyz
[XX
]*ibox
[1]*ibox
[2])/ibox
[2];
822 nxyz
[ZZ
] = imin
% ibox
[2];
823 for (i
= 0; (i
< ibox
[0]); i
++)
826 for (j
= 0; (j
< ibox
[1]); j
++)
828 WW
[i
][j
] = W
[index3(ibox
, i
, j
, nxyz
[ZZ
])];
831 snew(buf
, strlen(xpm
)+4);
832 sprintf(buf
, "%s", xpm
);
833 sprintf(&buf
[strlen(xpm
)-4], "12.xpm");
834 fp
= gmx_ffopen(buf
, "w");
835 write_xpm(fp
, flags
, "Gibbs Energy Landscape", "W (kJ/mol)", "PC1", "PC2",
836 ibox
[0], ibox
[1], axis_x
, axis_y
, WW
, 0, gmax
, rlo
, rhi
, &nlevels
);
838 for (i
= 0; (i
< ibox
[0]); i
++)
840 for (j
= 0; (j
< ibox
[2]); j
++)
842 WW
[i
][j
] = W
[index3(ibox
, i
, nxyz
[YY
], j
)];
845 sprintf(&buf
[strlen(xpm
)-4], "13.xpm");
846 fp
= gmx_ffopen(buf
, "w");
847 write_xpm(fp
, flags
, "SHAM Energy Landscape", "kJ/mol", "PC1", "PC3",
848 ibox
[0], ibox
[2], axis_x
, axis_z
, WW
, 0, gmax
, rlo
, rhi
, &nlevels
);
850 for (i
= 0; (i
< ibox
[1]); i
++)
852 for (j
= 0; (j
< ibox
[2]); j
++)
854 WW
[i
][j
] = W
[index3(ibox
, nxyz
[XX
], i
, j
)];
857 sprintf(&buf
[strlen(xpm
)-4], "23.xpm");
858 fp
= gmx_ffopen(buf
, "w");
859 write_xpm(fp
, flags
, "SHAM Energy Landscape", "kJ/mol", "PC2", "PC3",
860 ibox
[1], ibox
[2], axis_y
, axis_z
, WW
, 0, gmax
, rlo
, rhi
, &nlevels
);
871 static void ehisto(const char *fh
, int n
, real
**enerT
, const output_env_t oenv
)
874 int i
, j
, k
, nbin
, blength
;
876 real
*T
, bmin
, bmax
, bwidth
;
884 for (j
= 1; (j
< n
); j
++)
886 for (k
= 0; (k
< nbin
); k
++)
888 if (T
[k
] == enerT
[1][j
])
897 T
[nbin
] = enerT
[1][j
];
900 bmin
= min(enerT
[0][j
], bmin
);
901 bmax
= max(enerT
[0][j
], bmax
);
904 blength
= (bmax
- bmin
)/bwidth
+ 2;
906 for (i
= 0; (i
< nbin
); i
++)
908 snew(histo
[i
], blength
);
910 for (j
= 0; (j
< n
); j
++)
912 k
= (enerT
[0][j
]-bmin
)/bwidth
;
913 histo
[bindex
[j
]][k
]++;
915 fp
= xvgropen(fh
, "Energy distribution", "E (kJ/mol)", "", oenv
);
916 for (j
= 0; (j
< blength
); j
++)
918 fprintf(fp
, "%8.3f", bmin
+j
*bwidth
);
919 for (k
= 0; (k
< nbin
); k
++)
921 fprintf(fp
, " %6d", histo
[k
][j
]);
928 int gmx_sham(int argc
, char *argv
[])
930 const char *desc
[] = {
931 "[THISMODULE] makes multi-dimensional free-energy, enthalpy and entropy plots.",
932 "[THISMODULE] reads one or more [TT].xvg[tt] files and analyzes data sets.",
933 "The basic purpose of [THISMODULE] is to plot Gibbs free energy landscapes",
934 "(option [TT]-ls[tt])",
935 "by Bolzmann inverting multi-dimensional histograms (option [TT]-lp[tt]),",
937 "make enthalpy (option [TT]-lsh[tt]) and entropy (option [TT]-lss[tt])",
938 "plots. The histograms can be made for any quantities the user supplies.",
939 "A line in the input file may start with a time",
940 "(see option [TT]-time[tt]) and any number of [IT]y[it]-values may follow.",
941 "Multiple sets can also be",
942 "read when they are separated by & (option [TT]-n[tt]),",
943 "in this case only one [IT]y[it]-value is read from each line.",
944 "All lines starting with # and @ are skipped.",
946 "Option [TT]-ge[tt] can be used to supply a file with free energies",
947 "when the ensemble is not a Boltzmann ensemble, but needs to be biased",
948 "by this free energy. One free energy value is required for each",
949 "(multi-dimensional) data point in the [TT]-f[tt] input.",
951 "Option [TT]-ene[tt] can be used to supply a file with energies.",
952 "These energies are used as a weighting function in the single",
953 "histogram analysis method by Kumar et al. When temperatures",
954 "are supplied (as a second column in the file), an experimental",
955 "weighting scheme is applied. In addition the vales",
956 "are used for making enthalpy and entropy plots.",
958 "With option [TT]-dim[tt], dimensions can be gives for distances.",
959 "When a distance is 2- or 3-dimensional, the circumference or surface",
960 "sampled by two particles increases with increasing distance.",
961 "Depending on what one would like to show, one can choose to correct",
962 "the histogram and free-energy for this volume effect.",
963 "The probability is normalized by r and r^2 for dimensions of 2 and 3, ",
965 "A value of -1 is used to indicate an angle in degrees between two",
966 "vectors: a sin(angle) normalization will be applied.",
967 "[BB]Note[bb] that for angles between vectors the inner-product or cosine",
968 "is the natural quantity to use, as it will produce bins of the same",
971 static real tb
= -1, te
= -1, frac
= 0.5, filtlen
= 0;
972 static gmx_bool bHaveT
= TRUE
, bDer
= FALSE
, bSubAv
= TRUE
, bAverCorr
= FALSE
, bXYdy
= FALSE
;
973 static gmx_bool bEESEF
= FALSE
, bEENLC
= FALSE
, bEeFitAc
= FALSE
, bPower
= FALSE
;
974 static gmx_bool bShamEner
= TRUE
, bSham
= TRUE
;
975 static real Tref
= 298.15, pmin
= 0, ttol
= 0, pmax
= 0, gmax
= 0, emin
= 0, emax
= 0;
976 static rvec nrdim
= {1, 1, 1};
977 static rvec nrbox
= {32, 32, 32};
978 static rvec xmin
= {0, 0, 0}, xmax
= {1, 1, 1};
979 static int nsets_in
= 1, nb_min
= 4, resol
= 10, nlevels
= 25;
980 static const char *mname
= "";
982 { "-time", FALSE
, etBOOL
, {&bHaveT
},
983 "Expect a time in the input" },
984 { "-b", FALSE
, etREAL
, {&tb
},
985 "First time to read from set" },
986 { "-e", FALSE
, etREAL
, {&te
},
987 "Last time to read from set" },
988 { "-ttol", FALSE
, etREAL
, {&ttol
},
989 "Tolerance on time in appropriate units (usually ps)" },
990 { "-n", FALSE
, etINT
, {&nsets_in
},
991 "Read this number of sets separated by lines containing only an ampersand" },
992 { "-d", FALSE
, etBOOL
, {&bDer
},
993 "Use the derivative" },
994 { "-sham", FALSE
, etBOOL
, {&bSham
},
995 "Turn off energy weighting even if energies are given" },
996 { "-tsham", FALSE
, etREAL
, {&Tref
},
997 "Temperature for single histogram analysis" },
998 { "-pmin", FALSE
, etREAL
, {&pmin
},
999 "Minimum probability. Anything lower than this will be set to zero" },
1000 { "-dim", FALSE
, etRVEC
, {nrdim
},
1001 "Dimensions for distances, used for volume correction (max 3 values, dimensions > 3 will get the same value as the last)" },
1002 { "-ngrid", FALSE
, etRVEC
, {nrbox
},
1003 "Number of bins for energy landscapes (max 3 values, dimensions > 3 will get the same value as the last)" },
1004 { "-xmin", FALSE
, etRVEC
, {xmin
},
1005 "Minimum for the axes in energy landscape (see above for > 3 dimensions)" },
1006 { "-xmax", FALSE
, etRVEC
, {xmax
},
1007 "Maximum for the axes in energy landscape (see above for > 3 dimensions)" },
1008 { "-pmax", FALSE
, etREAL
, {&pmax
},
1009 "Maximum probability in output, default is calculate" },
1010 { "-gmax", FALSE
, etREAL
, {&gmax
},
1011 "Maximum free energy in output, default is calculate" },
1012 { "-emin", FALSE
, etREAL
, {&emin
},
1013 "Minimum enthalpy in output, default is calculate" },
1014 { "-emax", FALSE
, etREAL
, {&emax
},
1015 "Maximum enthalpy in output, default is calculate" },
1016 { "-nlevels", FALSE
, etINT
, {&nlevels
},
1017 "Number of levels for energy landscape" },
1018 { "-mname", FALSE
, etSTR
, {&mname
},
1019 "Legend label for the custom landscape" },
1021 #define NPA asize(pa)
1024 int n
, e_n
, d_n
, nlast
, s
, nset
, e_nset
, d_nset
, i
, j
= 0, *idim
, *ibox
;
1025 real
**val
, **et_val
, **dt_val
, *t
, *e_t
, e_dt
, d_dt
, *d_t
, dt
, tot
, error
;
1027 double *av
, *sig
, cum1
, cum2
, cum3
, cum4
, db
;
1028 const char *fn_ge
, *fn_ene
;
1030 gmx_int64_t num_grid_points
;
1033 { efXVG
, "-f", "graph", ffREAD
},
1034 { efXVG
, "-ge", "gibbs", ffOPTRD
},
1035 { efXVG
, "-ene", "esham", ffOPTRD
},
1036 { efXVG
, "-dist", "ener", ffOPTWR
},
1037 { efXVG
, "-histo", "edist", ffOPTWR
},
1038 { efNDX
, "-bin", "bindex", ffOPTWR
},
1039 { efXPM
, "-lp", "prob", ffOPTWR
},
1040 { efXPM
, "-ls", "gibbs", ffOPTWR
},
1041 { efXPM
, "-lsh", "enthalpy", ffOPTWR
},
1042 { efXPM
, "-lss", "entropy", ffOPTWR
},
1043 { efXPM
, "-map", "map", ffOPTWR
},
1044 { efPDB
, "-ls3", "gibbs3", ffOPTWR
},
1045 { efXVG
, "-mdata", "mapdata", ffOPTRD
},
1046 { efLOG
, "-g", "shamlog", ffOPTWR
}
1048 #define NFILE asize(fnm)
1053 if (!parse_common_args(&argc
, argv
, PCA_CAN_VIEW
| PCA_BE_NICE
,
1054 NFILE
, fnm
, npargs
, pa
, asize(desc
), desc
, 0, NULL
, &oenv
))
1059 val
= read_xvg_time(opt2fn("-f", NFILE
, fnm
), bHaveT
,
1060 opt2parg_bSet("-b", npargs
, pa
), tb
-ttol
,
1061 opt2parg_bSet("-e", npargs
, pa
), te
+ttol
,
1062 nsets_in
, &nset
, &n
, &dt
, &t
);
1063 printf("Read %d sets of %d points, dt = %g\n\n", nset
, n
, dt
);
1065 fn_ge
= opt2fn_null("-ge", NFILE
, fnm
);
1066 fn_ene
= opt2fn_null("-ene", NFILE
, fnm
);
1068 if (fn_ge
&& fn_ene
)
1070 gmx_fatal(FARGS
, "Can not do free energy and energy corrections at the same time");
1073 if (fn_ge
|| fn_ene
)
1075 et_val
= read_xvg_time(fn_ge
? fn_ge
: fn_ene
, bHaveT
,
1076 opt2parg_bSet("-b", npargs
, pa
), tb
-ttol
,
1077 opt2parg_bSet("-e", npargs
, pa
), te
+ttol
,
1078 1, &e_nset
, &e_n
, &e_dt
, &e_t
);
1083 gmx_fatal(FARGS
, "Can only handle one free energy component in %s",
1089 if (e_nset
!= 1 && e_nset
!= 2)
1091 gmx_fatal(FARGS
, "Can only handle one energy component or one energy and one T in %s",
1097 gmx_fatal(FARGS
, "Number of energies (%d) does not match number of entries (%d) in %s", e_n
, n
, opt2fn("-f", NFILE
, fnm
));
1105 if (opt2fn_null("-mdata", NFILE
, fnm
) != NULL
)
1107 dt_val
= read_xvg_time(opt2fn("-mdata", NFILE
, fnm
), bHaveT
,
1108 FALSE
, tb
, FALSE
, te
,
1109 nsets_in
, &d_nset
, &d_n
, &d_dt
, &d_t
);
1112 gmx_fatal(FARGS
, "Can only handle one mapping data column in %s",
1113 opt2fn("-mdata", NFILE
, fnm
));
1121 if (fn_ene
&& et_val
)
1123 ehisto(opt2fn("-histo", NFILE
, fnm
), e_n
, et_val
, oenv
);
1126 snew(idim
, max(3, nset
));
1127 snew(ibox
, max(3, nset
));
1128 snew(rmin
, max(3, nset
));
1129 snew(rmax
, max(3, nset
));
1130 for (i
= 0; (i
< min(3, nset
)); i
++)
1137 for (; (i
< nset
); i
++)
1145 /* Check that the grid size is manageable. */
1146 num_grid_points
= ibox
[0];
1147 for (i
= 1; i
< nset
; i
++)
1150 if (!check_int_multiply_for_overflow(num_grid_points
, ibox
[i
], &result
))
1153 "The number of dimensions and grid points is too large for this tool.\n");
1155 num_grid_points
= result
;
1157 /* The number of grid points fits in a gmx_int64_t. */
1159 do_sham(opt2fn("-dist", NFILE
, fnm
), opt2fn("-bin", NFILE
, fnm
),
1160 opt2fn("-lp", NFILE
, fnm
),
1161 opt2fn("-ls", NFILE
, fnm
), opt2fn("-lsh", NFILE
, fnm
),
1162 opt2fn("-lss", NFILE
, fnm
), opt2fn("-map", NFILE
, fnm
),
1163 opt2fn("-ls3", NFILE
, fnm
), opt2fn("-g", NFILE
, fnm
),
1164 n
, nset
, val
, fn_ge
!= NULL
, e_nset
, et_val
, d_n
, d_t
, dt_val
, Tref
,
1166 opt2parg_bSet("-emin", NPA
, pa
) ? &emin
: NULL
,
1167 opt2parg_bSet("-emax", NPA
, pa
) ? &emax
: NULL
,
1170 opt2parg_bSet("-xmin", NPA
, pa
), rmin
,
1171 opt2parg_bSet("-xmax", NPA
, pa
), rmax
);