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43 #include "gromacs/math/units.h"
45 #include "gromacs/utility/smalloc.h"
46 #include "gromacs/utility/futil.h"
47 #include "gromacs/commandline/pargs.h"
49 #include "gromacs/math/vec.h"
52 #include "gromacs/utility/fatalerror.h"
53 #include "gromacs/fileio/xvgr.h"
56 #include "gromacs/fileio/trnio.h"
60 static void dump_dih_trn(int nframes
, int nangles
, real
**dih
, const char *fn
,
63 int i
, j
, k
, l
, m
, na
;
66 matrix box
= {{2, 0, 0}, {0, 2, 0}, {0, 0, 2}};
77 printf("There are %d dihedrals. Will fill %d atom positions with cos/sin\n",
80 trn
= open_trn(fn
, "w");
81 for (i
= 0; (i
< nframes
); i
++)
84 for (j
= 0; (j
< nangles
); j
++)
86 for (m
= 0; (m
< 2); m
++)
88 x
[k
][l
] = (m
== 0) ? cos(dih
[j
][i
]) : sin(dih
[j
][i
]);
97 fwrite_trn(trn
, i
, time
[i
], 0, box
, na
, x
, NULL
, NULL
);
103 int gmx_g_angle(int argc
, char *argv
[])
105 static const char *desc
[] = {
106 "[THISMODULE] computes the angle distribution for a number of angles",
107 "or dihedrals.[PAR]",
108 "With option [TT]-ov[tt], you can plot the average angle of",
109 "a group of angles as a function of time. With the [TT]-all[tt] option,",
110 "the first graph is the average and the rest are the individual angles.[PAR]",
111 "With the [TT]-of[tt] option, [THISMODULE] also calculates the fraction of trans",
112 "dihedrals (only for dihedrals) as function of time, but this is",
113 "probably only fun for a select few.[PAR]",
114 "With option [TT]-oc[tt], a dihedral correlation function is calculated.[PAR]",
115 "It should be noted that the index file must contain",
116 "atom triplets for angles or atom quadruplets for dihedrals.",
117 "If this is not the case, the program will crash.[PAR]",
118 "With option [TT]-or[tt], a trajectory file is dumped containing cos and",
119 "sin of selected dihedral angles, which subsequently can be used as",
120 "input for a principal components analysis using [gmx-covar].[PAR]",
121 "Option [TT]-ot[tt] plots when transitions occur between",
122 "dihedral rotamers of multiplicity 3 and [TT]-oh[tt]",
123 "records a histogram of the times between such transitions,",
124 "assuming the input trajectory frames are equally spaced in time."
126 static const char *opt
[] = { NULL
, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL
};
127 static gmx_bool bALL
= FALSE
, bChandler
= FALSE
, bAverCorr
= FALSE
, bPBC
= TRUE
;
128 static real binwidth
= 1;
130 { "-type", FALSE
, etENUM
, {opt
},
131 "Type of angle to analyse" },
132 { "-all", FALSE
, etBOOL
, {&bALL
},
133 "Plot all angles separately in the averages file, in the order of appearance in the index file." },
134 { "-binwidth", FALSE
, etREAL
, {&binwidth
},
135 "binwidth (degrees) for calculating the distribution" },
136 { "-periodic", FALSE
, etBOOL
, {&bPBC
},
137 "Print dihedral angles modulo 360 degrees" },
138 { "-chandler", FALSE
, etBOOL
, {&bChandler
},
139 "Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi < -60 or phi > 60." },
140 { "-avercorr", FALSE
, etBOOL
, {&bAverCorr
},
141 "Average the correlation functions for the individual angles/dihedrals" }
143 static const char *bugs
[] = {
144 "Counting transitions only works for dihedrals with multiplicity 3"
152 real maxang
, Jc
, S2
, norm_fac
, maxstat
;
154 int nframes
, maxangstat
, mult
, *angstat
;
155 int i
, j
, total
, nangles
, natoms
, nat2
, first
, last
, angind
;
156 gmx_bool bAver
, bRb
, bPeriodic
,
157 bFrac
, /* calculate fraction too? */
158 bTrans
, /* worry about transtions too? */
159 bCorr
; /* correlation function ? */
160 real t
, aa
, aver
, aver2
, aversig
, fraction
; /* fraction trans dihedrals */
163 real
**dih
= NULL
; /* mega array with all dih. angles at all times*/
165 real
*time
, *trans_frac
, *aver_angle
;
167 { efTRX
, "-f", NULL
, ffREAD
},
168 { efNDX
, NULL
, "angle", ffREAD
},
169 { efXVG
, "-od", "angdist", ffWRITE
},
170 { efXVG
, "-ov", "angaver", ffOPTWR
},
171 { efXVG
, "-of", "dihfrac", ffOPTWR
},
172 { efXVG
, "-ot", "dihtrans", ffOPTWR
},
173 { efXVG
, "-oh", "trhisto", ffOPTWR
},
174 { efXVG
, "-oc", "dihcorr", ffOPTWR
},
175 { efTRR
, "-or", NULL
, ffOPTWR
}
177 #define NFILE asize(fnm)
183 ppa
= add_acf_pargs(&npargs
, pa
);
184 if (!parse_common_args(&argc
, argv
, PCA_CAN_VIEW
| PCA_CAN_TIME
| PCA_BE_NICE
,
185 NFILE
, fnm
, npargs
, ppa
, asize(desc
), desc
, asize(bugs
), bugs
,
209 if (opt2bSet("-or", NFILE
, fnm
))
213 gmx_fatal(FARGS
, "Can not combine angles with trn dump");
217 please_cite(stdout
, "Mu2005a");
221 /* Calculate bin size */
222 maxangstat
= (int)(maxang
/binwidth
+0.5);
223 binwidth
= maxang
/maxangstat
;
225 rd_index(ftp2fn(efNDX
, NFILE
, fnm
), 1, &isize
, &index
, &grpname
);
226 nangles
= isize
/mult
;
227 if ((isize
% mult
) != 0)
229 gmx_fatal(FARGS
, "number of index elements not multiple of %d, "
230 "these can not be %s\n",
231 mult
, (mult
== 3) ? "angle triplets" : "dihedral quadruplets");
235 /* Check whether specific analysis has to be performed */
236 bCorr
= opt2bSet("-oc", NFILE
, fnm
);
237 bAver
= opt2bSet("-ov", NFILE
, fnm
);
238 bTrans
= opt2bSet("-ot", NFILE
, fnm
);
239 bFrac
= opt2bSet("-of", NFILE
, fnm
);
240 if (bTrans
&& opt
[0][0] != 'd')
242 fprintf(stderr
, "Option -ot should only accompany -type dihedral. Disabling -ot.\n");
246 if (bChandler
&& !bCorr
)
253 fprintf(stderr
, "Warning:"
254 " calculating fractions as defined in this program\n"
255 "makes sense for Ryckaert Bellemans dihs. only. Ignoring -of\n\n");
259 if ( (bTrans
|| bFrac
|| bCorr
) && mult
== 3)
261 gmx_fatal(FARGS
, "Can only do transition, fraction or correlation\n"
262 "on dihedrals. Select -d\n");
266 * We need to know the nr of frames so we can allocate memory for an array
267 * with all dihedral angles at all timesteps. Works for me.
269 if (bTrans
|| bCorr
|| bALL
|| opt2bSet("-or", NFILE
, fnm
))
274 snew(angstat
, maxangstat
);
276 read_ang_dih(ftp2fn(efTRX
, NFILE
, fnm
), (mult
== 3),
277 bALL
|| bCorr
|| bTrans
|| opt2bSet("-or", NFILE
, fnm
),
278 bRb
, bPBC
, maxangstat
, angstat
,
279 &nframes
, &time
, isize
, index
, &trans_frac
, &aver_angle
, dih
,
282 dt
= (time
[nframes
-1]-time
[0])/(nframes
-1);
286 sprintf(title
, "Average Angle: %s", grpname
);
287 out
= xvgropen(opt2fn("-ov", NFILE
, fnm
),
288 title
, "Time (ps)", "Angle (degrees)", oenv
);
289 for (i
= 0; (i
< nframes
); i
++)
291 fprintf(out
, "%10.5f %8.3f", time
[i
], aver_angle
[i
]*RAD2DEG
);
294 for (j
= 0; (j
< nangles
); j
++)
299 fprintf(out
, " %8.3f", atan2(sin(dd
), cos(dd
))*RAD2DEG
);
303 fprintf(out
, " %8.3f", dih
[j
][i
]*RAD2DEG
);
311 if (opt2bSet("-or", NFILE
, fnm
))
313 dump_dih_trn(nframes
, nangles
, dih
, opt2fn("-or", NFILE
, fnm
), time
);
318 sprintf(title
, "Trans fraction: %s", grpname
);
319 out
= xvgropen(opt2fn("-of", NFILE
, fnm
),
320 title
, "Time (ps)", "Fraction", oenv
);
322 for (i
= 0; (i
< nframes
); i
++)
324 fprintf(out
, "%10.5f %10.3f\n", time
[i
], trans_frac
[i
]);
325 tfrac
+= trans_frac
[i
];
330 fprintf(stderr
, "Average trans fraction: %g\n", tfrac
);
336 ana_dih_trans(opt2fn("-ot", NFILE
, fnm
), opt2fn("-oh", NFILE
, fnm
),
337 dih
, nframes
, nangles
, grpname
, time
, bRb
, oenv
);
342 /* Autocorrelation function */
345 fprintf(stderr
, "Not enough frames for correlation function\n");
352 real dval
, sixty
= DEG2RAD
*60;
355 for (i
= 0; (i
< nangles
); i
++)
357 for (j
= 0; (j
< nframes
); j
++)
362 bTest
= (dval
> -sixty
) && (dval
< sixty
);
366 bTest
= (dval
< -sixty
) || (dval
> sixty
);
370 dih
[i
][j
] = dval
-tfrac
;
387 do_autocorr(opt2fn("-oc", NFILE
, fnm
), oenv
,
388 "Dihedral Autocorrelation Function",
389 nframes
, nangles
, dih
, dt
, mode
, bAverCorr
);
394 /* Determine the non-zero part of the distribution */
395 for (first
= 0; (first
< maxangstat
-1) && (angstat
[first
+1] == 0); first
++)
399 for (last
= maxangstat
-1; (last
> 0) && (angstat
[last
-1] == 0); last
--)
405 for (i
= 0; (i
< nframes
); i
++)
407 aver
+= RAD2DEG
*aver_angle
[i
];
408 aver2
+= sqr(RAD2DEG
*aver_angle
[i
]);
410 aver
/= (real
) nframes
;
411 aver2
/= (real
) nframes
;
412 aversig
= sqrt(aver2
-sqr(aver
));
413 printf("Found points in the range from %d to %d (max %d)\n",
414 first
, last
, maxangstat
);
415 printf(" < angle > = %g\n", aver
);
416 printf("< angle^2 > = %g\n", aver2
);
417 printf("Std. Dev. = %g\n", aversig
);
421 sprintf(title
, "Angle Distribution: %s", grpname
);
425 sprintf(title
, "Dihedral Distribution: %s", grpname
);
427 calc_distribution_props(maxangstat
, angstat
, -180.0, 0, NULL
, &S2
);
428 fprintf(stderr
, "Order parameter S^2 = %g\n", S2
);
431 bPeriodic
= (mult
== 4) && (first
== 0) && (last
== maxangstat
-1);
433 out
= xvgropen(opt2fn("-od", NFILE
, fnm
), title
, "Degrees", "", oenv
);
434 if (output_env_get_print_xvgr_codes(oenv
))
436 fprintf(out
, "@ subtitle \"average angle: %g\\So\\N\"\n", aver
);
438 norm_fac
= 1.0/(nangles
*nframes
*binwidth
);
442 for (i
= first
; (i
<= last
); i
++)
444 maxstat
= max(maxstat
, angstat
[i
]*norm_fac
);
446 fprintf(out
, "@with g0\n");
447 fprintf(out
, "@ world xmin -180\n");
448 fprintf(out
, "@ world xmax 180\n");
449 fprintf(out
, "@ world ymin 0\n");
450 fprintf(out
, "@ world ymax %g\n", maxstat
*1.05);
451 fprintf(out
, "@ xaxis tick major 60\n");
452 fprintf(out
, "@ xaxis tick minor 30\n");
453 fprintf(out
, "@ yaxis tick major 0.005\n");
454 fprintf(out
, "@ yaxis tick minor 0.0025\n");
456 for (i
= first
; (i
<= last
); i
++)
458 fprintf(out
, "%10g %10f\n", i
*binwidth
+180.0-maxang
, angstat
[i
]*norm_fac
);
462 /* print first bin again as last one */
463 fprintf(out
, "%10g %10f\n", 180.0, angstat
[0]*norm_fac
);
468 do_view(oenv
, opt2fn("-od", NFILE
, fnm
), "-nxy");
471 do_view(oenv
, opt2fn("-ov", NFILE
, fnm
), "-nxy");