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44 #include "gromacs/commandline/pargs.h"
45 #include "gromacs/legacyheaders/typedefs.h"
46 #include "gromacs/utility/smalloc.h"
47 #include "gromacs/legacyheaders/macros.h"
48 #include "gromacs/math/vec.h"
49 #include "gromacs/utility/futil.h"
50 #include "gromacs/topology/index.h"
52 #include "gromacs/pbcutil/rmpbc.h"
53 #include "gromacs/legacyheaders/txtdump.h"
54 #include "gromacs/fileio/tpxio.h"
55 #include "gromacs/fileio/trxio.h"
56 #include "gromacs/fileio/xvgr.h"
62 calc_principal_axes(t_topology
* top
,
71 sub_xcm(x
, n
, index
, top
->atoms
.atom
, xcm
, FALSE
);
72 principal_comp(n
, index
, top
->atoms
.atom
, x
, axes
, inertia
);
75 int gmx_principal(int argc
, char *argv
[])
77 const char *desc
[] = {
78 "[THISMODULE] calculates the three principal axes of inertia for a group",
79 "of atoms. NOTE: Old versions of Gromacs wrote the output data in a",
80 "strange transposed way. As of Gromacs-5.0, the output file paxis1.dat",
81 "contains the x/y/z components of the first (major) principal axis for",
82 "each frame, and similarly for the middle and minor axes in paxis2.dat",
85 static gmx_bool foo
= FALSE
;
88 { "-foo", FALSE
, etBOOL
, {&foo
}, "Dummy option to avoid empty array" }
97 char *grpname
, title
[256];
98 int i
, j
, m
, gnx
, nam
, mol
;
100 rvec a1
, a2
, a3
, moi
;
107 gmx_rmpbc_t gpbc
= NULL
;
111 { efTRX
, "-f", NULL
, ffREAD
},
112 { efTPS
, NULL
, NULL
, ffREAD
},
113 { efNDX
, NULL
, NULL
, ffOPTRD
},
114 { efXVG
, "-a1", "paxis1", ffWRITE
},
115 { efXVG
, "-a2", "paxis2", ffWRITE
},
116 { efXVG
, "-a3", "paxis3", ffWRITE
},
117 { efXVG
, "-om", "moi", ffWRITE
}
119 #define NFILE asize(fnm)
121 if (!parse_common_args(&argc
, argv
,
122 PCA_CAN_TIME
| PCA_TIME_UNIT
| PCA_CAN_VIEW
| PCA_BE_NICE
,
123 NFILE
, fnm
, asize(pa
), pa
, asize(desc
), desc
, 0, NULL
, &oenv
))
129 for (i
= 0; i
< DIM
; i
++)
131 snew(legend
[i
], STRLEN
);
132 sprintf(legend
[i
], "%c component", 'X'+i
);
135 axis1
= xvgropen(opt2fn("-a1", NFILE
, fnm
), "Principal axis 1 (major axis)",
136 output_env_get_xvgr_tlabel(oenv
), "Component (nm)", oenv
);
137 xvgr_legend(axis1
, DIM
, (const char **)legend
, oenv
);
139 axis2
= xvgropen(opt2fn("-a2", NFILE
, fnm
), "Principal axis 2 (middle axis)",
140 output_env_get_xvgr_tlabel(oenv
), "Component (nm)", oenv
);
141 xvgr_legend(axis2
, DIM
, (const char **)legend
, oenv
);
143 axis3
= xvgropen(opt2fn("-a3", NFILE
, fnm
), "Principal axis 3 (minor axis)",
144 output_env_get_xvgr_tlabel(oenv
), "Component (nm)", oenv
);
145 xvgr_legend(axis3
, DIM
, (const char **)legend
, oenv
);
147 sprintf(legend
[XX
], "Axis 1 (major)");
148 sprintf(legend
[YY
], "Axis 2 (middle)");
149 sprintf(legend
[ZZ
], "Axis 3 (minor)");
151 fmoi
= xvgropen(opt2fn("-om", NFILE
, fnm
), "Moments of inertia around inertial axes",
152 output_env_get_xvgr_tlabel(oenv
), "I (au nm\\S2\\N)", oenv
);
153 xvgr_legend(fmoi
, DIM
, (const char **)legend
, oenv
);
155 for (i
= 0; i
< DIM
; i
++)
161 read_tps_conf(ftp2fn(efTPS
, NFILE
, fnm
), title
, &top
, &ePBC
, NULL
, NULL
, box
, TRUE
);
163 get_index(&top
.atoms
, ftp2fn_null(efNDX
, NFILE
, fnm
), 1, &gnx
, &index
, &grpname
);
165 natoms
= read_first_x(oenv
, &status
, ftp2fn(efTRX
, NFILE
, fnm
), &t
, &x
, box
);
167 gpbc
= gmx_rmpbc_init(&top
.idef
, ePBC
, natoms
);
171 gmx_rmpbc(gpbc
, natoms
, box
, x
);
173 calc_principal_axes(&top
, x
, index
, gnx
, axes
, moi
);
175 fprintf(axis1
, "%15.10f %15.10f %15.10f %15.10f\n", t
, axes
[XX
][XX
], axes
[XX
][YY
], axes
[XX
][ZZ
]);
176 fprintf(axis2
, "%15.10f %15.10f %15.10f %15.10f\n", t
, axes
[YY
][XX
], axes
[YY
][YY
], axes
[YY
][ZZ
]);
177 fprintf(axis3
, "%15.10f %15.10f %15.10f %15.10f\n", t
, axes
[ZZ
][XX
], axes
[ZZ
][YY
], axes
[ZZ
][ZZ
]);
178 fprintf(fmoi
, "%15.10f %15.10f %15.10f %15.10f\n", t
, moi
[XX
], moi
[YY
], moi
[ZZ
]);
180 while (read_next_x(oenv
, status
, &t
, x
, box
));
182 gmx_rmpbc_done(gpbc
);