[gmx-developers] how to write a xtc file in c
Dongsheng Zhang
dong at pampas.chem.purdue.edu
Sat Aug 12 16:43:17 CEST 2006
Dear Yang Ye,
The problem is I can't find libgmx.o anywhere. I have tried to use find
command to search it. Could you please tell me where it supposes to be
after gromacs installed?
All the best!
Dongsheng
On Sat, 2006-08-12 at 22:19 +0800, Yang Ye wrote:
> Hi, Dong sheng
>
> It wasn't the problem of "Append -lgmx to LIBS". The parameters required by GCC are to be spread into different variable to make it clearer.
>
> Your current Makefile doesn't make LDFLAGS work.
>
> Try this
>
> CC=gcc
> CFLAGS=-c -Wall -I/hielo/include/gromacs
> LDFLAGS=-L/hielo/lib
> LIBS=-lgmx -lm
>
> all: xtc
>
> xtc:
> $(CC) $(CFLAGS) ${LDFLAGS} ${LIBS} accessXtc.c -o accessXTC
>
>
>
> Make sure that under /hield/lib, there is libgmx.o and under
> /hielo/include/gromacs, there are all the .h files.
>
> Yang Ye
>
> Dongsheng Zhang wrote:
> > Dear Yang Ye,
> >
> > Thank you very much for your great help to give me the basic work flow.
> > I still have trouble to compile my file accessXtc.c. the following is my
> > simple Makefile:
> >
> >
> > CC=gcc
> > CFLAGS=-c -Wall -I/hielo/include/gromacs
> > LDFLAGS=-L/hielo/lib
> > LIBS=-lgmx
> >
> > all: xtc
> >
> > xtc: xtc.o
> > gcc xtc.o -o a.out
> > xtc.o: accessXtc.c
> > $(CC) $(CFLAGS) $(LIBS) accessXtc.c -o xtc.o
> >
> >
> > I believe I miss your fourth point "Append -lgmx to LIBS". I don't know
> > what -lgmx really means. Where is gmx library? The make command gives
> > me the following error message:
> >
> > xtc.o(.text+0x1f): In function `main':
> > : undefined reference to `open_xtc'
> > xtc.o(.text+0x6d): In function `main':
> > : undefined reference to `close_xtc'
> > xtc.o(.text+0x103): In function `writeXtc':
> > : undefined reference to `cos'
> > xtc.o(.text+0x117): In function `writeXtc':
> > : undefined reference to `sin'
> > xtc.o(.text+0x130): In function `writeXtc':
> > : undefined reference to `open_xtc'
> > xtc.o(.text+0x176): In function `writeXtc':
> > : undefined reference to `read_first_xtc'
> > xtc.o(.text+0x1db): In function `writeXtc':
> > : undefined reference to `read_next_xtc'
> > xtc.o(.text+0x20e): In function `writeXtc':
> > : undefined reference to `close_xtc'
> > xtc.o(.text+0x2e5): In function `writeXtc':
> > : undefined reference to `open_xtc'
> > xtc.o(.text+0x32b): In function `writeXtc':
> > : undefined reference to `read_first_xtc'
> > xtc.o(.text+0x390): In function `writeXtc':
> > : undefined reference to `read_next_xtc'
> > xtc.o(.text+0x3c3): In function `writeXtc':
> > : undefined reference to `close_xtc'
> > xtc.o(.text+0x4f1): In function `writeXtc':
> > : undefined reference to `write_xtc'
> > collect2: ld returned 1 exit status
> > make: *** [xtc] Error 1
> >
> >
> > Please give me more help.
> >
> >
> > Have a nice weekend!
> >
> > Dongsheng
> >
> > On Sat, 2006-08-12 at 09:09 +0800, Yang Ye wrote:
> >
> >> 1. Use #include in the C file
> >> In Makefile
> >> 2. Append -I/gromacs/include to CFLAGS
> >> 3. Append -L/gromacs/lib to LDFLAGS
> >> 4. Append -lgmx to LIBS
> >>
> >> Yang Ye
> >>
> >> Dongsheng Zhang wrote:
> >>
> >>> Dear Yang Ye or other gmx developers,
> >>>
> >>> I have finished writing the code to read and write a xtc file, but I
> >>> have trouble to compile it. from the web site:
> >>>
> >>> http://www.gromacs.org/documentation/reference/online/xtc.html
> >>>
> >>> I find:
> >>>
> >>> To use the library function include "xtcio.h" in your file and link with
> >>> -lgmx.$(CPU)
> >>>
> >>>
> >>> Could you please tell me how to specify the link?
> >>>
> >>>
> >>> Thanks a lot!
> >>>
> >>> Dongsheng
> >>>
> >>>
> >>> On Thu, 2006-08-10 at 17:39 +0800, Yang Ye wrote:
> >>>
> >>>
> >>>> Mark Abraham wrote:
> >>>>
> >>>>
> >>>>> Dongsheng Zhang wrote:
> >>>>>
> >>>>>
> >>>>>> Dear GMX developers,
> >>>>>>
> >>>>>> I want to write a xtc file to do rerun to get a special potential
> >>>>>> energy. Could you please tell me how to write a xtc file in c from a gro
> >>>>>> file (with multiple frames got from a xtc file, without velocity)? Thank
> >>>>>> you for your help!
> >>>>>>
> >>>>>>
> >>>>> Read the source code - to find the right functions to call look how
> >>>>> trjconv or something does it, then grep the src/*/*.c files for the
> >>>>> function definition.
> >>>>>
> >>>>> Also http://www.gromacs.org/documentation/reference/online/xtc.html
> >>>>>
> >>>>>
> >>>> This document shall help you.
> >>>>
> >>>> Here is basic workflow:
> >>>>
> >>>> 1. Open XTC
> >>>> int xfile = -1;
> >>>> char *xfilename = "out.xtc";
> >>>>
> >>>> xfile = open_xtc(xfilename, "w");
> >>>>
> >>>> 2. Close
> >>>> if (xfile!=-1) {
> >>>> close_xtc(xfile);
> >>>> xfile = -1;
> >>>> //OK
> >>>> } else {
> >>>> //Error
> >>>> }
> >>>>
> >>>> 3. Write XTC
> >>>> long step = -1;
> >>>> double sim_time = 0.0;
> >>>>
> >>>> matrix mat;
> >>>> int i;
> >>>> rvec *x_data;
> >>>> double ppos[3];
> >>>> int img[3];
> >>>> int pnode;
> >>>>
> >>>> int n_total_particles;
> >>>>
> >>>> Particle p_data;
> >>>>
> >>>> if (xfile==-1) {
> >>>> //Error
> >>>> }
> >>>>
> >>>> if (n_total_particles <1) {
> >>>> //Error
> >>>> }
> >>>>
> >>>> mat[0][0] = CONV_UNIT_L(box_l[0]);
> >>>> mat[0][1] = 0.0;
> >>>> mat[0][2] = 0.0;
> >>>> mat[1][0] = 0.0;
> >>>> mat[1][1] = CONV_UNIT_L(box_l[1]);
> >>>> mat[1][2] = 0.0;
> >>>> mat[2][0] = 0.0;
> >>>> mat[2][1] = 0.0;
> >>>> mat[2][2] = CONV_UNIT_L(box_l[2]);
> >>>>
> >>>> x_data = (rvec *)malloc(sizeof(rvec)*(n_total_particles+1));
> >>>>
> >>>> for (i = 0; i < n_total_particles; i++) {
> >>>> x_data[i][0] = X;
> >>>> x_data[i][1] = Y;
> >>>> x_data[i][2] = Z;
> >>>> }
> >>>>
> >>>> write_xtc(xfile, n_total_particles, step, sim_time, mat, x_data, 1000);
> >>>> step++;
> >>>>
> >>>> free(x_data);
> >>>>
> >>>> return OK;
> >>>>
> >>>>
> >>>>
> >>>>> Mark
> >>>>> _______________________________________________
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> >>>>>
> >>>>>
> >>>>>
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> >>>>
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> >>>
> >>
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