[gmx-developers] how to write a xtc file in c

[Dongsheng Zhang]

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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> >>> gmx-developers at gromacs.org
> >>> http://www.gromacs.org/mailman/listinfo/gmx-developers
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> >>>
> >>>       
> >>
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> >>     
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> >   
> 
> 
> 
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