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

[Yang Ye]

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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