int main(int argc,char* argv[])
{
FILE* fp=NULL;
//printf("no of argc=%d\n",argc);
fp=argChk(argc,argv);
if(fp == NULL || fp == 0)
{
fprintf(stderr, "Quitting the Program because - %s\n", strerror(errno));
exit(0);
}
My402List *list; //------creating a list-----//
list=(My402List*)malloc(sizeof(My402List));
if(!My402ListInit(list))
{
fprintf(stderr,"Error: Error in Initializing the list\n");
exit(0);
}
if(!Read_input(fp,list))
{
printf("error\n");
exit(0);
}
if(list->num_members==0)
{
fprintf(stderr,"Error:Invalid input\n");
exit(0);
}
sort(list);
display(list);
fclose(fp);
cleanup(list);
return TRUE;
}
int main()
{
int Num_particles;
int struct_index;
double cutoff;
double force_constant;
double energy_offset;
double step_size;
double step_size_reduction_factor;
double rmsd_pathway;
double delta_rmsd_zero;
double energy_from_ref_tol;
long int Max_num_iterations;
FR_DAT fr_ref, fr_ref_for_alignment, fr_ts, fr_start, fr_end;
double **pair_distances_structure;
char Filename[1000];
int i;
double *Reference_x, *Reference_y, *Reference_z;
int Num_struct_written;
FILE *out_num, *out;
double energy_ref, rmsd_from_ref_final;
long int iteration_number_end;
int is_step_size_adequate;
/********************************************************************************/
Read_input(&Num_particles, &struct_index, &cutoff, &force_constant, &energy_offset, &step_size, &step_size_reduction_factor, &rmsd_pathway, &delta_rmsd_zero, &energy_from_ref_tol, &Max_num_iterations);
pair_distances_structure = (double**)malloc(Num_particles * sizeof(double*));
for(i = 0 ; i < Num_particles ; i++)
{
pair_distances_structure[i] = (double*)malloc(Num_particles * sizeof(double));
}
fr_ref.natoms = Num_particles;
fr_ref.x = (rvec*)malloc(Num_particles * sizeof(rvec));
fr_ref.f = (rvec*)malloc(Num_particles * sizeof(rvec));
fr_ref_for_alignment.natoms = Num_particles;
fr_ref_for_alignment.x = (rvec*)malloc(Num_particles * sizeof(rvec));
fr_ts.natoms = Num_particles;
fr_ts.x = (rvec*)malloc(Num_particles * sizeof(rvec));
fr_start.natoms = Num_particles;
fr_start.x = (rvec*)malloc(Num_particles * sizeof(rvec));
fr_end.natoms = Num_particles;
fr_end.x = (rvec*)malloc(Num_particles * sizeof(rvec));
fr_end.f = (rvec*)malloc(Num_particles * sizeof(rvec));
/*Lei's code uses array whose indices start from 1.*/
Reference_x = (double*)malloc((Num_particles + 1) * sizeof(double));
Reference_y = (double*)malloc((Num_particles + 1) * sizeof(double));
Reference_z = (double*)malloc((Num_particles + 1) * sizeof(double));
/********************************************************************************/
sprintf(Filename, "INPUT_STRUCTURE_%d", struct_index);
Read_config_simple_3d(Num_particles, &fr_ref, Filename);
sprintf(Filename, "minimized_struct_on_cusp");
Read_config_simple_3d(Num_particles, &fr_ts, Filename);
sprintf(Filename, "REFERENCE_FOR_ALIGNMENT");
Read_config_simple_3d(Num_particles, &fr_ref_for_alignment, Filename);
for(i = 0 ; i < Num_particles ; i++)
{
Reference_x[i+1] = fr_ref_for_alignment.x[i][0];
Reference_y[i+1] = fr_ref_for_alignment.x[i][1];
Reference_z[i+1] = fr_ref_for_alignment.x[i][2];
}
//Align_two_structures_lei(Reference_x, Reference_y, Reference_z, &fr_ref);
//Align_two_structures_lei(Reference_x, Reference_y, Reference_z, &fr_ts);
Calc_pair_distances_one_structure(Num_particles, fr_ref, pair_distances_structure);
for(i = 0 ; i < Num_particles ; i++)
{
fr_start.x[i][0] = fr_ts.x[i][0];
fr_start.x[i][1] = fr_ts.x[i][1];
fr_start.x[i][2] = fr_ts.x[i][2];
}
is_step_size_adequate = 0;
while(is_step_size_adequate == 0)
{
is_step_size_adequate = Check_step_size_offset(Num_particles, force_constant, cutoff, energy_offset, pair_distances_structure, Reference_x, Reference_y, Reference_z, rmsd_pathway, delta_rmsd_zero, &fr_start, step_size);
if(is_step_size_adequate == 1)
{
printf("Step-size is %lf and it is adequate\n", step_size);
}
else
{
printf("Step-size is %lf and it is not adequate\n", step_size);
step_size = step_size * step_size_reduction_factor;
}
}
getforces_enm_offset(&fr_ref, pair_distances_structure, cutoff, force_constant, energy_offset);
energy_ref = fr_ref.U;
Num_struct_written = 0;
Slide_down_single_step_size_offset(Num_particles, force_constant, cutoff, energy_offset, pair_distances_structure, Max_num_iterations, Reference_x, Reference_y, Reference_z, struct_index, rmsd_pathway, delta_rmsd_zero, &fr_ref, &fr_start, step_size, energy_ref, energy_from_ref_tol, &Num_struct_written, &fr_end, &iteration_number_end, step_size_reduction_factor);
sprintf(Filename, "num_structures_written_%d", struct_index);
out_num = fopen(Filename, "w");
fprintf(out_num, "%d\n", Num_struct_written);
fclose(out_num);
getforces_enm_offset(&fr_end, pair_distances_structure, cutoff, force_constant, energy_offset);
rmsd_from_ref_final = Calc_rmsd_one_structure(&fr_ref, &fr_end);
sprintf(Filename, "final_struct_info_%d", struct_index);
out = fopen(Filename, "w");
fprintf(out, "Energy of the reference strucutre: %.8f\n", energy_ref);
fprintf(out, "Number of iterations: %lu\n", iteration_number_end);
fprintf(out, "Energy of final strucutre from minimization: %.8f\n", fr_end.U);
fprintf(out, "RMSD of final strucutre from minimization from the reference strucutre: %.8f\n", rmsd_from_ref_final);
fclose(out);
sprintf(Filename, "final_struct_from_min_%d", struct_index);
Write_config_simple(&fr_end, Filename);
return 0;
}
