- t_topology top;
- gmx_mtop_t *mtop = NULL;
- gmx_conect gc = NULL;
- int ePBC = -1;
- t_atoms *atoms = NULL, useatoms;
- matrix top_box;
- atom_id *index, *cindex;
- char *grpnm;
- int *frindex, nrfri;
- char *frname;
- int ifit, irms, my_clust = -1;
- atom_id *ind_fit, *ind_rms;
- char *gn_fit, *gn_rms;
- t_cluster_ndx *clust = NULL;
- t_trxstatus **clust_status = NULL;
- int *clust_status_id = NULL;
- int ntrxopen = 0;
- int *nfwritten = NULL;
- int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0;
- double **dropval;
- real tshift = 0, t0 = -1, dt = 0.001, prec;
- gmx_bool bFit, bFitXY, bPFit, bReset;
- int nfitdim;
- gmx_rmpbc_t gpbc = NULL;
- gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster;
- gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE, bDTset = FALSE;
- gmx_bool bExec, bTimeStep = FALSE, bDumpFrame = FALSE, bSetPrec, bNeedPrec;
- gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE;
- gmx_bool bSubTraj = FALSE, bDropUnder = FALSE, bDropOver = FALSE, bTrans = FALSE;
- gmx_bool bWriteFrame, bSplitHere;
- const char *top_file, *in_file, *out_file = NULL;
- char out_file2[256], *charpt;
- char *outf_base = NULL;
- const char *outf_ext = NULL;
- char top_title[256], title[256], command[256], filemode[5];
- int xdr = 0;
- gmx_bool bWarnCompact = FALSE;
- const char *warn;
- output_env_t oenv;
-
- t_filenm fnm[] = {
+ t_topology top;
+ gmx_mtop_t *mtop = NULL;
+ gmx_conect gc = NULL;
+ int ePBC = -1;
+ t_atoms *atoms = NULL, useatoms;
+ matrix top_box;
+ atom_id *index, *cindex;
+ char *grpnm;
+ int *frindex, nrfri;
+ char *frname;
+ int ifit, my_clust = -1;
+ atom_id *ind_fit;
+ char *gn_fit;
+ t_cluster_ndx *clust = NULL;
+ t_trxstatus **clust_status = NULL;
+ int *clust_status_id = NULL;
+ int ntrxopen = 0;
+ int *nfwritten = NULL;
+ int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0;
+ double **dropval;
+ real tshift = 0, t0 = -1, dt = 0.001, prec;
+ gmx_bool bFit, bPFit, bReset;
+ int nfitdim;
+ gmx_rmpbc_t gpbc = NULL;
+ gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster;
+ gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE, bDTset = FALSE;
+ gmx_bool bExec, bTimeStep = FALSE, bDumpFrame = FALSE, bSetPrec, bNeedPrec;
+ gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE;
+ gmx_bool bSubTraj = FALSE, bDropUnder = FALSE, bDropOver = FALSE, bTrans = FALSE;
+ gmx_bool bWriteFrame, bSplitHere;
+ const char *top_file, *in_file, *out_file = NULL;
+ char out_file2[256], *charpt;
+ char *outf_base = NULL;
+ const char *outf_ext = NULL;
+ char top_title[256], title[256], filemode[5];
+ gmx_bool bWarnCompact = FALSE;
+ const char *warn;
+ output_env_t oenv;
+
+ t_filenm fnm[] = {