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47 void read_eigenvectors(const char *file,int *natoms,gmx_bool *bFit,
48 rvec **xref,gmx_bool *bDMR,
49 rvec **xav,gmx_bool *bDMA,
50 int *nvec, int **eignr,
51 rvec ***eigvec,real **eigval)
62 /* read (reference (t=-1) and) average (t=0) structure */
63 status=open_trn(file,"r");
64 fread_trnheader(status,&head,&bOK);
67 fread_htrn(status,&head,box,*xav,NULL,NULL);
69 if ((head.t>=-1.1) && (head.t<=-0.9))
72 for(i=0; i<*natoms; i++)
73 copy_rvec((*xav)[i],(*xref)[i]);
74 *bDMR = (head.lambda > 0.5);
75 *bFit = (head.lambda > -0.5);
78 fprintf(stderr,"Read %smass weighted reference structure with %d atoms from %s\n", *bDMR ? "" : "non ",*natoms,file);
82 fprintf(stderr,"Eigenvectors in %s were determined without fitting\n",file);
86 fread_trnheader(status,&head,&bOK);
87 fread_htrn(status,&head,box,*xav,NULL,NULL);
94 *bDMA = (head.lambda > 0.5);
95 if ((head.t<=-0.01) || (head.t>=0.01))
97 fprintf(stderr,"WARNING: %s does not start with t=0, which should be the "
98 "average structure. This might not be a eigenvector file. "
99 "Some things might go wrong.\n",
105 "Read %smass weighted average/minimum structure with %d atoms from %s\n",
106 *bDMA ? "" : "non ",*natoms,file);
111 snew(*eignr,snew_size);
112 snew(*eigval,snew_size);
113 snew(*eigvec,snew_size);
116 while (fread_trnheader(status,&head,&bOK))
118 fread_htrn(status,&head,box,x,NULL,NULL);
119 if (*nvec >= snew_size)
122 srenew(*eignr,snew_size);
123 srenew(*eigval,snew_size);
124 srenew(*eigvec,snew_size);
127 (*eigval)[*nvec]=head.t;
129 snew((*eigvec)[*nvec],*natoms);
130 for(i=0; i<*natoms; i++)
132 copy_rvec(x[i],(*eigvec)[*nvec][i]);
137 fprintf(stderr,"Read %d eigenvectors (for %d atoms)\n\n",*nvec,*natoms);
141 void write_eigenvectors(const char *trnname,int natoms,real mat[],
142 gmx_bool bReverse,int begin,int end,
143 int WriteXref,rvec *xref,gmx_bool bDMR,
144 rvec xav[], gmx_bool bDMA,real eigval[])
156 "\nWriting %saverage structure & eigenvectors %d--%d to %s\n",
157 (WriteXref==eWXR_YES) ? "reference, " : "",
160 trnout = open_tpx(trnname,"w");
161 if (WriteXref == eWXR_YES)
163 /* misuse lambda: 0/1 mass weighted fit no/yes */
164 fwrite_trn(trnout,-1,-1,bDMR ? 1.0 : 0.0,zerobox,natoms,xref,NULL,NULL);
166 else if (WriteXref == eWXR_NOFIT)
168 /* misuse lambda: -1 no fit */
169 fwrite_trn(trnout,-1,-1,-1.0,zerobox,natoms,x,NULL,NULL);
172 /* misuse lambda: 0/1 mass weighted analysis no/yes */
173 fwrite_trn(trnout,0,0,bDMA ? 1.0 : 0.0,zerobox,natoms,xav,NULL,NULL);
175 for(i=0; i<=(end-begin); i++)
183 for (j=0; j<natoms; j++)
185 x[j][d]=mat[vec*ndim+DIM*j+d];
187 /* Store the eigenvalue in the time field */
188 fwrite_trn(trnout,begin+i,eigval[vec],0,zerobox,natoms,x,NULL,NULL);