NAMD
Public Member Functions | Public Attributes | List of all members
parm Struct Reference

#include <parm.h>

Public Member Functions

 parm ()
 
 ~parm ()
 
FILE * genopen (const char *name)
 
void genclose (FILE *)
 
char * get (int)
 
void preadln (FILE *, const char *, char *)
 
int readparm (char *)
 
int firstwat ()
 
int read_fortran_12I6 (FILE *, int *, int)
 
int moveto (FILE *, const char *)
 

Public Attributes

char ititl [81]
 
int IfBox
 
int Nmxrs
 
int IfCap
 
int Natom
 
int Ntypes
 
int Nbonh
 
int Mbona
 
int Ntheth
 
int Mtheta
 
int Nphih
 
int Mphia
 
int Nhparm
 
int Nparm
 
int Nnb
 
int Nres
 
int Nbona
 
int Ntheta
 
int Nphia
 
int Numbnd
 
int Numang
 
int Nptra
 
int Natyp
 
int Nphb
 
int Nat3
 
int Ntype2d
 
int Nttyp
 
int Nspm
 
int Iptres
 
int Nspsol
 
int Ipatm
 
int Natcap
 
char * AtomNames
 
char * ResNames
 
char * AtomSym
 
char * AtomTree
 
_REALCharges
 
_REALMasses
 
_REALRk
 
_REALReq
 
_REALTk
 
_REALTeq
 
_REALPk
 
_REALPn
 
_REALPhase
 
_REALSolty
 
_REALCn1
 
_REALCn2
 
_REALHB12
 
_REALHB6
 
_REAL Box [3]
 
_REAL Cutcap
 
_REAL Xcap
 
_REAL Ycap
 
_REAL Zcap
 
int * Iac
 
int * Iblo
 
int * Cno
 
int * Ipres
 
int * ExclAt
 
int * TreeJoin
 
int * AtomRes
 
int * BondHAt1
 
int * BondHAt2
 
int * BondHNum
 
int * BondAt1
 
int * BondAt2
 
int * BondNum
 
int * AngleHAt1
 
int * AngleHAt2
 
int * AngleHAt3
 
int * AngleHNum
 
int * AngleAt1
 
int * AngleAt2
 
int * AngleAt3
 
int * AngleNum
 
int * DihHAt1
 
int * DihHAt2
 
int * DihHAt3
 
int * DihHAt4
 
int * DihHNum
 
int * DihAt1
 
int * DihAt2
 
int * DihAt3
 
int * DihAt4
 
int * DihNum
 
int * Boundary
 
int popn
 
int data_read
 

Detailed Description

Definition at line 15 of file parm.h.

Constructor & Destructor Documentation

Ambertoppar::parm ( )

Definition at line 1124 of file parm.C.

References AngleAt1, AngleAt2, AngleAt3, AngleHAt1, AngleHAt2, AngleHAt3, AngleHNum, AngleNum, AtomNames, AtomRes, AtomSym, AtomTree, BondAt1, BondAt2, BondHAt1, BondHAt2, BondHNum, BondNum, Boundary, Charges, Cn1, Cn2, Cno, data_read, DihAt1, DihAt2, DihAt3, DihAt4, DihHAt1, DihHAt2, DihHAt3, DihHAt4, DihHNum, DihNum, ExclAt, HB12, HB6, Iac, Iblo, Ipres, Masses, Phase, Pk, Pn, Req, ResNames, Rk, Solty, Teq, Tk, and TreeJoin.

1125 {
1126  data_read = 0; // No data are read yet
1127  AtomNames = ResNames = AtomSym = AtomTree = NULL;
1128  Charges = Masses = Rk = Req = Tk = Teq = Pk = Pn = Phase = NULL;
1129  Solty = Cn1 = Cn2 = HB12 = HB6 = NULL;
1130  Iac = Iblo = Cno = Ipres = ExclAt = TreeJoin = AtomRes = NULL;
1131  BondHAt1 = BondHAt2 = BondHNum = BondAt1 = BondAt2 = NULL;
1133  AngleAt1 = AngleAt2 = AngleAt3 = AngleNum = DihHAt1 = NULL;
1134  DihHAt2 = DihHAt3 = DihHAt4 = DihHNum = DihAt1 = DihAt2 = NULL;
1135  DihAt3 = DihAt4 = DihNum = Boundary = NULL;
1136 }
_REAL * Pk
Definition: parm.h:24
int * DihHAt1
Definition: parm.h:27
_REAL * Teq
Definition: parm.h:24
char * AtomTree
Definition: parm.h:23
int * BondHNum
Definition: parm.h:27
int * DihAt3
Definition: parm.h:27
_REAL * Phase
Definition: parm.h:24
int * AngleHNum
Definition: parm.h:27
int * BondAt2
Definition: parm.h:27
int * DihHAt4
Definition: parm.h:27
_REAL * Tk
Definition: parm.h:24
int * Iblo
Definition: parm.h:27
char * ResNames
Definition: parm.h:23
int * DihAt4
Definition: parm.h:27
_REAL * Masses
Definition: parm.h:24
int * AngleHAt1
Definition: parm.h:27
_REAL * HB6
Definition: parm.h:24
_REAL * HB12
Definition: parm.h:24
int * AngleNum
Definition: parm.h:27
int * DihHNum
Definition: parm.h:27
int * Iac
Definition: parm.h:27
_REAL * Charges
Definition: parm.h:24
int * DihAt1
Definition: parm.h:27
int * BondNum
Definition: parm.h:27
int * DihNum
Definition: parm.h:27
int * BondHAt1
Definition: parm.h:27
int * AngleHAt3
Definition: parm.h:27
char * AtomNames
Definition: parm.h:23
_REAL * Cn2
Definition: parm.h:24
int * Boundary
Definition: parm.h:27
int * AtomRes
Definition: parm.h:27
int * AngleAt3
Definition: parm.h:27
int * AngleAt1
Definition: parm.h:27
char * AtomSym
Definition: parm.h:23
int * BondAt1
Definition: parm.h:27
_REAL * Rk
Definition: parm.h:24
int data_read
Definition: parm.h:34
int * DihHAt2
Definition: parm.h:27
_REAL * Cn1
Definition: parm.h:24
int * TreeJoin
Definition: parm.h:27
int * DihAt2
Definition: parm.h:27
_REAL * Req
Definition: parm.h:24
_REAL * Solty
Definition: parm.h:24
int * AngleAt2
Definition: parm.h:27
int * ExclAt
Definition: parm.h:27
int * AngleHAt2
Definition: parm.h:27
int * Ipres
Definition: parm.h:27
int * BondHAt2
Definition: parm.h:27
int * Cno
Definition: parm.h:27
_REAL * Pn
Definition: parm.h:24
int * DihHAt3
Definition: parm.h:27
Ambertoppar::~parm ( )

Definition at line 1141 of file parm.C.

References AngleAt1, AngleAt2, AngleAt3, AngleHAt1, AngleHAt2, AngleHAt3, AngleHNum, AngleNum, AtomNames, AtomRes, AtomSym, AtomTree, BondAt1, BondAt2, BondHAt1, BondHAt2, BondHNum, BondNum, Charges, Cn1, Cn2, Cno, DihAt1, DihAt2, DihAt3, DihAt4, DihHAt1, DihHAt2, DihHAt3, DihHAt4, DihHNum, DihNum, ExclAt, HB12, HB6, Iac, Iblo, Ipres, Masses, Phase, Pk, Pn, Req, ResNames, Rk, Solty, Teq, Tk, and TreeJoin.

1142 {
1143  free(AtomNames);
1144  free(Charges);
1145  free(Masses);
1146  free(Iac);
1147  free(Iblo);
1148  free(Cno);
1149  free(ResNames);
1150  free(Ipres);
1151  free(Rk);
1152  free(Req);
1153  free(Tk);
1154  free(Teq);
1155  free(Pk);
1156  free(Pn);
1157  free(Phase);
1158  free(Solty);
1159  free(Cn1);
1160  free(Cn2);
1161  free(BondHAt1);
1162  free(BondHAt2);
1163  free(BondHNum);
1164  free(BondAt1);
1165  free(BondAt2);
1166  free(BondNum);
1167  free(AngleHAt1);
1168  free(AngleHAt2);
1169  free(AngleHAt3);
1170  free(AngleHNum);
1171  free(AngleAt1);
1172  free(AngleAt2);
1173  free(AngleAt3);
1174  free(AngleNum);
1175  free(DihHAt1);
1176  free(DihHAt2);
1177  free(DihHAt3);
1178  free(DihHAt4);
1179  free(DihHNum);
1180  free(DihAt1);
1181  free(DihAt2);
1182  free(DihAt3);
1183  free(DihAt4);
1184  free(DihNum);
1185  free(ExclAt);
1186  free(HB12);
1187  free(HB6);
1188  free(AtomSym);
1189  free(AtomTree);
1190  free(TreeJoin);
1191  free(AtomRes);
1192 }
_REAL * Pk
Definition: parm.h:24
int * DihHAt1
Definition: parm.h:27
_REAL * Teq
Definition: parm.h:24
char * AtomTree
Definition: parm.h:23
int * BondHNum
Definition: parm.h:27
int * DihAt3
Definition: parm.h:27
_REAL * Phase
Definition: parm.h:24
int * AngleHNum
Definition: parm.h:27
int * BondAt2
Definition: parm.h:27
int * DihHAt4
Definition: parm.h:27
_REAL * Tk
Definition: parm.h:24
int * Iblo
Definition: parm.h:27
char * ResNames
Definition: parm.h:23
int * DihAt4
Definition: parm.h:27
_REAL * Masses
Definition: parm.h:24
int * AngleHAt1
Definition: parm.h:27
_REAL * HB6
Definition: parm.h:24
_REAL * HB12
Definition: parm.h:24
int * AngleNum
Definition: parm.h:27
int * DihHNum
Definition: parm.h:27
int * Iac
Definition: parm.h:27
_REAL * Charges
Definition: parm.h:24
int * DihAt1
Definition: parm.h:27
int * BondNum
Definition: parm.h:27
int * DihNum
Definition: parm.h:27
int * BondHAt1
Definition: parm.h:27
int * AngleHAt3
Definition: parm.h:27
char * AtomNames
Definition: parm.h:23
_REAL * Cn2
Definition: parm.h:24
int * AtomRes
Definition: parm.h:27
int * AngleAt3
Definition: parm.h:27
int * AngleAt1
Definition: parm.h:27
char * AtomSym
Definition: parm.h:23
int * BondAt1
Definition: parm.h:27
_REAL * Rk
Definition: parm.h:24
int * DihHAt2
Definition: parm.h:27
_REAL * Cn1
Definition: parm.h:24
int * TreeJoin
Definition: parm.h:27
int * DihAt2
Definition: parm.h:27
_REAL * Req
Definition: parm.h:24
_REAL * Solty
Definition: parm.h:24
int * AngleAt2
Definition: parm.h:27
int * ExclAt
Definition: parm.h:27
int * AngleHAt2
Definition: parm.h:27
int * Ipres
Definition: parm.h:27
int * BondHAt2
Definition: parm.h:27
int * Cno
Definition: parm.h:27
_REAL * Pn
Definition: parm.h:24
int * DihHAt3
Definition: parm.h:27

Member Function Documentation

int Ambertoppar::firstwat ( )

Definition at line 1096 of file parm.C.

References AtomNames, Ipres, Nres, and ResNames.

1097 {
1098  char *restr = ResNames;
1099  char *lastres = ResNames + Nres * 4 + 1;
1100  int res = 0;
1101 
1102  /*
1103  * find 1st water residue
1104  */
1105 
1106  for (; restr<lastres; restr+=4) {
1107  if (!strncmp(restr, "WAT ", 4)) {
1108  printf("first water: res = %d, atom = %d (%.4s)\n",
1109  res+1, Ipres[res],
1110  &AtomNames[Ipres[res]]);
1111 #ifndef NAMD_NO_STDOUT_FLUSH
1112  fflush(stdout);
1113 #endif
1114  return(Ipres[res]-1);
1115  }
1116  res++;
1117  }
1118  return(0);
1119 }
char * ResNames
Definition: parm.h:23
char * AtomNames
Definition: parm.h:23
int Nres
Definition: parm.h:17
int * Ipres
Definition: parm.h:27
void Ambertoppar::genclose ( FILE *  fileptr)

Definition at line 86 of file parm.C.

References Fclose().

Referenced by readparm().

87 {
88  Fclose(fileptr);
89 }
int Fclose(FILE *fout)
Definition: common.C:359
FILE * Ambertoppar::genopen ( const char *  name)

Definition at line 72 of file parm.C.

References Fopen().

Referenced by readparm().

73 {
74  return(Fopen(name,"r"));
75 }
FILE * Fopen(const char *filename, const char *mode)
Definition: common.C:265
char * Ambertoppar::get ( int  size)

Definition at line 96 of file parm.C.

References NAMD_die().

97 {
98  char *ptr;
99 
100 #ifdef DEBUG
101  printf("malloc %d\n", size);
102 #ifndef NAMD_NO_STDOUT_FLUSH
103  fflush(stdout);
104 #endif
105 #endif
106  if (size ==0)
107  return((char *) NULL);
108 
109  if ((ptr = (char *) malloc((unsigned)size)) == NULL) {
110  printf("malloc %d", size);
111 #ifndef NAMD_NO_STDOUT_FLUSH
112  fflush(stdout);
113 #endif
114  NAMD_die("Memory allocation error in Ambertoppar::get()");
115  }
116  return(ptr);
117 }
void NAMD_die(const char *err_msg)
Definition: common.C:83
int Ambertoppar::moveto ( FILE *  fp,
const char *  label 
)

Definition at line 1226 of file parm.C.

References endi(), iout, iWARN(), and preadln().

Referenced by readparm().

1227 {
1228  char s[76],buf[81];
1229 
1230  while ( 1 ) {
1231  // Find the string "%FLAG"
1232  do preadln(fp, "parm file", buf);
1233  while (strncmp(buf,"%FLAG",5));
1234 
1235  // See if the label is what we expected
1236  sscanf(buf+5,"%s",s);
1237  if (strcasecmp(s,label))
1238  iout << iWARN << "Skipping " << s << " in parm file while seeking " << label << ".\n" << endi;
1239  else
1240  break;
1241  }
1242 
1243  // The next line should begin with "%FORMAT"
1244  preadln(fp, "parm file", buf);
1245  if (strncmp(buf,"%FORMAT",7))
1246  return 0;
1247 
1248  return 1;
1249 }
void preadln(FILE *, const char *, char *)
Definition: parm.C:123
std::ostream & iWARN(std::ostream &s)
Definition: InfoStream.C:108
#define iout
Definition: InfoStream.h:87
infostream & endi(infostream &s)
Definition: InfoStream.C:38
void Ambertoppar::preadln ( FILE *  file,
const char *  name,
char *  string 
)

Definition at line 123 of file parm.C.

References NAMD_die().

Referenced by moveto(), and readparm().

124 {
125  int i, j;
126 
127  for (i=0; i<81; i++) {
128  if ((j = getc(file)) == EOF) {
129  NAMD_die("Unexpected EOF in Amber parm file");
130  printf("Error: unexpected EOF in %s\n", name);
131  }
132  string[i] = (char) j;
133  if (string[i] == '\n') {
134  break;
135  }
136  }
137  if (i == 80 && string[i] != '\n') {
138  NAMD_die("Line too long in Amber parm file");
139  printf("Error: line too long in %s:\n%.80s", name, string);
140  }
141 }
void NAMD_die(const char *err_msg)
Definition: common.C:83
int Ambertoppar::read_fortran_12I6 ( FILE *  fp,
int *  data,
int  count 
)

Definition at line 1201 of file parm.C.

References readtoeoln().

Referenced by readparm().

1202 {
1203  int i,j;
1204  char buf[7];
1205 
1206  for (i=0; i<count; ++i)
1207  { for (j=0; j<6; ++j)
1208  { buf[j]=getc(fp);
1209  if (buf[j]=='\n' || buf[j]=='\0' || buf[j]==EOF)
1210  return 0;
1211  }
1212  buf[6] = '\0';
1213  if (sscanf(buf,"%d",data+i) != 1)
1214  return 0;
1215  if (i%12==11 && i<count-1)
1216  readtoeoln(fp);
1217  }
1218 
1219  return 1;
1220 }
static int readtoeoln(FILE *f)
Definition: parm.C:51
int Ambertoppar::readparm ( char *  name)

Definition at line 151 of file parm.C.

References _REAL, AngleAt1, AngleAt2, AngleAt3, AngleHAt1, AngleHAt2, AngleHAt3, AngleHNum, AngleNum, AtomNames, AtomRes, AtomSym, AtomTree, BondAt1, BondAt2, BondHAt1, BondHAt2, BondHNum, BondNum, Boundary, Charges, Cn1, Cn2, Cno, Cutcap, data_read, debug, DihAt1, DihAt2, DihAt3, DihAt4, DihHAt1, DihHAt2, DihHAt3, DihHAt4, DihHNum, DihNum, endi(), ExclAt, genclose(), genopen(), HB12, HB6, Iac, Iblo, IfBox, IfCap, iout, Ipatm, Ipres, Iptres, ititl, Masses, Mbona, moveto(), Mphia, Mtheta, Nat3, Natcap, Natom, Natyp, Nbona, Nbonh, Nhparm, Nmxrs, Nnb, Nparm, Nphb, Nphia, Nphih, Nptra, Nres, Nspm, Nspsol, Ntheta, Ntheth, Nttyp, Ntype2d, Ntypes, Numang, Numbnd, Phase, Pk, Pn, preadln(), read_fortran_12I6(), readtoeoln(), Req, ResNames, Rk, Solty, Teq, Tk, TreeJoin, Xcap, Ycap, and Zcap.

Referenced by NamdState::loadStructure().

152 {
153  _REAL *H;
154  int i, idum, res, ifpert;
155  int *buffer, amber7_format;
156  FILE *file;
157 
158  if (data_read)
159  { iout << "Duplicate parm data in one object!\n" << endi;
160  return(0);
161  }
162 
163 // printf("Reading parm file (%s)\n", name);
164  iout << "Reading parm file (" << name << ") ...\n" << endi;
165 
166 // if ((file = genopen(name, "parm")) == NULL)
167  if ((file = genopen(name)) == NULL)
168  return(0);
169 
170  /* READ TITLE */
171 
172  preadln(file, name, ititl);
173 // "ititle" doesn't guarantee to have '\0' (as the end of a string),
174 // so the following is disabled in order to avoid strange output
175 // printf("%s title:\n%s", name, ititl);
176 
177  // Check whether it's in AMBER 7 format or in old format
178 
179  if (strncmp(ititl,"%VERSION",8))
180  amber7_format = 0; // old format
181  else
182  { amber7_format = 1; // AMBER 7 format
183  iout << "PARM file in AMBER 7 format\n" << endi;
184  if (!moveto(file,"TITLE"))
185  { genclose(file);
186  return 0;
187  }
188  preadln(file, name, ititl);
189  }
190 
191  /* READ CONTROL INTEGERS */
192 
193  if (amber7_format)
194  { if (!moveto(file,"POINTERS"))
195  { genclose(file);
196  return 0;
197  }
198 // fscanf(file, f9118,
199  fscanf(file, "%d%d%d%d%d%d%d%d%d%d%d%d",
200  &Natom, &Ntypes, &Nbonh, &Mbona,
201  &Ntheth, &Mtheta, &Nphih, &Mphia,
202  &Nhparm, &Nparm, &Nnb, &Nres);
203 
204 // fscanf(file, f9118,
205  fscanf(file, "%d%d%d%d%d%d%d%d%d%d%d%d",
206  &Nbona, &Ntheta, &Nphia, &Numbnd,
207  &Numang, &Nptra, &Natyp, &Nphb,
208  &ifpert, &idum, &idum, &idum);
209 
210  fscanf(file, " %d %d %d %d %d %d",
211  &idum, &idum,&idum,&IfBox,&Nmxrs,&IfCap);
212  }
213  else
214  { buffer = new int[30];
215  if (!read_fortran_12I6(file,buffer,30))
216  { genclose(file);
217  return 0;
218  }
219  Natom = buffer[0];
220  Ntypes = buffer[1];
221  Nbonh = buffer[2];
222  Mbona = buffer[3];
223  Ntheth = buffer[4];
224  Mtheta = buffer[5];
225  Nphih = buffer[6];
226  Mphia = buffer[7];
227  Nhparm = buffer[8];
228  Nparm = buffer[9];
229  Nnb = buffer[10];
230  Nres = buffer[11];
231  Nbona = buffer[12];
232  Ntheta = buffer[13];
233  Nphia = buffer[14];
234  Numbnd = buffer[15];
235  Numang = buffer[16];
236  Nptra = buffer[17];
237  Natyp = buffer[18];
238  Nphb = buffer[19];
239  ifpert = buffer[20];
240  IfBox = buffer[27];
241  Nmxrs = buffer[28];
242  IfCap = buffer[29];
243  delete [] buffer;
244 // skipeoln(file);
245  readtoeoln(file);
246  }
247 
248  if (ifpert) {
249  printf("not equipped to read perturbation prmtop\n");
250  return(0);
251  }
252 
253  /* ALLOCATE MEMORY */
254 
255  Nat3 = 3 * Natom;
256  Ntype2d = Ntypes * Ntypes;
257  Nttyp = Ntypes*(Ntypes+1)/2;
258 
259  /*
260  * get most of the indirect stuff; some extra allowed for char arrays
261  */
262 
263  AtomNames = (char *) get(4*Natom+81);
264  Charges = (_REAL *) get(sizeof(_REAL)*Natom);
265  Masses = (_REAL *) get(sizeof(_REAL)*Natom);
266  Iac = (int *) get(sizeof(int)*Natom);
267  Iblo = (int *) get(sizeof(int)*Natom);
268  Cno = (int *) get(sizeof(int)* Ntype2d);
269  ResNames = (char *) get(4* Nres+81);
270  Ipres = (int *) get(sizeof(int)*( Nres+1));
271  Rk = (_REAL *) get(sizeof(_REAL)* Numbnd);
272  Req = (_REAL *) get(sizeof(_REAL)* Numbnd);
273  Tk = (_REAL *) get(sizeof(_REAL)* Numang);
274  Teq = (_REAL *) get(sizeof(_REAL)* Numang);
275  Pk = (_REAL *) get(sizeof(_REAL)* Nptra);
276  Pn = (_REAL *) get(sizeof(_REAL)* Nptra);
277  Phase = (_REAL *) get(sizeof(_REAL)* Nptra);
278  Solty = (_REAL *) get(sizeof(_REAL)* Natyp);
279  Cn1 = (_REAL *) get(sizeof(_REAL)* Nttyp);
280  Cn2 = (_REAL *) get(sizeof(_REAL)* Nttyp);
281  BondHAt1 = (int *) get(sizeof(int)* Nbonh);
282  BondHAt2 = (int *) get(sizeof(int)* Nbonh);
283  BondHNum = (int *) get(sizeof(int)* Nbonh);
284  BondAt1 = (int *) get(sizeof(int)* Nbona);
285  BondAt2 = (int *) get(sizeof(int)* Nbona);
286  BondNum = (int *) get(sizeof(int)* Nbona);
287  AngleHAt1 = (int *) get(sizeof(int)* Ntheth);
288  AngleHAt2 = (int *) get(sizeof(int)* Ntheth);
289  AngleHAt3 = (int *) get(sizeof(int)* Ntheth);
290  AngleHNum = (int *) get(sizeof(int)* Ntheth);
291  AngleAt1 = (int *) get(sizeof(int)* Ntheta);
292  AngleAt2 = (int *) get(sizeof(int)*Ntheta);
293  AngleAt3 = (int *) get(sizeof(int)*Ntheta);
294  AngleNum = (int *) get(sizeof(int)*Ntheta);
295  DihHAt1 = (int *) get(sizeof(int)*Nphih);
296  DihHAt2 = (int *) get(sizeof(int)*Nphih);
297  DihHAt3 = (int *) get(sizeof(int)*Nphih);
298  DihHAt4 = (int *) get(sizeof(int)*Nphih);
299  DihHNum = (int *) get(sizeof(int)*Nphih);
300  DihAt1 = (int *) get(sizeof(int)*Nphia);
301  DihAt2 = (int *) get(sizeof(int)*Nphia);
302  DihAt3 = (int *) get(sizeof(int)*Nphia);
303  DihAt4 = (int *) get(sizeof(int)*Nphia);
304  DihNum = (int *) get(sizeof(int)*Nphia);
305  ExclAt = (int *) get(sizeof(int)*Nnb);
306  HB12 = (_REAL *) get(sizeof(_REAL)*Nphb);
307  HB6 = (_REAL *) get(sizeof(_REAL)*Nphb);
308  AtomSym = (char *) get(4*Natom+81);
309  AtomTree = (char *) get(4*Natom+81);
310  TreeJoin = (int *) get(sizeof(int)*Natom);
311  AtomRes = (int *) get(sizeof(int)*Natom);
312 
313  /*
314  * READ ATOM NAMES -IH(M04)
315  */
316 
317  if (amber7_format)
318  if (!moveto(file,"ATOM_NAME"))
319  { genclose(file);
320  return 0;
321  }
322  for (i=0; i<(Natom/20 + (Natom%20 ? 1 : 0)); i++)
323  preadln(file, "", &AtomNames[i*80]);
324 
325  /*
326  * READ ATOM CHARGES -X(L15)
327  * (pre-multiplied by an energy factor of 18.2223 == sqrt(332)
328  * for faster force field calculations)
329  */
330 
331  if (amber7_format)
332  if (!moveto(file,"CHARGE"))
333  { genclose(file);
334  return 0;
335  }
336  for (i=0; i<Natom; i++)
337 #ifdef DOUBLE
338  fscanf(file, " %lf", &Charges[i]);
339 #else
340  fscanf(file, " %f", &Charges[i]);
341 #endif
342 // skipeoln(file);
343  readtoeoln(file);
344 
345  /*
346  * READ ATOM MASSES -X(L20)
347  */
348 
349  if (amber7_format)
350  if (!moveto(file,"MASS"))
351  { genclose(file);
352  return 0;
353  }
354  for (i=0; i<Natom; i++)
355 #ifdef DOUBLE
356  fscanf(file, " %le", &Masses[i]);
357 #else
358  fscanf(file, " %e", &Masses[i]);
359 #endif
360 // skipeoln(file);
361  readtoeoln(file);
362 
363  /*
364  * READ ATOM L-J TYPES -IX(I04)
365  */
366 
367  if (amber7_format)
368  { if (!moveto(file,"ATOM_TYPE_INDEX"))
369  { genclose(file);
370  return 0;
371  }
372  for (i=0; i<Natom; i++)
373  fscanf(file, " %d", &Iac[i]);
374  }
375  else
376  { if (!read_fortran_12I6(file,Iac,Natom))
377  { genclose(file);
378  return 0;
379  }
380 // skipeoln(file);
381  readtoeoln(file);
382  }
383 
384  /*
385  * READ ATOM INDEX TO 1st IN EXCLUDED ATOM LIST "NATEX" -IX(I08)
386  */
387 
388  if (amber7_format)
389  { if (!moveto(file,"NUMBER_EXCLUDED_ATOMS"))
390  { genclose(file);
391  return 0;
392  }
393  for (i=0; i<Natom; i++)
394  fscanf(file, " %d", &Iblo[i]);
395  }
396  else
397  { if (!read_fortran_12I6(file,Iblo,Natom))
398  { genclose(file);
399  return 0;
400  }
401 // skipeoln(file);
402  readtoeoln(file);
403  }
404 
405  /*
406  * READ TYPE INDEX TO N-B TYPE -IX(I06)
407  */
408 
409  if (amber7_format)
410  { if (!moveto(file,"NONBONDED_PARM_INDEX"))
411  { genclose(file);
412  return 0;
413  }
414  for (i=0; i<Ntype2d; i++)
415  fscanf(file, " %d", &Cno[i]);
416  }
417  else
418  { if (!read_fortran_12I6(file,Cno,Ntype2d))
419  { genclose(file);
420  return 0;
421  }
422 // skipeoln(file);
423  readtoeoln(file);
424  }
425 
426  /*
427  * READ RES NAMES (4 chars each, 4th blank) -IH(M02)
428  */
429 
430  if (amber7_format)
431  if (!moveto(file,"RESIDUE_LABEL"))
432  { genclose(file);
433  return 0;
434  }
435  for (i=0; i<(Nres/20 + (Nres%20 ? 1 : 0)); i++)
436  preadln(file, "", &ResNames[i*80]);
437 
438  /*
439  * READ RES POINTERS TO 1st ATOM -IX(I02)
440  */
441 
442  if (amber7_format)
443  { if (!moveto(file,"RESIDUE_POINTER"))
444  { genclose(file);
445  return 0;
446  }
447  for (i=0; i<Nres; i++)
448  fscanf(file, " %d", &Ipres[i]);
449  }
450  else
451  { if (!read_fortran_12I6(file,Ipres,Nres))
452  { genclose(file);
453  return 0;
454  }
455 // skipeoln(file);
456  readtoeoln(file);
457  }
458  Ipres[Nres] = Natom + 1;
459 
460  /*
461  * READ BOND FORCE CONSTANTS -RK()
462  */
463 
464  if (amber7_format)
465  if (!moveto(file,"BOND_FORCE_CONSTANT"))
466  { genclose(file);
467  return 0;
468  }
469  for (i=0; i< Numbnd; i++)
470 #ifdef DOUBLE
471  fscanf(file, " %lf", &Rk[i]);
472 #else
473  fscanf(file, " %f", &Rk[i]);
474 #endif
475 // skipeoln(file);
476  readtoeoln(file);
477 
478  /*
479  * READ BOND LENGTH OF MINIMUM ENERGY -REQ()
480  */
481 
482  if (amber7_format)
483  if (!moveto(file,"BOND_EQUIL_VALUE"))
484  { genclose(file);
485  return 0;
486  }
487  for (i=0; i< Numbnd; i++)
488 #ifdef DOUBLE
489  fscanf(file, " %lf", &Req[i]);
490 #else
491  fscanf(file, " %f", &Req[i]);
492 #endif
493 // skipeoln(file);
494  readtoeoln(file);
495 
496  /*
497  * READ BOND ANGLE FORCE CONSTANTS (following Rk nomen) -TK()
498  */
499 
500  if (amber7_format)
501  if (!moveto(file,"ANGLE_FORCE_CONSTANT"))
502  { genclose(file);
503  return 0;
504  }
505  for (i=0; i< Numang; i++)
506 #ifdef DOUBLE
507  fscanf(file, " %lf", &Tk[i]);
508 #else
509  fscanf(file, " %f", &Tk[i]);
510 #endif
511 // skipeoln(file);
512  readtoeoln(file);
513 
514  /*
515  * READ BOND ANGLE OF MINIMUM ENERGY (following Req nomen) -TEQ()
516  */
517 
518  if (amber7_format)
519  if (!moveto(file,"ANGLE_EQUIL_VALUE"))
520  { genclose(file);
521  return 0;
522  }
523  for (i=0; i< Numang; i++)
524 #ifdef DOUBLE
525  fscanf(file, " %lf", &Teq[i]);
526 #else
527  fscanf(file, " %f", &Teq[i]);
528 #endif
529 // skipeoln(file);
530  readtoeoln(file);
531 
532  /*
533  * READ DIHEDRAL PEAK MAGNITUDE -PK()
534  */
535 
536  if (amber7_format)
537  if (!moveto(file,"DIHEDRAL_FORCE_CONSTANT"))
538  { genclose(file);
539  return 0;
540  }
541  for (i=0; i< Nptra; i++)
542 #ifdef DOUBLE
543  fscanf(file, " %lf", &Pk[i]);
544 #else
545  fscanf(file, " %f", &Pk[i]);
546 #endif
547 // skipeoln(file);
548  readtoeoln(file);
549 
550  /*
551  * READ DIHEDRAL PERIODICITY -PN()
552  */
553 
554  if (amber7_format)
555  if (!moveto(file,"DIHEDRAL_PERIODICITY"))
556  { genclose(file);
557  return 0;
558  }
559  for (i=0; i< Nptra; i++)
560 #ifdef DOUBLE
561  fscanf(file, " %lf", &Pn[i]);
562 #else
563  fscanf(file, " %f", &Pn[i]);
564 #endif
565 // skipeoln(file);
566  readtoeoln(file);
567 
568  /*
569  * READ DIHEDRAL PHASE -PHASE()
570  */
571 
572  if (amber7_format)
573  if (!moveto(file,"DIHEDRAL_PHASE"))
574  { genclose(file);
575  return 0;
576  }
577  for (i=0; i< Nptra; i++)
578 #ifdef DOUBLE
579  fscanf(file, " %lf", &Phase[i]);
580 #else
581  fscanf(file, " %f", &Phase[i]);
582 #endif
583 // skipeoln(file);
584  readtoeoln(file);
585 
586  /*
587  * ?? "RESERVED" -SOLTY()
588  */
589 
590  if (amber7_format)
591  if (!moveto(file,"SOLTY"))
592  { genclose(file);
593  return 0;
594  }
595  for (i=0; i< Natyp; i++)
596 #ifdef DOUBLE
597  fscanf(file, " %lf", &Solty[i]);
598 #else
599  fscanf(file, " %f", &Solty[i]);
600 #endif
601 // skipeoln(file);
602  readtoeoln(file);
603 
604  /*
605  * READ L-J R**12 FOR ALL PAIRS OF ATOM TYPES -CN1()
606  * (SHOULD BE 0 WHERE H-BONDS)
607  */
608 
609  if (amber7_format)
610  if (!moveto(file,"LENNARD_JONES_ACOEF"))
611  { genclose(file);
612  return 0;
613  }
614  for (i=0; i< Nttyp; i++)
615 #ifdef DOUBLE
616  fscanf(file, " %lf", &Cn1[i]);
617 #else
618  fscanf(file, " %f", &Cn1[i]);
619 #endif
620 // skipeoln(file);
621  readtoeoln(file);
622 
623  /*
624  * READ L-J R**6 FOR ALL PAIRS OF ATOM TYPES -CN2()
625  * (SHOULD BE 0 WHERE H-BONDS)
626  */
627 
628  if (amber7_format)
629  if (!moveto(file,"LENNARD_JONES_BCOEF"))
630  { genclose(file);
631  return 0;
632  }
633  for (i=0; i< Nttyp; i++)
634 #ifdef DOUBLE
635  fscanf(file, " %lf", &Cn2[i]);
636 #else
637  fscanf(file, " %f", &Cn2[i]);
638 #endif
639 // skipeoln(file);
640  readtoeoln(file);
641 
642  /*
643  * READ COVALENT BOND W/ HYDROGEN (3*(atnum-1)):
644  * IBH = ATOM1 -IX(I12)
645  * JBH = ATOM2 -IX(I14)
646  * ICBH = BOND ARRAY PTR -IX(I16)
647  */
648 
649  if (amber7_format)
650  { if (!moveto(file,"BONDS_INC_HYDROGEN"))
651  { genclose(file);
652  return 0;
653  }
654  for (i=0; i<Nbonh; i++)
655  fscanf(file, " %d %d %d",
656  &BondHAt1[i], &BondHAt2[i], &BondHNum[i]);
657  }
658  else
659  { buffer = new int[3*Nbonh];
660  if (!read_fortran_12I6(file,buffer,3*Nbonh))
661  { genclose(file);
662  return 0;
663  }
664  for (i=0; i<Nbonh; i++)
665  { BondHAt1[i] = buffer[3*i];
666  BondHAt2[i] = buffer[3*i+1];
667  BondHNum[i] = buffer[3*i+2];
668  }
669  delete [] buffer;
670 // skipeoln(file);
671  readtoeoln(file);
672  }
673 
674  /*
675  * READ COVALENT BOND W/OUT HYDROGEN (3*(atnum-1)):
676  * IB = ATOM1 -IX(I18)
677  * JB = ATOM2 -IX(I20)
678  * ICB = BOND ARRAY PTR -IX(I22)
679  */
680 
681  if (amber7_format)
682  { if (!moveto(file,"BONDS_WITHOUT_HYDROGEN"))
683  { genclose(file);
684  return 0;
685  }
686  for (i=0; i<Nbona; i++)
687  fscanf(file, " %d %d %d",
688  &BondAt1[i], &BondAt2[i], &BondNum[i]);
689  }
690  else
691  { buffer = new int[3*Nbona];
692  if (!read_fortran_12I6(file,buffer,3*Nbona))
693  { genclose(file);
694  return 0;
695  }
696  for (i=0; i<Nbona; i++)
697  { BondAt1[i] = buffer[3*i];
698  BondAt2[i] = buffer[3*i+1];
699  BondNum[i] = buffer[3*i+2];
700  }
701  delete [] buffer;
702 // skipeoln(file);
703  readtoeoln(file);
704  }
705 
706  /*
707  * READ ANGLE W/ HYDROGEN:
708  * ITH = ATOM1 -IX(I24)
709  * JTH = ATOM2 -IX(I26)
710  * KTH = ATOM3 -IX(I28)
711  * ICTH = ANGLE ARRAY PTR -IX(I30)
712  */
713 
714  if (amber7_format)
715  { if (!moveto(file,"ANGLES_INC_HYDROGEN"))
716  { genclose(file);
717  return 0;
718  }
719  for (i=0; i<Ntheth; i++)
720  fscanf(file, " %d %d %d %d",
721  &AngleHAt1[i], &AngleHAt2[i],
722  &AngleHAt3[i], &AngleHNum[i]);
723  }
724  else
725  { buffer = new int[4*Ntheth];
726  if (!read_fortran_12I6(file,buffer,4*Ntheth))
727  { genclose(file);
728  return 0;
729  }
730  for (i=0; i<Ntheth; i++)
731  { AngleHAt1[i] = buffer[4*i];
732  AngleHAt2[i] = buffer[4*i+1];
733  AngleHAt3[i] = buffer[4*i+2];
734  AngleHNum[i] = buffer[4*i+3];
735  }
736  delete [] buffer;
737 // skipeoln(file);
738  readtoeoln(file);
739  }
740 
741  /*
742  * READ ANGLE W/OUT HYDROGEN:
743  * IT = ATOM1 -IX(I32)
744  * JT = ATOM2 -IX(I34)
745  * KT = ATOM3 -IX(I36)
746  * ICT = ANGLE ARRAY PTR -IX(I38)
747  */
748 
749  if (amber7_format)
750  { if (!moveto(file,"ANGLES_WITHOUT_HYDROGEN"))
751  { genclose(file);
752  return 0;
753  }
754  for (i=0; i<Ntheta; i++)
755  fscanf(file, " %d %d %d %d",
756  &AngleAt1[i], &AngleAt2[i],
757  &AngleAt3[i], &AngleNum[i]);
758  }
759  else
760  { buffer = new int[4*Ntheta];
761  if (!read_fortran_12I6(file,buffer,4*Ntheta))
762  { genclose(file);
763  return 0;
764  }
765  for (i=0; i<Ntheta; i++)
766  { AngleAt1[i] = buffer[4*i];
767  AngleAt2[i] = buffer[4*i+1];
768  AngleAt3[i] = buffer[4*i+2];
769  AngleNum[i] = buffer[4*i+3];
770  }
771  delete [] buffer;
772 // skipeoln(file);
773  readtoeoln(file);
774  }
775 
776  /*
777  * READ DIHEDRAL W/ HYDROGEN:
778  * ITH = ATOM1 -IX(40)
779  * JTH = ATOM2 -IX(42)
780  * KTH = ATOM3 -IX(44)
781  * LTH = ATOM4 -IX(46)
782  * ICTH = DIHEDRAL ARRAY PTR -IX(48)
783  */
784 
785  if (amber7_format)
786  { if (!moveto(file,"DIHEDRALS_INC_HYDROGEN"))
787  { genclose(file);
788  return 0;
789  }
790  for (i=0; i<Nphih; i++)
791  fscanf(file, " %d %d %d %d %d",
792  &DihHAt1[i], &DihHAt2[i], &DihHAt3[i],
793  &DihHAt4[i], &DihHNum[i]);
794  }
795  else
796  { buffer = new int[5*Nphih];
797  if (!read_fortran_12I6(file,buffer,5*Nphih))
798  { genclose(file);
799  return 0;
800  }
801  for (i=0; i<Nphih; i++)
802  { DihHAt1[i] = buffer[5*i];
803  DihHAt2[i] = buffer[5*i+1];
804  DihHAt3[i] = buffer[5*i+2];
805  DihHAt4[i] = buffer[5*i+3];
806  DihHNum[i] = buffer[5*i+4];
807  }
808  delete [] buffer;
809 // skipeoln(file);
810  readtoeoln(file);
811  }
812 
813  /*
814  * READ DIHEDRAL W/OUT HYDROGEN:
815  * IT = ATOM1
816  * JT = ATOM2
817  * KT = ATOM3
818  * LT = ATOM4
819  * ICT = DIHEDRAL ARRAY PTR
820  */
821 
822  if (amber7_format)
823  { if (!moveto(file,"DIHEDRALS_WITHOUT_HYDROGEN"))
824  { genclose(file);
825  return 0;
826  }
827  for (i=0; i<Nphia; i++)
828  fscanf(file, " %d %d %d %d %d",
829  &DihAt1[i], &DihAt2[i], &DihAt3[i],
830  &DihAt4[i], &DihNum[i]);
831  }
832  else
833  { buffer = new int[5*Nphia];
834  if (!read_fortran_12I6(file,buffer,5*Nphia))
835  { genclose(file);
836  return 0;
837  }
838  for (i=0; i<Nphia; i++) {
839  DihAt1[i] = buffer[5*i];
840  DihAt2[i] = buffer[5*i+1];
841  DihAt3[i] = buffer[5*i+2];
842  DihAt4[i] = buffer[5*i+3];
843  DihNum[i] = buffer[5*i+4];
844  }
845  delete [] buffer;
846 // skipeoln(file);
847  readtoeoln(file);
848  }
849 
850  /*
851  * READ EXCLUDED ATOM LIST -IX(I10)
852  */
853 
854  if (amber7_format)
855  { if (!moveto(file,"EXCLUDED_ATOMS_LIST"))
856  { genclose(file);
857  return 0;
858  }
859  for (i=0; i<Nnb; i++)
860  fscanf(file, " %d", &ExclAt[i]);
861  }
862  else
863  { if (!read_fortran_12I6(file,ExclAt,Nnb))
864  { genclose(file);
865  return 0;
866  }
867 // skipeoln(file);
868  readtoeoln(file);
869  }
870 
871  /*
872  * READ H-BOND R**12 TERM FOR ALL N-B TYPES -ASOL()
873  */
874 
875  if (amber7_format)
876  if (!moveto(file,"HBOND_ACOEF"))
877  { genclose(file);
878  return 0;
879  }
880  for (i=0; i<Nphb; i++)
881 #ifdef DOUBLE
882  fscanf(file, " %lf", &HB12[i]);
883 #else
884  fscanf(file, " %f", &HB12[i]);
885 #endif
886 // skipeoln(file);
887  readtoeoln(file);
888 
889  /*
890  * READ H-BOND R**6 TERM FOR ALL N-B TYPES -BSOL()
891  */
892 
893  if (amber7_format)
894  if (!moveto(file,"HBOND_BCOEF"))
895  { genclose(file);
896  return 0;
897  }
898  for (i=0; i<Nphb; i++)
899 #ifdef DOUBLE
900  fscanf(file, " %lf", &HB6[i]);
901 #else
902  fscanf(file, " %f", &HB6[i]);
903 #endif
904 // skipeoln(file);
905  readtoeoln(file);
906 
907  /*
908  * READ H-BOND CUTOFF (NOT USED) ?? -HBCUT()
909  */
910 
911  if (amber7_format)
912  if (!moveto(file,"HBCUT"))
913  { genclose(file);
914  return 0;
915  }
916  H = (_REAL *) get(Nphb * sizeof(_REAL));
917  for (i=0; i<Nphb; i++)
918 #ifdef DOUBLE
919  fscanf(file, " %lf", &H[i]);
920 #else
921  fscanf(file, " %f", &H[i]);
922 #endif
923  free((char *)H);
924 
925 // skipeoln(file);
926  readtoeoln(file);
927 
928  /*
929  * READ ATOM SYMBOLS (FOR ANALYSIS PROGS) -IH(M06)
930  */
931 
932  if (amber7_format)
933  if (!moveto(file,"AMBER_ATOM_TYPE"))
934  { genclose(file);
935  return 0;
936  }
937  for (i=0; i<(Natom/20 + (Natom%20 ? 1 : 0)); i++)
938  preadln(file, "", &AtomSym[i*80]);
939 
940  /*
941  * READ TREE SYMBOLS (FOR ANALYSIS PROGS) -IH(M08)
942  */
943 
944  if (amber7_format)
945  if (!moveto(file,"TREE_CHAIN_CLASSIFICATION"))
946  { genclose(file);
947  return 0;
948  }
949  for (i=0; i<(Natom/20 + (Natom%20 ? 1 : 0)); i++)
950  preadln(file, "", &AtomTree[i*80]);
951 
952  /*
953  * READ TREE JOIN INFO (FOR ANALYSIS PROGS) -IX(I64)
954  */
955 
956  if (amber7_format)
957  { if (!moveto(file,"JOIN_ARRAY"))
958  { genclose(file);
959  return 0;
960  }
961  for (i=0; i<Natom; i++)
962  fscanf(file, " %d", &TreeJoin[i]);
963  }
964  else
965  { if (!read_fortran_12I6(file,TreeJoin,Natom))
966  { genclose(file);
967  return 0;
968  }
969 // skipeoln(file);
970  readtoeoln(file);
971  }
972 
973  /*
974  * READ PER-ATOM RES NUMBER -IX(I66)
975  * NOTE: this appears to be something entirely different
976  * NOTE: overwriting this with correct PER-ATOM RES NUMBERs
977  */
978 
979  if (amber7_format)
980  { if (!moveto(file,"IROTAT"))
981  { genclose(file);
982  return 0;
983  }
984  for (i=0; i<Natom; i++)
985  fscanf(file, " %d", &AtomRes[i]);
986  }
987  else
988  if (!read_fortran_12I6(file,AtomRes,Natom))
989  { genclose(file);
990  return 0;
991  }
992  res = 0;
993  for (i=0; i<Natom; i++) {
994  if (i+1 == Ipres[res+1]) /* atom is 1st of next res */
995  res++;
996  AtomRes[i] = res;
997  }
998 
999  /*
1000  * BOUNDARY CONDITION STUFF
1001  */
1002 
1003  if (!IfBox) {
1004  Nspm = 1;
1005  Boundary = (int *) get(sizeof(int)*Nspm);
1006  Boundary[0] = Natom;
1007  } else {
1008  if (amber7_format)
1009  { if (!moveto(file,"SOLVENT_POINTERS"))
1010  { genclose(file);
1011  return 0;
1012  }
1013  fscanf(file, " %d %d %d", &Iptres, &Nspm,
1014  &Nspsol);
1015  }
1016  else
1017  {
1018 // skipeoln(file);
1019  readtoeoln(file);
1020  buffer = new int[3];
1021  if (!read_fortran_12I6(file,buffer,3))
1022  { genclose(file);
1023  return 0;
1024  }
1025  Iptres = buffer[0];
1026  Nspm = buffer[1];
1027  Nspsol = buffer[2];
1028  delete [] buffer;
1029 // skipeoln(file);
1030  readtoeoln(file);
1031  }
1032  Boundary = (int *) get(sizeof(int)*Nspm);
1033  if (amber7_format)
1034  { if (!moveto(file,"ATOMS_PER_MOLECULE"))
1035  { genclose(file);
1036  return 0;
1037  }
1038  for (i=0; i<Nspm; i++)
1039  fscanf(file, " %d", &Boundary[i]);
1040  }
1041  else
1042  { if (!read_fortran_12I6(file,Boundary,Nspm))
1043  { genclose(file);
1044  return 0;
1045  }
1046 // skipeoln(file);
1047  readtoeoln(file);
1048  }
1049  if (amber7_format)
1050  if (!moveto(file,"BOX_DIMENSIONS"))
1051  { genclose(file);
1052  return 0;
1053  }
1054 #ifdef DOUBLE
1055  fscanf(file, " %lf %lf %lf",
1056 #else
1057  fscanf(file, " %f %f %f",
1058 #endif
1059  &Box[0], &Box[1], &Box[2]);
1060 // skipeoln(file);
1061  readtoeoln(file);
1062  if (Iptres)
1063  Ipatm = Ipres[Iptres] - 1;
1064  /* IF(IPTRES.GT.0) IPTATM = IX(I02+IPTRES-1+1)-1 */
1065  }
1066 
1067  /*
1068  * ----- LOAD THE CAP INFORMATION IF NEEDED -----
1069  */
1070 
1071  // I don't know the label for it, so I don't read it if
1072  // it's AMBER 7 format. It's not used in NAMD anyway.
1073 // if (IfCap) {
1074  if (IfCap && !amber7_format) {
1075  /* if (IfBox)
1076  skipeoln(file); */
1077 #ifdef DOUBLE
1078  fscanf(file, " %d %lf %lf %lf %lf",
1079 #else
1080  fscanf(file, " %d %f %f %f %f",
1081 #endif
1082  &Natcap, &Cutcap,
1083  &Xcap, &Ycap, &Zcap);
1084  }
1085  genclose(file);
1086  if (debug) {
1087  printf("rdprm done\n");
1088 #ifndef NAMD_NO_STDOUT_FLUSH
1089  fflush(stdout);
1090 #endif
1091  }
1092  data_read = 1;
1093  return(1);
1094 }
_REAL * Pk
Definition: parm.h:24
int * DihHAt1
Definition: parm.h:27
_REAL Zcap
Definition: parm.h:26
int Nttyp
Definition: parm.h:17
_REAL Ycap
Definition: parm.h:26
_REAL * Teq
Definition: parm.h:24
char * AtomTree
Definition: parm.h:23
int * BondHNum
Definition: parm.h:27
void preadln(FILE *, const char *, char *)
Definition: parm.C:123
int * DihAt3
Definition: parm.h:27
char ititl[81]
Definition: parm.h:16
int Natom
Definition: parm.h:17
int IfBox
Definition: parm.h:17
_REAL * Phase
Definition: parm.h:24
int Natyp
Definition: parm.h:17
int Nphih
Definition: parm.h:17
int * AngleHNum
Definition: parm.h:27
int Iptres
Definition: parm.h:17
int Mtheta
Definition: parm.h:17
void genclose(FILE *)
Definition: parm.C:86
int * BondAt2
Definition: parm.h:27
int Nbonh
Definition: parm.h:17
static int readtoeoln(FILE *f)
Definition: parm.C:51
static int debug
Definition: parm.C:36
int * DihHAt4
Definition: parm.h:27
_REAL * Tk
Definition: parm.h:24
#define iout
Definition: InfoStream.h:87
int Natcap
Definition: parm.h:17
int Mbona
Definition: parm.h:17
int Nhparm
Definition: parm.h:17
int * Iblo
Definition: parm.h:27
char * ResNames
Definition: parm.h:23
int * DihAt4
Definition: parm.h:27
int Mphia
Definition: parm.h:17
_REAL * Masses
Definition: parm.h:24
int * AngleHAt1
Definition: parm.h:27
int Numbnd
Definition: parm.h:17
_REAL * HB6
Definition: parm.h:24
_REAL * HB12
Definition: parm.h:24
int * AngleNum
Definition: parm.h:27
int * DihHNum
Definition: parm.h:27
int * Iac
Definition: parm.h:27
_REAL * Charges
Definition: parm.h:24
int Ntypes
Definition: parm.h:17
int * DihAt1
Definition: parm.h:27
int * BondNum
Definition: parm.h:27
int * DihNum
Definition: parm.h:27
_REAL Xcap
Definition: parm.h:26
int Nbona
Definition: parm.h:17
int Nmxrs
Definition: parm.h:17
int * BondHAt1
Definition: parm.h:27
int * AngleHAt3
Definition: parm.h:27
char * AtomNames
Definition: parm.h:23
_REAL * Cn2
Definition: parm.h:24
int * Boundary
Definition: parm.h:27
int * AtomRes
Definition: parm.h:27
FILE * genopen(const char *name)
Definition: parm.C:72
int Ntheta
Definition: parm.h:17
int * AngleAt3
Definition: parm.h:27
int * AngleAt1
Definition: parm.h:27
int Nparm
Definition: parm.h:17
char * AtomSym
Definition: parm.h:23
int * BondAt1
Definition: parm.h:27
int Ntype2d
Definition: parm.h:17
int Nspm
Definition: parm.h:17
int Ntheth
Definition: parm.h:17
_REAL * Rk
Definition: parm.h:24
Definition: Box.h:14
int data_read
Definition: parm.h:34
int Nnb
Definition: parm.h:17
int Nat3
Definition: parm.h:17
int IfCap
Definition: parm.h:17
int * DihHAt2
Definition: parm.h:27
int Nphb
Definition: parm.h:17
_REAL * Cn1
Definition: parm.h:24
int * TreeJoin
Definition: parm.h:27
int * DihAt2
Definition: parm.h:27
int Numang
Definition: parm.h:17
_REAL * Req
Definition: parm.h:24
int read_fortran_12I6(FILE *, int *, int)
Definition: parm.C:1201
int Ipatm
Definition: parm.h:17
_REAL * Solty
Definition: parm.h:24
int Nphia
Definition: parm.h:17
int * AngleAt2
Definition: parm.h:27
int moveto(FILE *, const char *)
Definition: parm.C:1226
infostream & endi(infostream &s)
Definition: InfoStream.C:38
int * ExclAt
Definition: parm.h:27
int * AngleHAt2
Definition: parm.h:27
int Nres
Definition: parm.h:17
int * Ipres
Definition: parm.h:27
int Nptra
Definition: parm.h:17
#define _REAL
Definition: parm.h:11
int Nspsol
Definition: parm.h:17
int * BondHAt2
Definition: parm.h:27
int * Cno
Definition: parm.h:27
_REAL * Pn
Definition: parm.h:24
int * DihHAt3
Definition: parm.h:27
_REAL Cutcap
Definition: parm.h:26

Member Data Documentation

int * parm::AngleAt1

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::AngleAt2

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::AngleAt3

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::AngleHAt1

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::AngleHAt2

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::AngleHAt3

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::AngleHNum

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::AngleNum

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

char* parm::AtomNames

Definition at line 23 of file parm.h.

Referenced by firstwat(), parm(), PDB::PDB(), readparm(), and ~parm().

int * parm::AtomRes

Definition at line 27 of file parm.h.

Referenced by parm(), PDB::PDB(), readparm(), and ~parm().

char * parm::AtomSym

Definition at line 23 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

char * parm::AtomTree

Definition at line 23 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::BondAt1

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::BondAt2

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::BondHAt1

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::BondHAt2

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::BondHNum

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::BondNum

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::Boundary

Definition at line 27 of file parm.h.

Referenced by parm(), and readparm().

_REAL parm::Box[3]

Definition at line 26 of file parm.h.

_REAL* parm::Charges

Definition at line 24 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

_REAL * parm::Cn1

Definition at line 24 of file parm.h.

Referenced by parm(), Parameters::read_parm(), readparm(), and ~parm().

_REAL * parm::Cn2

Definition at line 24 of file parm.h.

Referenced by parm(), Parameters::read_parm(), readparm(), and ~parm().

int * parm::Cno

Definition at line 27 of file parm.h.

Referenced by parm(), Parameters::read_parm(), readparm(), and ~parm().

_REAL parm::Cutcap

Definition at line 26 of file parm.h.

Referenced by readparm().

int parm::data_read

Definition at line 34 of file parm.h.

Referenced by parm(), Parameters::read_parm(), and readparm().

int * parm::DihAt1

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::DihAt2

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::DihAt3

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::DihAt4

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::DihHAt1

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::DihHAt2

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::DihHAt3

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::DihHAt4

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::DihHNum

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::DihNum

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::ExclAt

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

_REAL * parm::HB12

Definition at line 24 of file parm.h.

Referenced by parm(), Parameters::read_parm(), readparm(), and ~parm().

_REAL * parm::HB6

Definition at line 24 of file parm.h.

Referenced by parm(), Parameters::read_parm(), readparm(), and ~parm().

int* parm::Iac

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int * parm::Iblo

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int parm::IfBox

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::IfCap

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Ipatm

Definition at line 17 of file parm.h.

Referenced by readparm().

int * parm::Ipres

Definition at line 27 of file parm.h.

Referenced by firstwat(), parm(), readparm(), and ~parm().

int parm::Iptres

Definition at line 17 of file parm.h.

Referenced by readparm().

char parm::ititl[81]

Definition at line 16 of file parm.h.

Referenced by readparm().

_REAL * parm::Masses

Definition at line 24 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

int parm::Mbona

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Mphia

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Mtheta

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Nat3

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Natcap

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Natom

Definition at line 17 of file parm.h.

Referenced by PDB::PDB(), and readparm().

int parm::Natyp

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Nbona

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Nbonh

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Nhparm

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Nmxrs

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Nnb

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Nparm

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Nphb

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Nphia

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Nphih

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Nptra

Definition at line 17 of file parm.h.

Referenced by Parameters::read_parm(), and readparm().

int parm::Nres

Definition at line 17 of file parm.h.

Referenced by firstwat(), and readparm().

int parm::Nspm

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Nspsol

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Ntheta

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Ntheth

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Nttyp

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Ntype2d

Definition at line 17 of file parm.h.

Referenced by readparm().

int parm::Ntypes

Definition at line 17 of file parm.h.

Referenced by Parameters::read_parm(), and readparm().

int parm::Numang

Definition at line 17 of file parm.h.

Referenced by Parameters::read_parm(), and readparm().

int parm::Numbnd

Definition at line 17 of file parm.h.

Referenced by Parameters::read_parm(), and readparm().

_REAL * parm::Phase

Definition at line 24 of file parm.h.

Referenced by parm(), Parameters::read_parm(), readparm(), and ~parm().

_REAL * parm::Pk

Definition at line 24 of file parm.h.

Referenced by parm(), Parameters::read_parm(), readparm(), and ~parm().

_REAL * parm::Pn

Definition at line 24 of file parm.h.

Referenced by parm(), Parameters::read_parm(), readparm(), and ~parm().

int parm::popn

Definition at line 33 of file parm.h.

_REAL * parm::Req

Definition at line 24 of file parm.h.

Referenced by parm(), Parameters::read_parm(), readparm(), and ~parm().

char * parm::ResNames

Definition at line 23 of file parm.h.

Referenced by firstwat(), parm(), PDB::PDB(), readparm(), and ~parm().

_REAL * parm::Rk

Definition at line 24 of file parm.h.

Referenced by parm(), Parameters::read_parm(), readparm(), and ~parm().

_REAL * parm::Solty

Definition at line 24 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

_REAL * parm::Teq

Definition at line 24 of file parm.h.

Referenced by parm(), Parameters::read_parm(), readparm(), and ~parm().

_REAL * parm::Tk

Definition at line 24 of file parm.h.

Referenced by parm(), Parameters::read_parm(), readparm(), and ~parm().

int * parm::TreeJoin

Definition at line 27 of file parm.h.

Referenced by parm(), readparm(), and ~parm().

_REAL parm::Xcap

Definition at line 26 of file parm.h.

Referenced by readparm().

_REAL parm::Ycap

Definition at line 26 of file parm.h.

Referenced by readparm().

_REAL parm::Zcap

Definition at line 26 of file parm.h.

Referenced by readparm().


The documentation for this struct was generated from the following files: