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root/freemol/trunk/src/mengine/src/get_mem.c
Revision: 104
Committed: Fri Feb 20 14:09:46 2009 UTC (12 years, 5 months ago) by gilbertke
File size: 9512 byte(s)
Log Message:
full dynamic memory allocation of molecule
Line File contents
1 #define EXTERN extern
2
3 #include "pcwin.h"
4 #include "pcmod.h"
5 #include "attached.h"
6 #include "derivs.h"
7 #include "hess.h"
8 #include "utility.h"
9 #include "nonbond.h"
10 #include "torsions.h"
11
12 void max_torsions(void);
13 void get_molecule_memory(int);
14 int use_solv(void);
15
16
17 #define STILL 1
18 #define HCT 2
19
20 EXTERN struct t_solvent {
21 int type;
22 double EPSin, EPSsolv;
23 double doffset, p1,p2,p3,p4,p5;
24 double *shct,*asolv,*rsolv,*vsolv,*gpol,*rborn;
25 } solvent;
26
27 // =======================================
28 void get_molecule_memory(int niatom)
29 {
30 int i,j;
31
32 atom.type = ivector(0,niatom+10);
33 atom.tclass = ivector(0,niatom+10);
34 atom.mmx_type = ivector(0,niatom+10);
35 atom.mm3_type = ivector(0,niatom+10);
36 atom.mmff_type = ivector(0,niatom+10);
37 atom.atomnum = ivector(0,niatom+10);
38 atom.use = ivector(0,niatom+10);
39 atom.flags = ilvector(0,niatom+10);
40 atom.iat = imatrix(0, niatom+10,0,MAXIAT);
41 atom.bo = imatrix(0,niatom+10, 0, MAXIAT);
42 atom.x = dvector(0,niatom+10);
43 atom.y = dvector(0,niatom+10);
44 atom.z = dvector(0,niatom+10);
45 atom.charge = dvector(0,niatom+10);
46 atom.formal_charge = dvector(0,niatom+10);
47 atom.sigma_charge = dvector(0,niatom+10);
48 atom.atomwt = dvector(0,niatom+10);
49 atom.radius = dvector(0,niatom+10);
50 atom.name = malloc( (niatom+10)*sizeof(LABEL));
51
52 for (i=0; i <= niatom; i++)
53 {
54 atom.type[i] = 0;
55 atom.tclass[i] = 0;
56 atom.mmx_type[i] = 0;
57 atom.mm3_type[i] = 0;
58 atom.mmff_type[i] = 0;
59 atom.atomnum[i] = 0;
60 atom.use[i] = 0;
61 atom.flags[i] = 0;
62 atom.x[i] = 0.0;
63 atom.y[i] = 0.0;
64 atom.z[i] = 0.0;
65 atom.charge[i] = 0.0;
66 atom.formal_charge[i] = 0.0;
67 atom.sigma_charge[i] = 0.0;
68 atom.atomwt[i] = 0.0;
69 for (j=0; j < MAXIAT; j++)
70 {
71 atom.iat[i][j] = 0;
72 atom.bo[i][j] = 0;
73 }
74 strcpy(atom.name[i],"");
75 }
76
77 }
78 /* ================================================================ */
79 void get_memory()
80 {
81 int i, j;
82 int ntor;
83 int ntypes, found, itype[MAXATOMTYPE];
84
85 skip = imatrix(0,natom+1,0,natom+1);
86 for (i=1; i <= natom; i++)
87 {
88 for (j=1; j <=natom; j++)
89 skip[i][j] = 0;
90 }
91
92 deriv.d1 = dmatrix(0,natom+1, 0,3);
93 deriv.deb = dmatrix(0,natom+1, 0,3);
94 deriv.dea = dmatrix(0,natom+1, 0,3);
95 deriv.destb = dmatrix(0,natom+1, 0,3);
96 deriv.deopb = dmatrix(0,natom+1, 0,3);
97 deriv.detor = dmatrix(0,natom+1, 0,3);
98 deriv.de14 = dmatrix(0,natom+1, 0,3);
99 deriv.devdw = dmatrix(0,natom+1, 0,3);
100 deriv.deqq = dmatrix(0,natom+1, 0,3);
101 deriv.deaa = dmatrix(0,natom+1, 0,3);
102 deriv.destor = dmatrix(0,natom+1, 0,3);
103 deriv.dehb = dmatrix(0,natom+1, 0,3);
104 deriv.deimprop = dmatrix(0,natom+1, 0,3);
105 deriv.deub = dmatrix(0,natom+1, 0,3);
106 deriv.desolv = dmatrix(0,natom+1, 0,3);
107 deriv.degeom = dmatrix(0,natom+1, 0,3);
108 deriv.drb = dvector(0,natom+1);
109
110 ntypes = 0;
111 nonbond.maxnbtype = 0;
112
113 for (i=1; i <= natom; i++)
114 {
115 found = FALSE;
116 if (atom.type[i] > nonbond.maxnbtype)
117 nonbond.maxnbtype = atom.type[i];
118 for (j=0; j < ntypes; j++)
119 {
120 if (atom.type[i] == itype[j])
121 {
122 found = TRUE;
123 break;
124 }
125 }
126 if (found == FALSE)
127 {
128 itype[ntypes] = atom.type[i];
129 ntypes++;
130 }
131 }
132
133 j=0;
134 for (i=0; i <= ntypes; i++)
135 j+= i;
136
137 nonbond.nonbond = j;
138 nonbond.iNBtype = imatrix(0,nonbond.maxnbtype+1, 0,nonbond.maxnbtype+1);
139 nonbond.ipif = imatrix(0,nonbond.maxnbtype+1, 0,nonbond.maxnbtype+1);
140 nonbond.vrad = dmatrix(0,nonbond.maxnbtype+1, 0,nonbond.maxnbtype+1);
141 nonbond.veps = dmatrix(0,nonbond.maxnbtype+1, 0,nonbond.maxnbtype+1);
142 nonbond.vrad14 = dmatrix(0,nonbond.maxnbtype+1, 0,nonbond.maxnbtype+1);
143 nonbond.veps14 = dmatrix(0,nonbond.maxnbtype+1, 0,nonbond.maxnbtype+1);
144
145 max_torsions();
146 ntor = torsions.ntor;
147 if (ntor > 0)
148 {
149 torsions.i14 = imatrix(0,ntor,0,4);
150 torsions.v1 = vector(0,ntor);
151 torsions.v2 = vector(0,ntor);
152 torsions.v3 = vector(0,ntor);
153 torsions.v4 = vector(0,ntor);
154 torsions.v5 = vector(0,ntor);
155 torsions.v6 = vector(0,ntor);
156 torsions.ph1 = ivector(0,ntor);
157 torsions.ph2 = ivector(0,ntor);
158 torsions.ph3 = ivector(0,ntor);
159 torsions.ph4 = ivector(0,ntor);
160 torsions.ph5 = ivector(0,ntor);
161 torsions.ph6 = ivector(0,ntor);
162 for (i=0; i < ntor; i++)
163 {
164 torsions.v1[i] = 0.0;
165 torsions.v2[i] = 0.0;
166 torsions.v3[i] = 0.0;
167 torsions.v4[i] = 0.0;
168 torsions.v5[i] = 0.0;
169 torsions.v6[i] = 0.0;
170 torsions.ph1[i] = 0;
171 torsions.ph2[i] = 0;
172 torsions.ph3[i] = 0;
173 torsions.ph4[i] = 0;
174 torsions.ph5[i] = 0;
175 torsions.ph6[i] = 0;
176 }
177 }
178 hess.hessx = matrix(0,natom+1, 0,3);
179 hess.hessy = matrix(0,natom+1, 0,3);
180 hess.hessz = matrix(0,natom+1, 0,3);
181
182 attached.n13 = ivector(0,natom+1);
183 attached.n14 = ivector(0,natom+1);
184 attached.i13 = imatrix(0, 20, 0,natom+1);
185 attached.i14 = imatrix(0,144, 0,natom+1);
186
187 for(i=0; i <= natom; i++)
188 {
189 for (j=0; j < 3; j++)
190 {
191 deriv.d1[i][j] = 0.0;
192 deriv.deb[i][j] = 0.0;
193 deriv.dea[i][j] = 0.0;
194 deriv.destb[i][j] = 0.0;
195 deriv.deopb[i][j] = 0.0;
196 deriv.detor[i][j] = 0.0;
197 deriv.de14[i][j] = 0.0;
198 deriv.devdw[i][j] = 0.0;
199 deriv.deqq[i][j] = 0.0;
200 deriv.deaa[i][j] = 0.0;
201 deriv.destor[i][j] = 0.0;
202 deriv.dehb[i][j] = 0.0;
203 deriv.deimprop[i][j] = 0.0;
204 deriv.deub[i][j] = 0.0;
205
206 hess.hessx[i][j] = 0.0;
207 hess.hessy[i][j] = 0.0;
208 hess.hessz[i][j] = 0.0;
209 }
210 }
211 if (use_solv())
212 {
213 solvent.asolv = dvector(0,natom+1);
214 solvent.rsolv = dvector(0,natom+1);
215 solvent.rborn = dvector(0,natom+1);
216 if (solvent.type == STILL)
217 {
218 solvent.vsolv = dvector(0,natom+1);
219 solvent.gpol = dvector(0,natom+1);
220 } else if (solvent.type == HCT)
221 {
222 solvent.shct = dvector(0,natom+1);
223 }
224 }
225 }
226
227 void free_memory()
228 {
229 int ntor;
230 free_imatrix(skip, 0, natom+1,0,natom+1);
231 free_dmatrix(deriv.d1, 0,natom+1, 0,3);
232 free_dmatrix(deriv.deb, 0,natom+1, 0,3);
233 free_dmatrix(deriv.dea, 0,natom+1, 0,3);
234 free_dmatrix(deriv.destb, 0,natom+1, 0,3);
235 free_dmatrix(deriv.deopb, 0,natom+1, 0,3);
236 free_dmatrix(deriv.detor, 0,natom+1, 0,3);
237 free_dmatrix(deriv.de14, 0,natom+1, 0,3);
238 free_dmatrix(deriv.devdw, 0,natom+1, 0,3);
239 free_dmatrix(deriv.deqq, 0,natom+1, 0,3);
240 free_dmatrix(deriv.deaa, 0,natom+1, 0,3);
241 free_dmatrix(deriv.destor, 0,natom+1, 0,3);
242 free_dmatrix(deriv.dehb, 0,natom+1, 0,3);
243 free_dmatrix(deriv.deimprop,0,natom+1, 0,3);
244 free_dmatrix(deriv.deub, 0,natom+1, 0,3);
245 free_dmatrix(deriv.desolv ,0,natom+1, 0,3);
246 free_dmatrix(deriv.degeom ,0,natom+1, 0,3);
247 free_dvector(deriv.drb ,0,natom+1);
248
249 free_imatrix(nonbond.iNBtype ,0,nonbond.maxnbtype+1, 0,nonbond.maxnbtype+1);
250 free_imatrix(nonbond.ipif ,0,nonbond.maxnbtype+1, 0,nonbond.maxnbtype+1);
251 free_dmatrix(nonbond.vrad ,0,nonbond.maxnbtype+1, 0,nonbond.maxnbtype+1);
252 free_dmatrix(nonbond.veps ,0,nonbond.maxnbtype+1, 0,nonbond.maxnbtype+1);
253 free_dmatrix(nonbond.vrad14 ,0,nonbond.maxnbtype+1, 0,nonbond.maxnbtype+1);
254 free_dmatrix(nonbond.veps14 ,0,nonbond.maxnbtype+1, 0,nonbond.maxnbtype+1);
255
256 // ntor = 9*natom;
257 ntor = torsions.ntor;
258 if (ntor > 0)
259 {
260 free_imatrix(torsions.i14 ,0,ntor,0,4);
261 free_vector(torsions.v1 ,0,ntor);
262 free_vector(torsions.v2 ,0,ntor);
263 free_vector(torsions.v3 ,0,ntor);
264 free_vector(torsions.v4 ,0,ntor);
265 free_vector(torsions.v5 ,0,ntor);
266 free_vector(torsions.v6 ,0,ntor);
267 free_ivector(torsions.ph1 ,0,ntor);
268 free_ivector(torsions.ph2 ,0,ntor);
269 free_ivector(torsions.ph3 ,0,ntor);
270 free_ivector(torsions.ph4 ,0,ntor);
271 free_ivector(torsions.ph5 ,0,ntor);
272 free_ivector(torsions.ph6 ,0,ntor);
273 }
274
275 free_matrix(hess.hessx, 0,natom+1, 0,3);
276 free_matrix(hess.hessy, 0,natom+1, 0,3);
277 free_matrix(hess.hessz, 0,natom+1, 0,3);
278
279 free_ivector(attached.n13 ,0,natom+1);
280 free_ivector(attached.n14 ,0,natom+1);
281 free_imatrix(attached.i13 ,0, 20, 0,natom+1);
282 free_imatrix(attached.i14 ,0,144, 0,natom+1);
283
284 if (use_solv())
285 {
286 free_dvector(solvent.asolv ,0,natom+1);
287 free_dvector(solvent.rsolv ,0,natom+1);
288 free_dvector(solvent.rborn ,0,natom+1);
289 if (solvent.type == STILL)
290 {
291 free_dvector(solvent.vsolv ,0,natom+1);
292 free_dvector(solvent.gpol ,0,natom+1);
293 } else if (solvent.type == HCT)
294 {
295 free_dvector(solvent.shct ,0,natom+1);
296 }
297 }
298 }
299