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root/group/trunk/tcProps/rmsd.c
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Comparing trunk/tcProps/rmsd.c (file contents):
Revision 1073 by mmeineke, Sat Feb 28 16:45:57 2004 UTC vs.
Revision 1085 by mmeineke, Fri Mar 5 03:10:29 2004 UTC

# Line 28 | Line 28 | void calcRMSDpair( int bin, int i, int j, enum atomNam
28  
29   void calcRMSDpair( int bin, int i, int j, enum atomNames rType );
30  
31 < void rmsd( enum atomNames rType, double startTime, char* outPrefix ){
31 > void rmsd( enum atomNames rType, double startTime, char* outPrefix,
32 >           char* theName){
33  
34    // list of 'a priori' constants
35  
# Line 56 | Line 57 | void rmsd( enum atomNames rType, double startTime, cha
57    double rmsdDt;
58    double timeOut, outVal;
59  
60 +  struct atomCoord* atoms;
61 +
62    framesFinished = 0;
63    
64    startFound = 0;
# Line 91 | Line 94 | void rmsd( enum atomNames rType, double startTime, cha
94                 index,
95                 corrFrames );
96      }
97 <  
97 >    
98 >    // initialize the arrays
99 >    
100 >    atoms = myFrames[index].atoms;
101 >    for(j=0;j<nLipids;j++){
102 >      
103 >      atoms[nLipAtoms*j+0].type = HEAD;
104 >      atoms[nLipAtoms*j+0].mass = 72;
105 >      atoms[nLipAtoms*j+0].u[0] = 0.0;
106 >      atoms[nLipAtoms*j+0].u[1] = 0.0;
107 >      atoms[nLipAtoms*j+0].u[2] = 1.0;
108 >      
109 >      
110 >      
111 >      atoms[nLipAtoms*j+1].type = CH2;
112 >      atoms[nLipAtoms*j+1].mass = 14.03;
113 >      
114 >      atoms[nLipAtoms*j+2].type = CH;
115 >      atoms[nLipAtoms*j+2].mass = 13.02;
116 >      
117 >      atoms[nLipAtoms*j+3].type = CH2;
118 >      atoms[nLipAtoms*j+3].mass = 14.03;
119 >      
120 >      atoms[nLipAtoms*j+4].type = CH2;
121 >      atoms[nLipAtoms*j+4].mass = 14.03;
122 >      
123 >      atoms[nLipAtoms*j+5].type = CH2;
124 >      atoms[nLipAtoms*j+5].mass = 14.03;
125 >      
126 >      atoms[nLipAtoms*j+6].type = CH2;
127 >      atoms[nLipAtoms*j+6].mass = 14.03;
128 >      
129 >      atoms[nLipAtoms*j+7].type = CH2;
130 >      atoms[nLipAtoms*j+7].mass = 14.03;
131 >      
132 >      atoms[nLipAtoms*j+8].type = CH2;
133 >      atoms[nLipAtoms*j+8].mass = 14.03;
134 >      
135 >      atoms[nLipAtoms*j+9].type = CH2;
136 >      atoms[nLipAtoms*j+9].mass = 14.03;
137 >      
138 >      atoms[nLipAtoms*j+10].type = CH3;
139 >      atoms[nLipAtoms*j+10].mass = 15.04;
140 >      
141 >      atoms[nLipAtoms*j+11].type = CH2;
142 >      atoms[nLipAtoms*j+11].mass = 14.03;
143 >      
144 >      atoms[nLipAtoms*j+12].type = CH2;
145 >      atoms[nLipAtoms*j+12].mass = 14.03;
146 >      
147 >      atoms[nLipAtoms*j+13].type = CH2;    
148 >      atoms[nLipAtoms*j+13].mass = 14.03;
149 >      
150 >      atoms[nLipAtoms*j+14].type = CH2;
151 >      atoms[nLipAtoms*j+14].mass = 14.03;
152 >      
153 >      atoms[nLipAtoms*j+15].type = CH2;
154 >      atoms[nLipAtoms*j+15].mass = 14.03;
155 >      
156 >      atoms[nLipAtoms*j+16].type = CH2;
157 >      atoms[nLipAtoms*j+16].mass = 14.03;
158 >      
159 >      atoms[nLipAtoms*j+17].type = CH2;
160 >      atoms[nLipAtoms*j+17].mass = 14.03;
161 >      
162 >      atoms[nLipAtoms*j+18].type = CH3;
163 >      atoms[nLipAtoms*j+18].mass = 15.04;
164 >    }
165 >    
166 >    for(j=(nLipAtoms*nLipids);j<nAtoms;j++){
167 >      atoms[j].type = SSD;
168 >      atoms[j].mass = 18.03;
169 >      atoms[j].u[0] = 0.0;
170 >      atoms[j].u[1] = 0.0;
171 >      atoms[j].u[2] = 1.0;
172 >    }
173      myFrames[index].time = frameTimes[i];
174 <    readFrame(i, myFrames[index].atoms, myFrames[index].Hmat );
174 >    readFrame(i, atoms, myFrames[index].Hmat );
175 >    
176 >    index++;
177    }
178  
179    // initialize the counts and the correlation
# Line 117 | Line 197 | void rmsd( enum atomNames rType, double startTime, cha
197      for(j=i+1;j<corrFrames;j++){
198  
199        diffTime = myFrames[j].time - myFrames[i].time;
200 <      if( diffTime > 0.0 ){
200 >      
201 >      if( diffTime > 0.0 ){      
202          
203          percentComplete =
204            (int)( 100.0 * (double)index / (double) nCounts );
205          
206          fprintf( stdout,
207 <                 "\rRMSD corr %3d%% complete.",
207 >                 "\rMSD corr %3d%% complete.",
208                   percentComplete );
209          fflush( stdout );
210          
# Line 138 | Line 219 | void rmsd( enum atomNames rType, double startTime, cha
219  
220    // print out the correlation
221  
222 <  sprintf( outName, "%s.rmsd", outPrefix );
222 >  sprintf( outName, "%s-%s.msd", outPrefix, theName );
223    outFile = fopen( outName, "w" );
224  
225    fprintf( outFile,
226 <           "#time\trmsd\n");
226 >           "#time\tmsd\n");
227  
228    for(i=0;i<RMSDBINS;i++){
229      
# Line 164 | Line 245 | void rmsd( enum atomNames rType, double startTime, cha
245      (int)( 100.0 * (double)index / (double) nCounts );
246    
247    fprintf( stdout,
248 <           "\rRMSD corr %3d%% complete.",
248 >           "\rMSD corr %3d%% complete.\n",
249             percentComplete );
250    fflush( stdout );
251  
# Line 202 | Line 283 | void calcRMSDpair( int bin, int frameI, int frameJ, en
283    atomsI = myFrames[frameI].atoms;
284    atomsJ = myFrames[frameJ].atoms;
285  
286 +  accum = 0.0;
287 +
288    if( rType != COM ){
289      
290      nAccums = 0;
# Line 216 | Line 299 | void calcRMSDpair( int bin, int frameI, int frameJ, en
299          for(j=0;j<3;j++)
300            dSqr += d[j] * d[j];
301          
302 <        accum += sqrt(dSqr);
302 >        accum += dSqr;
303          nAccums++;
304        }    
305      }
# Line 257 | Line 340 | void calcRMSDpair( int bin, int frameI, int frameJ, en
340        for(j=0;j<3;j++)
341          dSqr += d[j] * d[j];
342        
343 <      accum += sqrt(dSqr);
343 >      accum += dSqr;
344        nAccums++;
345      }
346    }

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