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root/group/trunk/tcProps/rmsd.c
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Comparing trunk/tcProps/rmsd.c (file contents):
Revision 1079 by mmeineke, Sat Feb 28 16:45:57 2004 UTC vs.
Revision 1080 by mmeineke, Wed Mar 3 15:16:15 2004 UTC

# Line 56 | Line 56 | void rmsd( enum atomNames rType, double startTime, cha
56    double rmsdDt;
57    double timeOut, outVal;
58  
59 +  struct atomCoord* atoms;
60 +
61    framesFinished = 0;
62    
63    startFound = 0;
# Line 91 | Line 93 | void rmsd( enum atomNames rType, double startTime, cha
93                 index,
94                 corrFrames );
95      }
96 <  
96 >    
97 >    // initialize the arrays
98 >    
99 >    atoms = myFrames[index].atoms;
100 >    for(j=0;j<nLipids;j++){
101 >      
102 >      atoms[nLipAtoms*j+0].type = HEAD;
103 >      atoms[nLipAtoms*j+0].mass = 72;
104 >      atoms[nLipAtoms*j+0].u[0] = 0.0;
105 >      atoms[nLipAtoms*j+0].u[1] = 0.0;
106 >      atoms[nLipAtoms*j+0].u[2] = 1.0;
107 >      
108 >      
109 >      
110 >      atoms[nLipAtoms*j+1].type = CH2;
111 >      atoms[nLipAtoms*j+1].mass = 14.03;
112 >      
113 >      atoms[nLipAtoms*j+2].type = CH;
114 >      atoms[nLipAtoms*j+2].mass = 13.02;
115 >      
116 >      atoms[nLipAtoms*j+3].type = CH2;
117 >      atoms[nLipAtoms*j+3].mass = 14.03;
118 >      
119 >      atoms[nLipAtoms*j+4].type = CH2;
120 >      atoms[nLipAtoms*j+4].mass = 14.03;
121 >      
122 >      atoms[nLipAtoms*j+5].type = CH2;
123 >      atoms[nLipAtoms*j+5].mass = 14.03;
124 >      
125 >      atoms[nLipAtoms*j+6].type = CH2;
126 >      atoms[nLipAtoms*j+6].mass = 14.03;
127 >      
128 >      atoms[nLipAtoms*j+7].type = CH2;
129 >      atoms[nLipAtoms*j+7].mass = 14.03;
130 >      
131 >      atoms[nLipAtoms*j+8].type = CH2;
132 >      atoms[nLipAtoms*j+8].mass = 14.03;
133 >      
134 >      atoms[nLipAtoms*j+9].type = CH2;
135 >      atoms[nLipAtoms*j+9].mass = 14.03;
136 >      
137 >      atoms[nLipAtoms*j+10].type = CH3;
138 >      atoms[nLipAtoms*j+10].mass = 15.04;
139 >      
140 >      atoms[nLipAtoms*j+11].type = CH2;
141 >      atoms[nLipAtoms*j+11].mass = 14.03;
142 >      
143 >      atoms[nLipAtoms*j+12].type = CH2;
144 >      atoms[nLipAtoms*j+12].mass = 14.03;
145 >      
146 >      atoms[nLipAtoms*j+13].type = CH2;    
147 >      atoms[nLipAtoms*j+13].mass = 14.03;
148 >      
149 >      atoms[nLipAtoms*j+14].type = CH2;
150 >      atoms[nLipAtoms*j+14].mass = 14.03;
151 >      
152 >      atoms[nLipAtoms*j+15].type = CH2;
153 >      atoms[nLipAtoms*j+15].mass = 14.03;
154 >      
155 >      atoms[nLipAtoms*j+16].type = CH2;
156 >      atoms[nLipAtoms*j+16].mass = 14.03;
157 >      
158 >      atoms[nLipAtoms*j+17].type = CH2;
159 >      atoms[nLipAtoms*j+17].mass = 14.03;
160 >      
161 >      atoms[nLipAtoms*j+18].type = CH3;
162 >      atoms[nLipAtoms*j+18].mass = 15.04;
163 >    }
164 >    
165 >    for(j=(nLipAtoms*nLipids);j<nAtoms;j++){
166 >      atoms[j].type = SSD;
167 >      atoms[j].mass = 18.03;
168 >      atoms[j].u[0] = 0.0;
169 >      atoms[j].u[1] = 0.0;
170 >      atoms[j].u[2] = 1.0;
171 >    }
172      myFrames[index].time = frameTimes[i];
173 <    readFrame(i, myFrames[index].atoms, myFrames[index].Hmat );
173 >    readFrame(i, atoms, myFrames[index].Hmat );
174    }
175  
176    // initialize the counts and the correlation

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