| 1 |
#include "SphereHarm.hpp" |
| 2 |
|
| 3 |
SphereHarm::SphereHarm( int bandWidth ){ |
| 4 |
bw = bandWidth; |
| 5 |
|
| 6 |
/*** ASSUMING WILL SEMINAIVE ALL ORDERS ***/ |
| 7 |
cutoff = bw; |
| 8 |
size = 2*bw; |
| 9 |
|
| 10 |
/* allocate memory */ |
| 11 |
rdata = (double *) fftw_malloc(sizeof(double) * (size * size)); |
| 12 |
idata = (double *) fftw_malloc(sizeof(double) * (size * size)); |
| 13 |
rcoeffs = (double *) fftw_malloc(sizeof(double) * (bw * bw)); |
| 14 |
icoeffs = (double *) fftw_malloc(sizeof(double) * (bw * bw)); |
| 15 |
weights = (double *) fftw_malloc(sizeof(double) * 4 * bw); |
| 16 |
seminaive_naive_tablespace = |
| 17 |
(double *) fftw_malloc(sizeof(double) * |
| 18 |
(Reduced_Naive_TableSize(bw,cutoff) + |
| 19 |
Reduced_SpharmonicTableSize(bw,cutoff))); |
| 20 |
workspace = (double *) fftw_malloc(sizeof(double) * |
| 21 |
((8 * (bw*bw)) + |
| 22 |
(7 * bw))); |
| 23 |
|
| 24 |
|
| 25 |
/**** |
| 26 |
At this point, check to see if all the memory has been |
| 27 |
allocated. If it has not, there's no point in going further. |
| 28 |
****/ |
| 29 |
|
| 30 |
if ( (rdata == NULL) || (idata == NULL) || |
| 31 |
(rcoeffs == NULL) || (icoeffs == NULL) || |
| 32 |
(seminaive_naive_tablespace == NULL) || |
| 33 |
(workspace == NULL) ) |
| 34 |
{ |
| 35 |
perror("Error in allocating memory"); |
| 36 |
exit( 1 ) ; |
| 37 |
} |
| 38 |
|
| 39 |
//precompute the Legendres |
| 40 |
fprintf(stdout,"Precomputing the Legendres...\n"); |
| 41 |
seminaive_naive_table = SemiNaive_Naive_Pml_Table( bw, cutoff, |
| 42 |
seminaive_naive_tablespace, |
| 43 |
workspace ); |
| 44 |
|
| 45 |
//construct fftw plans using the GURU interface |
| 46 |
/* forward DCT */ |
| 47 |
dctPlan = fftw_plan_r2r_1d( 2*bw, weights, rdata, |
| 48 |
FFTW_REDFT10, FFTW_ESTIMATE ) ; |
| 49 |
|
| 50 |
/* |
| 51 |
fftw "preamble" ; |
| 52 |
note that this plan places the output in a transposed array |
| 53 |
*/ |
| 54 |
rank = 1 ; |
| 55 |
dims[0].n = 2*bw ; |
| 56 |
dims[0].is = 1 ; |
| 57 |
dims[0].os = 2*bw ; |
| 58 |
howmany_rank = 1 ; |
| 59 |
howmany_dims[0].n = 2*bw ; |
| 60 |
howmany_dims[0].is = 2*bw ; |
| 61 |
howmany_dims[0].os = 1 ; |
| 62 |
|
| 63 |
/* forward fft */ |
| 64 |
fftPlan = fftw_plan_guru_split_dft( rank, dims, |
| 65 |
howmany_rank, howmany_dims, |
| 66 |
rdata, idata, |
| 67 |
workspace, workspace+(4*bw*bw), |
| 68 |
FFTW_ESTIMATE ); |
| 69 |
|
| 70 |
//make the weights |
| 71 |
makeweights( bw, weights ); |
| 72 |
} |
| 73 |
|
| 74 |
SphereHarm::~SphereHarm(){ |
| 75 |
//free up memory |
| 76 |
fftw_destroy_plan( fftPlan ); |
| 77 |
fftw_destroy_plan( dctPlan ); |
| 78 |
|
| 79 |
fftw_free(workspace); |
| 80 |
fftw_free(seminaive_naive_table); |
| 81 |
fftw_free(seminaive_naive_tablespace); |
| 82 |
fftw_free(weights); |
| 83 |
fftw_free(icoeffs); |
| 84 |
fftw_free(rcoeffs); |
| 85 |
fftw_free(idata); |
| 86 |
fftw_free(rdata); |
| 87 |
} |
| 88 |
|
| 89 |
void SphereHarm::doTransforms(vector<double> gridData){ |
| 90 |
int i; |
| 91 |
|
| 92 |
//load the data |
| 93 |
for (i=0; i<size*size; i++){ |
| 94 |
rdata[i] = gridData[i]; |
| 95 |
//our data is all real, so load the imaginary part with zeros |
| 96 |
idata[i] = 0.0; |
| 97 |
} |
| 98 |
|
| 99 |
//do the forward spherical transform |
| 100 |
FST_semi_memo(rdata, idata, |
| 101 |
rcoeffs, icoeffs, |
| 102 |
bw, |
| 103 |
seminaive_naive_table, |
| 104 |
workspace, |
| 105 |
0, |
| 106 |
cutoff, |
| 107 |
&dctPlan, |
| 108 |
&fftPlan, |
| 109 |
weights ); |
| 110 |
} |
| 111 |
|
| 112 |
void SphereHarm::printShapesFileStart(char name[200], char particle[80], |
| 113 |
double mass, double momInert[3][3]){ |
| 114 |
ofstream myShapes(name); |
| 115 |
printShapesStreamStart(myShapes, particle, mass, momInert); |
| 116 |
} |
| 117 |
|
| 118 |
void SphereHarm::printShapesStreamStart(ostream& shapes, char particle[80], |
| 119 |
double mass, double momInert[3][3]){ |
| 120 |
shapes << "begin ShapeInfo\n"; |
| 121 |
shapes << "#name\t\tmass\tI_xx\tI_yy\tI_zz\n"; |
| 122 |
shapes << particle << "\t" << mass << "\t" << momInert[0][0] << "\t" |
| 123 |
<< momInert[1][1] << "\t" << momInert[2][2] << "\n"; |
| 124 |
shapes << "end ShapeInfo\n"; |
| 125 |
} |
| 126 |
|
| 127 |
|
| 128 |
|
| 129 |
void SphereHarm::printToShapesFile(char name[200], int index, double tolVal){ |
| 130 |
ofstream shapes(name, ios::app); |
| 131 |
|
| 132 |
printToShapesStream(shapes, index, tolVal); |
| 133 |
} |
| 134 |
|
| 135 |
void SphereHarm::printToShapesStream(ostream& shapes, int index, double tolVal) { |
| 136 |
|
| 137 |
biggest = 0.0; |
| 138 |
nfuncs = 0; |
| 139 |
for ( l = 0 ; l < bw ; l++ ) { |
| 140 |
for (m = 0; m < l+1; m++) { |
| 141 |
dummy1 = seanindex(m, l, bw); |
| 142 |
dummy2 = seanindex(-m, l, bw); |
| 143 |
|
| 144 |
if (m == 0) { |
| 145 |
cm = normFactor(l,m)*rcoeffs[dummy1]; |
| 146 |
sm = normFactor(l,m)*icoeffs[dummy1]; |
| 147 |
} else { |
| 148 |
cm = normFactor(l,m)*(pow(-1.0,(double)m)*rcoeffs[dummy1] |
| 149 |
+ rcoeffs[dummy2]); |
| 150 |
sm = normFactor(l,m)*(pow(-1.0,(double)m)*icoeffs[dummy1] |
| 151 |
- icoeffs[dummy2]); |
| 152 |
} |
| 153 |
|
| 154 |
if (fabs(cm) > biggest) biggest = fabs(cm); |
| 155 |
if (fabs(sm) > biggest) biggest = fabs(sm); |
| 156 |
} |
| 157 |
} |
| 158 |
for ( l = 0 ; l < bw ; l++ ) { |
| 159 |
for (m = 0; m < l+1; m++) { |
| 160 |
dummy1 = seanindex(m, l, bw); |
| 161 |
dummy2 = seanindex(-m, l, bw); |
| 162 |
|
| 163 |
if (m == 0) { |
| 164 |
cm = normFactor(l,m)*rcoeffs[dummy1]; |
| 165 |
sm = normFactor(l,m)*icoeffs[dummy1]; |
| 166 |
} else { |
| 167 |
cm = normFactor(l,m)*(pow(-1.0,(double)m)*rcoeffs[dummy1] |
| 168 |
+ rcoeffs[dummy2]); |
| 169 |
sm = normFactor(l,m)*(pow(-1.0,(double)m)*icoeffs[dummy1] |
| 170 |
- icoeffs[dummy2]); |
| 171 |
} |
| 172 |
|
| 173 |
if (fabs(cm) > tolVal * biggest) nfuncs++; |
| 174 |
if (fabs(sm) > tolVal * biggest) nfuncs++; |
| 175 |
} |
| 176 |
} |
| 177 |
|
| 178 |
switch(index){ |
| 179 |
case 0:{ |
| 180 |
shapes << "\nbegin ContactFunctions\n"; |
| 181 |
shapes << "#l\tm\tsin or cos\tcoeff (Ang)\n"; |
| 182 |
}; break; |
| 183 |
case 1:{ |
| 184 |
shapes << "\nbegin RangeFunctions\n"; |
| 185 |
shapes << "#l\tm\tsin or cos\tcoeff (Ang)\n"; |
| 186 |
}; break; |
| 187 |
case 2:{ |
| 188 |
shapes << "\nbegin StrengthFunctions\n"; |
| 189 |
shapes << "#l\tm\tsin or cos\tcoeff (kcal/mol)\n"; |
| 190 |
}; break; |
| 191 |
} |
| 192 |
|
| 193 |
for ( l = 0 ; l < bw ; l++ ) { |
| 194 |
for (m = 0; m < l+1; m++) { |
| 195 |
dummy1 = seanindex(m, l, bw); |
| 196 |
dummy2 = seanindex(-m, l, bw); |
| 197 |
|
| 198 |
if (m == 0) { |
| 199 |
cm = normFactor(l,m)*rcoeffs[dummy1]; |
| 200 |
sm = normFactor(l,m)*icoeffs[dummy1]; |
| 201 |
} else { |
| 202 |
cm = normFactor(l,m)*(pow(-1.0,(double)m)*rcoeffs[dummy1] |
| 203 |
+ rcoeffs[dummy2]); |
| 204 |
sm = normFactor(l,m)*(pow(-1.0,(double)m)*icoeffs[dummy1] |
| 205 |
- icoeffs[dummy2]); |
| 206 |
} |
| 207 |
|
| 208 |
if (fabs(cm) > tolVal * biggest) |
| 209 |
shapes << l << "\t" << m << "\tcos\t\t" << cm << "\n"; |
| 210 |
if (fabs(sm) > tolVal * biggest) |
| 211 |
shapes << l << "\t" << m << "\tsin\t\t" << sm << "\n"; |
| 212 |
} |
| 213 |
} |
| 214 |
switch(index){ |
| 215 |
case 0:{ |
| 216 |
shapes << "end ContactFunctions\n"; |
| 217 |
}; break; |
| 218 |
case 1:{ |
| 219 |
shapes << "end RangeFunctions\n"; |
| 220 |
}; break; |
| 221 |
case 2:{ |
| 222 |
shapes << "end StrengthFunctions\n"; |
| 223 |
}; break; |
| 224 |
} |
| 225 |
} |
| 226 |
|
| 227 |
double SphereHarm::normFactor(int L, int M){ |
| 228 |
// normalization factor: |
| 229 |
if (L+M > 170){ |
| 230 |
printf("Warning: A coefficient was omitted because l + m > 170.\n" |
| 231 |
"\tThe double buffer overflows with factorial calculations\n" |
| 232 |
"\tof 170 and higher. You should consider using a smaller\n" |
| 233 |
"\tbandwidth if you aren't okay with the loss of the %i, %i\n" |
| 234 |
"\tspherical harmonic.\n", L, M); |
| 235 |
return 0.0; |
| 236 |
} |
| 237 |
else |
| 238 |
return sqrt( (2*L+1)/(4.0*M_PI)*factorialFunc((double)(L-M)) |
| 239 |
/ factorialFunc(double(L+M)) ); |
| 240 |
} |
| 241 |
|
| 242 |
double SphereHarm::factorialFunc(double n) { |
| 243 |
if (n < 0.0) return NAN; |
| 244 |
else { |
| 245 |
if (n < 2.0) return 1.0; |
| 246 |
else |
| 247 |
return n*factorialFunc(n-1.0); |
| 248 |
} |
| 249 |
} |
