libmaus2::math::GmpFloat::GmpFloat(
GmpFloat const &
#if defined(LIBMAUS2_HAVE_GMP)
o
#endif
)
: v(0)
{
#if defined(LIBMAUS2_HAVE_GMP)
v = new MpfContainer;
mpf_init_set(decode(v),decode(o.v));
//mpf_init2(decode(v),mpf_get_prec(decode(o.v)));
//mpf_set(decode(v),decode(o.v));
#endif
}
//Jianmin :: NLSystemContext* -> Effect -> IO
void Jianmin(NLSystemContext* ctx) {
uint32 i;
unsigned long exponent;
//Reactions:
bigFloat r[78]; //temp-storage during calculations
bigFloat r_f[78]; //forward reaction
bigFloat r_b[78]; //backward reaction
//Note: 'theta_H' is initialized in second bigFloat group below.
bigFloat theta_A, theta_B, theta_C, theta_D, theta_E, theta_F, theta_G, theta_I, theta_J, theta_K,
theta_L, theta_M, theta_N, theta_O, theta_P, theta_Q, theta_R, theta_S, theta_T, theta_U,
theta_V, theta_W, theta_X, theta_Y, theta_Z, theta_Z1;
bigFloat free, theta_H, theta_OH, theta_H2O, theta_CH, theta_CH2, theta_CH3, theta_CH4,
theta_CO, theta_CHO, theta_CH2O, theta_CH3O, theta_CH3OH;
bigFloat K_H;
bigFloat temp;
bigFloat e;
// define constants for forward and reverse rate constants.
//NOTE: constants for k_f[55]-k_f[70] are not defined! (same for k_b[].)
double in_k_f[78] = {
6.249e7, 1.831e3, 9.567e2, 8.447e3, 1.863e5, 5.509e8, 5.982, 2.106e10, 7.139e4, 2.243e8,
2.418e7, 1.247e8, 1.100e2, 5.791e12, 1.114e9, 9.955e3, 5.396e2, 3.706e3, 2.705e8, 7.040e9,
5.501e8, 2.335e4, 1.630e10, 6.622e2, 6.464e2, 2.109e8, 8.910, 3.268e5, 1.890e5, 9.014e11,
7.631e3, 6.303e2, 1.075e2, 9.362e7, 9.540e4, 2.636e8, 3.368e8, 1.615e10, 3.290e-3, 1.004e3,
1.457e5, 2.380e2, 3.845e7, 3.778e7, 9.432e3, 1.666e3, 3.094e8, 1.557e7, 6.575e1, 1.372e2,
3.003, 3.044e13, 1.047e16, 2.092e12, 1.020e3, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 5.056e9, 1.396e9, 4.831e9, 9.712e6, 4.000, 2.403e6, 1.404e-1};
double in_k_b[78] = {
5.885e4, 3.070e6, 2.885e7, 8.560e1, 8.721, 3.131e5, 6.828e-12, 4.823e3, 1.020e4, 1.566,
5.024e5, 3.056e6, 6.318e-1, 1.247e8, 8.518e-3, 6.388e10, 1.625e7, 1.514e5, 4.864e5, 1.941e2,
1.750e6, 8.974e1, 5.505e-2, 1.555e1, 2.380e7, 1.986, 1.865e7, 1.668, 1.108e7, 1.962,
1.902e11, 5.235e1, 1.311e7, 2.729, 2.606e8, 5.388e6, 4.689, 1.170e4, 2.457e-15, 1.833e-6,
7.225e-5, 5.142e8, 4.046e12, 9.921e9, 3.620e7, 2.431e7, 1.802e13, 2.232e8, 7.117e7, 6.635e7,
7.879e7, 1.230e8, 1.740e8, 1.640e8, 6.696e7, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 2.126e8, 1.611, 1.848e6, 1.828e2, 3.558e8, 1.593e5, 1.336e10};
bigFloat k_f[78];
bigFloat k_b[78];
// define partial pressures, Boltzman constant and temperature.
// guaiacol, H2, catechol, phenol, benzene, anisole.
bigFloat p_A, p_H2, p_M, p_S, p_X, p_K,
p_CO, p_H2O, p_CH4, p_CH3OH, KB, T;
double partialPressures[12] = {1.0, 1.0, 1.0e-5, 1.0e-5, 1.0e-5, 1.0e-5,
1.0e-6, 0.0, 0.0, 0.0, 8.6173324e-5, 573};
//---------------------------------------------------------
//INITIALIZATIONS:
//init r[]:
for(i = 0; i < 78; i++) {
mpf_init(r[i]);
}
//init r_f[]:
for(i = 0; i < 78; i++) {
mpf_init(r_f[i]);
}
//init r_b[]:
for(i = 0; i < 78; i++) {
mpf_init(r_b[i]);
}
//init forward and reverse rate constants:
initArray(k_f, in_k_f, 78);
initArray(k_b, in_k_b, 78);
//init the various thetas:
mpf_init_set(theta_A , ctx->state[0]);
mpf_init_set(theta_E , ctx->state[1]);
mpf_init_set(theta_F , ctx->state[2]);
mpf_init_set(theta_G , ctx->state[3]);
mpf_init_set(theta_I , ctx->state[4]);
mpf_init_set(theta_L , ctx->state[5]);
mpf_init_set(theta_M , ctx->state[6]);
mpf_init_set(theta_N , ctx->state[7]);
mpf_init_set(theta_O , ctx->state[8]);
mpf_init_set(theta_R , ctx->state[9]);
mpf_init_set(theta_S , ctx->state[10]);
mpf_init_set(theta_U , ctx->state[11]);
mpf_init_set(theta_V , ctx->state[12]);
mpf_init_set(theta_X , ctx->state[13]);
mpf_init_set(free , ctx->state[14]);
mpf_init_set(theta_H , ctx->state[15]);
mpf_init_set(theta_OH , ctx->state[16]);
mpf_init_set(theta_H2O , ctx->state[17]);
mpf_init_set(theta_CH , ctx->state[18]);
mpf_init_set(theta_CH2 , ctx->state[19]);
mpf_init_set(theta_CH3 , ctx->state[20]);
mpf_init_set(theta_CH4 , ctx->state[21]);
mpf_init_set(theta_CHO , ctx->state[22]);
mpf_init_set(theta_CH2O , ctx->state[23]);
mpf_init_set(theta_CH3O , ctx->state[24]);
mpf_init_set(theta_CH3OH , ctx->state[25]);
mpf_init_set(theta_W , ctx->state[26]);
mpf_init_set(theta_T , ctx->state[27]);
mpf_init_set(theta_B , ctx->state[28]);
mpf_init_set(theta_J , ctx->state[29]);
mpf_init_set(theta_P , ctx->state[30]);
mpf_init_set(theta_C , ctx->state[31]);
mpf_init_set(theta_D , ctx->state[32]);
mpf_init_set(theta_K , ctx->state[33]);
mpf_init_set(theta_Q , ctx->state[34]);
mpf_init_set(theta_Y , ctx->state[35]);
mpf_init_set(theta_Z , ctx->state[36]);
mpf_init_set(theta_Z1 , ctx->state[37]);
mpf_init_set(theta_CO , ctx->state[38]);
//init K_H, temp, and e:
mpf_init(K_H);
mpf_init(temp);
mpf_init(e);
//define e to 50 digits of precision:
gmp_sscanf("2.71828182845904523536028747135266249775724709369995", "%F", e);
//init partial pressures:
mpf_init_set_d(p_A , partialPressures[0]);
mpf_init_set_d(p_H2 , partialPressures[1]);
mpf_init_set_d(p_M , partialPressures[2]);
mpf_init_set_d(p_S , partialPressures[3]);
mpf_init_set_d(p_X , partialPressures[4]);
mpf_init_set_d(p_K , partialPressures[5]);
mpf_init_set_d(p_CO , partialPressures[6]);
mpf_init_set_d(p_H2O , partialPressures[7]);
mpf_init_set_d(p_CH4 , partialPressures[8]);
mpf_init_set_d(p_CH3OH , partialPressures[9]);
mpf_init_set_d(KB , partialPressures[10]);
mpf_init_set_d(T , partialPressures[11]);
//---------------------------------------------------------
//MAIN MATH KERNEL:
//FORWARD REACTION RATES:
// calculate rates for all elementary steps.
mpf_mul( r_f[0], k_f[0], p_A);
mpf_mul( r_f[0], r_f[0], free);
mpf_mul( r_f[0], r_f[0], free);
mpf_mul( r_f[0], r_f[0], free);
mpf_mul( r_f[0], r_f[0], free);
mpf_mul( r_f[1], k_f[1], theta_A);
mpf_mul( r_f[1], r_f[1], theta_H);
//r_f[2] and r_f[3] handled later on...
mpf_mul( r_f[4], k_f[4], theta_A);
mpf_mul( r_f[4], r_f[4], free);
mpf_mul( r_f[5], k_f[5], theta_A);
mpf_mul( r_f[5], r_f[5], free);
mpf_mul( r_f[6], k_f[6], theta_A);
mpf_mul( r_f[6], r_f[6], free);
mpf_mul( r_f[7], k_f[7], theta_A);
mpf_mul( r_f[7], r_f[7], free);
mpf_mul( r_f[8], k_f[8], theta_B);
mpf_mul( r_f[8], r_f[8], free);
mpf_mul( r_f[8], r_f[8], free);
//r_f[9] and r_f[10] handled later on...
mpf_mul( r_f[11], k_f[11], theta_E);
mpf_mul( r_f[11], r_f[11], theta_H);
mpf_mul( r_f[12], k_f[12], theta_F);
mpf_mul( r_f[12], r_f[12], free);
mpf_mul( r_f[13], k_f[13], theta_F);
mpf_mul( r_f[13], r_f[13], free);
mpf_mul( r_f[14], k_f[14], theta_F);
mpf_mul( r_f[15], k_f[15], theta_G);
mpf_mul( r_f[15], r_f[15], theta_H);
mpf_mul( r_f[16], k_f[16], theta_G);
mpf_mul( r_f[16], r_f[16], free);
mpf_mul( r_f[17], k_f[17], theta_I);
mpf_mul( r_f[17], r_f[17], free);
mpf_mul( r_f[18], k_f[18], theta_I);
mpf_mul( r_f[18], r_f[18], free);
mpf_mul( r_f[18], r_f[18], free);
mpf_mul( r_f[19], k_f[19], theta_J);
//r_f[20] handled later on...
mpf_mul( r_f[21], k_f[21], theta_L);
mpf_mul( r_f[21], r_f[21], free);
mpf_mul( r_f[22], k_f[22], theta_L);
mpf_mul( r_f[22], r_f[22], free);
mpf_mul( r_f[23], k_f[23], theta_M);
mpf_mul( r_f[23], r_f[23], free);
mpf_mul( r_f[24], k_f[24], theta_M);
mpf_mul( r_f[24], r_f[24], theta_H);
mpf_mul( r_f[25], k_f[25], theta_N);
mpf_mul( r_f[25], r_f[25], theta_H);
mpf_mul( r_f[26], k_f[26], theta_O);
mpf_mul( r_f[26], r_f[26], free);
mpf_mul( r_f[27], k_f[27], theta_O);
mpf_mul( r_f[27], r_f[27], free);
mpf_mul( r_f[28], k_f[28], theta_P);
mpf_mul( r_f[28], r_f[28], theta_H);
//r[29] handled later on...
mpf_mul( r_f[30], k_f[30], theta_R);
mpf_mul( r_f[30], r_f[30], theta_H);
mpf_mul( r_f[31], k_f[31], theta_S);
mpf_mul( r_f[31], r_f[31], free);
mpf_mul( r_f[32], k_f[32], theta_S);
mpf_mul( r_f[32], r_f[32], theta_H);
mpf_mul( r_f[33], k_f[33], theta_T);
mpf_mul( r_f[33], r_f[33], free);
mpf_mul( r_f[34], k_f[34], theta_U);
mpf_mul( r_f[34], r_f[34], theta_H);
mpf_mul( r_f[35], k_f[35], theta_V);
mpf_mul( r_f[35], r_f[35], theta_H);
mpf_mul( r_f[36], k_f[36], theta_W);
mpf_mul( r_f[37], k_f[37], theta_F);
mpf_mul( r_f[37], r_f[37], free);
//what happened to r_38?!
mpf_mul( r_f[39], k_f[39], theta_I);
mpf_mul( r_f[39], r_f[39], free);
mpf_mul( r_f[39], r_f[39], free);
mpf_mul( r_f[40], k_f[40], theta_B);
mpf_mul( r_f[40], r_f[40], free);
mpf_mul( r_f[40], r_f[40], free);
mpf_mul( r_f[41], k_f[41], theta_CH3O);
mpf_mul( r_f[41], r_f[41], theta_H);
mpf_mul( r_f[42], k_f[42], theta_CH);
mpf_mul( r_f[42], r_f[42], theta_H);
mpf_mul( r_f[43], k_f[43], theta_CH2);
mpf_mul( r_f[43], r_f[43], theta_H);
mpf_mul( r_f[44], k_f[44], theta_CH3);
mpf_mul( r_f[44], r_f[44], theta_H);
mpf_mul( r_f[45], k_f[45], theta_OH);
mpf_mul( r_f[45], r_f[45], theta_H);
mpf_mul( r_f[46], k_f[46], theta_CHO);
mpf_mul( r_f[46], r_f[46], theta_H);
mpf_mul( r_f[47], k_f[47], theta_CH2O);
mpf_mul( r_f[47], r_f[47], theta_H);
mpf_mul( r_f[48], k_f[48], theta_S);
mpf_mul( r_f[49], k_f[49], theta_M);
mpf_mul( r_f[50], k_f[50], theta_X);
mpf_mul( r_f[51], k_f[51], theta_CH3OH);
mpf_mul( r_f[52], k_f[52], theta_CH4);
mpf_mul( r_f[53], k_f[53], theta_H2O);
mpf_mul( r_f[54], k_f[54], theta_K);
//not using r_f[55] through r_f[74]?!
//also, consider making below assignments in-order (might help optimizer).
mpf_mul( r_f[71], k_f[71], theta_O);
mpf_mul( r_f[71], r_f[71], free);
mpf_mul( r_f[72], k_f[72], theta_Z);
mpf_mul( r_f[72], r_f[72], free);
mpf_mul( r_f[73], k_f[73], theta_Z);
mpf_mul( r_f[73], r_f[73], free);
mpf_mul( r_f[74], k_f[74], theta_Z1);
mpf_mul( r_f[75], k_f[75], theta_G);
mpf_mul( r_f[75], r_f[75], theta_H);
mpf_mul( r_f[76], k_f[76], theta_Y);
mpf_mul( r_f[76], r_f[76], free);
mpf_mul( r_f[77], k_f[77], theta_CO);
mpf_mul( r_f[77], r_f[77], theta_H);
//
// steps including C, D, K, Q.
mpf_mul( r_f[2], k_f[2], theta_A);
mpf_mul( r_f[2], r_f[2], theta_H);
mpf_mul( r_f[3], k_f[3], theta_A);
mpf_mul( r_f[3], r_f[3], free);
mpf_mul( r_f[9], k_f[9], theta_C);
mpf_mul( r_f[9], r_f[9], free);
mpf_mul( r_f[10], k_f[10], theta_D);
mpf_mul( r_f[10], r_f[10], theta_H);
mpf_mul( r_f[20], k_f[20], theta_K);
mpf_mul( r_f[20], r_f[20], free);
mpf_mul( r_f[29], k_f[29], theta_Q);
mpf_mul( r_f[29], r_f[29], free);
//REVERSE REACTION RATES:
mpf_mul( r_b[0], k_b[0], theta_A);
mpf_mul( r_b[1], k_b[1], theta_B);
mpf_mul( r_b[1], r_b[1], free);
//r[2] and r[3] handled later on...
mpf_mul( r_b[4], k_b[4], theta_E);
mpf_mul( r_b[4], r_b[4], theta_CH3O);
mpf_mul( r_b[5], k_b[5], theta_F);
mpf_mul( r_b[5], r_b[5], theta_H);
mpf_mul( r_b[6], k_b[6], theta_G);
mpf_mul( r_b[6], r_b[6], theta_CH3);
mpf_mul( r_b[7], k_b[7], theta_I);
mpf_mul( r_b[7], r_b[7], theta_H);
mpf_mul( r_b[8], k_b[8], theta_J);
mpf_mul( r_b[8], r_b[8], theta_H);
//r[9] and r[10] handled later on...
mpf_mul( r_b[11], k_b[11], theta_S);
mpf_mul( r_b[11], r_b[11], free);
mpf_mul( r_b[12], k_b[12], theta_E);
mpf_mul( r_b[12], r_b[12], theta_CH2O);
mpf_mul( r_b[13], k_b[13], theta_L);
mpf_mul( r_b[13], r_b[13], theta_H);
mpf_mul( r_b[14], k_b[14], theta_G);
mpf_mul( r_b[14], r_b[14], theta_CH2);
mpf_mul( r_b[15], k_b[15], theta_M);
mpf_mul( r_b[15], r_b[15], free);
mpf_mul( r_b[16], k_b[16], theta_N);
mpf_mul( r_b[16], r_b[16], theta_OH);
mpf_mul( r_b[17], k_b[17], theta_N);
mpf_mul( r_b[17], r_b[17], theta_CH3O);
mpf_mul( r_b[18], k_b[18], theta_O);
mpf_mul( r_b[18], r_b[18], theta_H);
mpf_mul( r_b[19], k_b[19], theta_P);
mpf_mul( r_b[19], r_b[19], theta_CH2);
//r[20] handled later on...
mpf_mul( r_b[21], k_b[21], theta_E);
mpf_mul( r_b[21], r_b[21], theta_CHO);
mpf_mul( r_b[22], k_b[22], theta_G);
mpf_mul( r_b[22], r_b[22], theta_CH);
mpf_mul( r_b[23], k_b[23], theta_E);
mpf_mul( r_b[23], r_b[23], theta_OH);
mpf_mul( r_b[24], k_b[24], theta_T);
mpf_mul( r_b[25], k_b[25], theta_R);
mpf_mul( r_b[25], r_b[25], free);
mpf_mul( r_b[26], k_b[26], theta_N);
mpf_mul( r_b[26], r_b[26], theta_CH2O);
mpf_mul( r_b[27], k_b[27], theta_U);
mpf_mul( r_b[27], r_b[27], theta_CH2);
mpf_mul( r_b[28], k_b[28], theta_T);
mpf_mul( r_b[28], r_b[28], free);
//r[29] handled later on...
mpf_mul( r_b[30], k_b[30], theta_S);
mpf_mul( r_b[30], r_b[30], free);
mpf_mul( r_b[31], k_b[31], theta_V);
mpf_mul( r_b[31], r_b[31], theta_OH);
mpf_mul( r_b[32], k_b[32], theta_W);
mpf_mul( r_b[32], r_b[32], free);
mpf_mul( r_b[33], k_b[33], theta_S);
mpf_mul( r_b[33], r_b[33], theta_OH);
mpf_mul( r_b[34], k_b[34], theta_G);
mpf_mul( r_b[34], r_b[34], free);
mpf_mul( r_b[34], r_b[34], free);
mpf_mul( r_b[35], k_b[35], theta_X);
mpf_mul( r_b[35], r_b[35], free);
mpf_mul( r_b[35], r_b[35], free);
mpf_mul( r_b[36], k_b[36], theta_X);
mpf_mul( r_b[36], r_b[36], theta_OH);
mpf_mul( r_b[37], k_b[37], theta_O);
mpf_mul( r_b[37], r_b[37], theta_H);
//what happened to r_38?!
mpf_mul( r_b[39], k_b[39], theta_U);
mpf_mul( r_b[39], r_b[39], theta_CH3);
mpf_mul( r_b[40], k_b[40], theta_S);
mpf_mul( r_b[40], r_b[40], theta_CH3O);
mpf_mul( r_b[41], k_b[41], theta_CH3OH);
mpf_mul( r_b[41], r_b[41], free);
mpf_mul( r_b[42], k_b[42], theta_CH2);
mpf_mul( r_b[42], r_b[42], free);
mpf_mul( r_b[43], k_b[43], theta_CH3);
mpf_mul( r_b[43], r_b[43], free);
mpf_mul( r_b[44], k_b[44], theta_CH4);
mpf_mul( r_b[44], r_b[44], free);
mpf_mul( r_b[45], k_b[45], theta_H2O);
mpf_mul( r_b[45], r_b[45], free);
mpf_mul( r_b[46], k_b[46], theta_CH2O);
mpf_mul( r_b[46], r_b[46], free);
mpf_mul( r_b[47], k_b[47], theta_CH3O);
mpf_mul( r_b[47], r_b[47], free);
mpf_mul( r_b[47], r_b[47], free);
mpf_mul( r_b[48], k_b[48], p_S);
mpf_mul( r_b[48], r_b[48], free);
mpf_mul( r_b[48], r_b[48], free);
mpf_mul( r_b[48], r_b[48], free);
mpf_mul( r_b[48], r_b[48], free);
mpf_mul( r_b[49], k_b[49], p_M);
mpf_mul( r_b[49], r_b[49], free);
mpf_mul( r_b[49], r_b[49], free);
mpf_mul( r_b[49], r_b[49], free);
mpf_mul( r_b[49], r_b[49], free);
mpf_mul( r_b[50], k_b[50], p_X);
mpf_mul( r_b[50], r_b[50], free);
mpf_mul( r_b[50], r_b[50], free);
mpf_mul( r_b[50], r_b[50], free);
mpf_mul( r_b[51], k_b[51], p_CH3OH);
mpf_mul( r_b[51], r_b[51], free);
mpf_mul( r_b[52], k_b[52], p_CH4);
mpf_mul( r_b[52], r_b[52], free);
mpf_mul( r_b[53], k_b[53], p_H2O);
mpf_mul( r_b[53], r_b[53], free);
mpf_mul( r_b[54], k_b[54], p_K);
mpf_mul( r_b[54], r_b[54], free);
mpf_mul( r_b[54], r_b[54], free);
mpf_mul( r_b[54], r_b[54], free);
mpf_mul( r_b[54], r_b[54], free);
//not using r[55] through r[74]?!
//also, consider making below assignments in-order (might help optimizer).
mpf_mul( r_b[71], k_b[71], theta_Z);
mpf_mul( r_b[71], r_b[71], theta_H);
mpf_mul( r_b[72], k_b[72], theta_U);
mpf_mul( r_b[72], r_b[72], theta_CH);
mpf_mul( r_b[73], k_b[73], theta_Z1);
mpf_mul( r_b[73], r_b[73], theta_H);
mpf_mul( r_b[74], k_b[74], theta_N);
mpf_mul( r_b[74], r_b[74], theta_CO);
mpf_mul( r_b[75], k_b[75], theta_Y);
mpf_mul( r_b[75], r_b[75], free);
mpf_mul( r_b[76], k_b[76], theta_R);
mpf_mul( r_b[76], r_b[76], theta_OH);
mpf_mul( r_b[77], k_b[77], theta_CHO);
//
// steps including C, D, K, Q.
mpf_mul( r_b[2], k_b[2], theta_C);
mpf_mul( r_b[2], r_b[2], free);
mpf_mul( r_b[3], k_b[3], theta_D);
mpf_mul( r_b[3], r_b[3], theta_OH);
mpf_mul( r_b[9], k_b[9], theta_K);
mpf_mul( r_b[9], r_b[9], theta_OH);
mpf_mul( r_b[10], k_b[10], theta_K);
mpf_mul( r_b[10], r_b[10], free);
mpf_mul( r_b[20], k_b[20], theta_Q);
mpf_mul( r_b[20], r_b[20], theta_H);
mpf_mul( r_b[29], k_b[29], theta_R);
mpf_mul( r_b[29], r_b[29], theta_CH2);
//OVERALL REACTION RATES:
for(i = 0; i < 78; i++) {
mpf_sub( r[i], r_f[i], r_b[i]);
}
//---------------------------------------------------------
// apply the steady state approximation for all thetas.
//NOTE: need to put in GNU MP ops + rewrite to array accesses.
/*out[0] = r_04 + r_12 + r_21 + r_23 - r_11; // d(theta_E)/dt=0
out[1] = r_05 - r_12 - r_13 - r_14 - r_37; // d(theta_F)/dt=0
out[2] = r_06 + r_14 + r_22 + r_34 - r_15 - r_16 - r_75; // d(theta_G)/dt=0
out[3] = r_07 - r_17 - r_18 - r_39; // d(theta_I)/dt=0
out[4] = r_13 - r_21 - r_22; // d(theta_L)/dt=0
out[5] = r_15 - r_23 - r_24 - r_49; // d(theta_M)/dt=0 catechol
out[6] = r_16 + r_17 + r_26 + r_74 - r_25; // d(theta_N)/dt=0
out[7] = r_18 + r_37 - r_26 - r_27 - r_71; // d(theta_O)/dt=0
out[8] = r_25 + r_29 + r_76 - r_30; // d(theta_R)/dt=0
out[9] = r_11 + r_30 + r_33 + r_40 - r_31 - r_32 - r_48; // d(theta_S)/dt=0 phenol
out[10] = r_27 + r_39 + r_72 - r_34; // d(theta_U)/dt=0
out[11] = r_31 - r_35; // d(theta_V)/dt=0
out[12] = r_35 + r_36 - r_50; // d(theta_X)/dt=0 benzene
out[13] = r_03 + r_09 + r_23 + r_31 + r_31 + r_33 - r_45; // d(theta_OH)/dt=0
out[14] = r_45 - r_53; // d(theta_H2O)/dt=0
out[15] = r_22 + r_72 - r_42; // d(theta_CH)/dt =0
out[16] = r_14 + r_19 + r_27 + r_29 + r_42 - r_43; // d(theta_CH2)/dt=0
out[17] = r_06 + r_43 - r_44; // d(theta_CH3)/dt=0
out[18] = r_44 - r_52; // d(theta_CH4)/dt=0
out[19] = r_21 + r_77 - r_46; // d(theta_CHO)/dt=0
out[20] = r_12 + r_26 + r_46 - r_47; // d(theta_CH2O)/dt=0
out[21] = r_04 + r_17 + r_47 - r_41; // d(theta_CH3O)/dt=0
out[22] = r_41 - r_51; // d(theta_CH3OH)/dt=0
out[23] = r_00 - r_01 - r_04 - r_05 - r_06 - r_07; // d(theta_A)/dt=0
// out[23] = theta_A - k_00_f/k_00_b*p_A*free*free*free*free; // d(theta_A)/dt=0 if step 0 is in equilibrium.
out[24] = r_32 - r_36; // d(theta_W)/dt=0
out[25] = r_24 + r_28 - r_33; // d(theta_T)/dt=0
out[26] = r_01 - r_08 - r_40; // d(theta_B)/dt=0
out[27] = r_08 - r_19; // d(theta_J)/dt=0
out[28] = r_19 - r_28; // d(theta_P)/dt=0
out[29] = theta_H - exp(-( (-1.374+0.076+0.683)/2 + 2*0.084*(theta_H-0.139))/KB/T)*pow(p_H2,0.5)*free; //theta_H
out[30] = r_02 - r_09; // d(theta_C)/dt=0
out[31] = r_03 - r_10; // d(theta_D)/dt=0
out[32] = r_09 + r_10 - r_20 - r_54; // d(theta_K)/dt=0
out[33] = r_20 - r_29; // d(theta_Q)/dt=0
out[34] = r_75 - r_76; // d(theta_Y)/dt=0
out[35] = r_71 - r_72 - r_73; // d(theta_Z)/dt=0
out[36] = r_73 - r_74; // d(theta_Z1)/dt=0
out[37] = theta_CO - exp(-(-2.131+0.028+1.764)/KB/T)*p_CO*free; // d(theta_CO)/dt=0*/
// finally the summation of all thetas should be 1.
//NOTE: need to put in GNU MP ops.
/*mpf_set(out[38], ( 4*ctx->state[0] + 4*ctx->state[1] + 4*ctx->state[2] + 4*ctx->state[3]
+ 4*ctx->state[4] + 4*ctx->state[5] + 4*ctx->state[6] + 4*ctx->state[7]
+ 4*ctx->state[8] + 4*ctx->state[9] + 4*ctx->state[10] + 5*ctx->state[11]
+ 3*ctx->state[12] + 3*ctx->state[13] + ctx->state[14] + ctx->state[15]
+ ctx->state[16] + ctx->state[17] + ctx->state[18] + 2*ctx->state[19]
+ ctx->state[20] + ctx->state[21] + 2*ctx->state[22] + 2*ctx->state[23]
+ ctx->state[24] + ctx->state[25] + 4*ctx->state[26] + 5*ctx->state[27]
+ 4*ctx->state[28] + 4*ctx->state[29] + 5*ctx->state[30] + 4*ctx->state[31]
+ 4*ctx->state[32] + 4*ctx->state[33] + 5*ctx->state[34] + 4*ctx->state[35]
+ 4*ctx->state[36] + 4*ctx->state[37] + ctx->state[38] - 1.00 )
);*/
//NOTE: need to put in GNU MP ops + rewrite to array accesses.
/*K_H = exp(-( (-1.374+0.076+0.683)/2 + 2*0.084*(theta_H-0.139))/KB/T);*/
//---------------------------------------------------------
//OUTPUT:
//To send output to a file, run this program like so:
//`$ ./theta.exe > output.txt`
printf("OVERALL REACTION RATES:\n");
for(i = 0; i < 78; i++) {
gmp_printf("r[%d] = %Fg\n", i, r[i]);
}
gmp_printf("K_H = %Fg\n", K_H);
printf("\nFORWARD REACTION RATES:\n");
for(i = 0; i < 78; i++) {
gmp_printf("r_f[%d] = %Fg\n", i, r_f[i]);
}
printf("\nREVERSE REACTION RATES:\n");
for(i = 0; i < 78; i++) {
gmp_printf("r_b[%d] = %Fg\n", i, r_b[i]);
}
//---------------------------------------------------------
//FREES:
//free up the memory GNU MP allocated behind the scenes:
//free r[]:
for(i = 0; i < 78; i++) {
mpf_clear(r[i]);
}
//free r_f[]:
for(i = 0; i < 78; i++) {
mpf_clear(r_f[i]);
}
//free r_b[]:
for(i = 0; i < 78; i++) {
mpf_clear(r_b[i]);
}
//free forward and reverse rate constants:
clearArray(k_f, 78);
clearArray(k_b, 78);
//free the various thetas:
mpf_clear(theta_A);
mpf_clear(theta_E);
mpf_clear(theta_F);
mpf_clear(theta_G);
mpf_clear(theta_I);
mpf_clear(theta_L);
mpf_clear(theta_M);
mpf_clear(theta_N);
mpf_clear(theta_O);
mpf_clear(theta_R);
mpf_clear(theta_S);
mpf_clear(theta_U);
mpf_clear(theta_V);
mpf_clear(theta_X);
mpf_clear(free);
mpf_clear(theta_H);
mpf_clear(theta_OH);
mpf_clear(theta_H2O);
mpf_clear(theta_CH);
mpf_clear(theta_CH2);
mpf_clear(theta_CH3);
mpf_clear(theta_CH4);
mpf_clear(theta_CHO);
mpf_clear(theta_CH2O);
mpf_clear(theta_CH3O);
mpf_clear(theta_CH3OH);
mpf_clear(theta_W);
mpf_clear(theta_T);
mpf_clear(theta_B);
mpf_clear(theta_J);
mpf_clear(theta_P);
mpf_clear(theta_C);
mpf_clear(theta_D);
mpf_clear(theta_K);
mpf_clear(theta_Q);
mpf_clear(theta_Y);
mpf_clear(theta_Z);
mpf_clear(theta_Z1);
mpf_clear(theta_CO);
//free K_H, temp, and e:
mpf_clear(K_H);
mpf_clear(temp);
mpf_clear(e);
//free partial pressures:
mpf_clear(p_A);
mpf_clear(p_H2);
mpf_clear(p_M);
mpf_clear(p_S);
mpf_clear(p_X);
mpf_clear(p_K);
mpf_clear(p_CO);
mpf_clear(p_H2O);
mpf_clear(p_CH4);
mpf_clear(p_CH3OH);
mpf_clear(KB);
mpf_clear(T);
//---------------------------------------------------------
}
Float::Float(const Float& f)
{
mpf_init_set(value, f.value);
}
//------------------------------------------------------------------------------
// Name:
//------------------------------------------------------------------------------
knumber_float::knumber_float(const knumber_float *value) {
mpf_init_set(mpf_, value->mpf_);
}
/* f_freq() -- frequency test on real numbers 0<=f<1*/
static void
f_freq (const unsigned l1runs, const unsigned l2runs,
mpf_t fvec[], const unsigned long n)
{
unsigned f;
mpf_t f_p, f_p_prob;
mpf_t f_m, f_m_prob;
mpf_t *l1res; /* level 1 result array */
mpf_init (f_p); mpf_init (f_m);
mpf_init (f_p_prob); mpf_init (f_m_prob);
/* Allocate space for 1st level results. */
l1res = (mpf_t *) malloc (l2runs * 2 * sizeof (mpf_t));
if (NULL == l1res)
{
fprintf (stderr, "stat: malloc failure\n");
exit (1);
}
printf ("\nEquidistribution/Frequency test on real numbers (0<=X<1):\n");
printf ("\tKp\t\tKm\n");
for (f = 0; f < l2runs; f++)
{
/* f_printvec (fvec, n); */
mpf_freqt (f_p, f_m, fvec + f * n, n);
/* what's the probability of getting these results? */
ks_table (f_p_prob, f_p, n);
ks_table (f_m_prob, f_m, n);
if (l1runs == 0)
{
/*printf ("%u:\t", f + 1);*/
print_ks_results (f_p, f_p_prob, f_m, f_m_prob, stdout);
}
else
{
/* save result */
mpf_init_set (l1res[f], f_p);
mpf_init_set (l1res[f + l2runs], f_m);
}
}
/* Now, apply the KS test on the results from the 1st level rounds
with the distribution
F(x) = 1 - pow(e, -2*x^2) [Knuth, vol 2, p.51] */
if (l1runs != 0)
{
/*printf ("-------------------------------------\n");*/
/* The Kp's. */
ks (f_p, f_m, l1res, Pks, l2runs);
ks_table (f_p_prob, f_p, l2runs);
ks_table (f_m_prob, f_m, l2runs);
printf ("Kp:\t");
print_ks_results (f_p, f_p_prob, f_m, f_m_prob, stdout);
/* The Km's. */
ks (f_p, f_m, l1res + l2runs, Pks, l2runs);
ks_table (f_p_prob, f_p, l2runs);
ks_table (f_m_prob, f_m, l2runs);
printf ("Km:\t");
print_ks_results (f_p, f_p_prob, f_m, f_m_prob, stdout);
}
mpf_clear (f_p); mpf_clear (f_m);
mpf_clear (f_p_prob); mpf_clear (f_m_prob);
free (l1res);
}
