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Changed the site weights to use doubles #20

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4 changes: 2 additions & 2 deletions src/core_derivatives.c
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Original file line number Diff line number Diff line change
Expand Up @@ -702,7 +702,7 @@ PLL_EXPORT int pll_core_likelihood_derivatives(unsigned int states,
unsigned int parent_sites,
unsigned int child_ids,
const int * invariant,
const unsigned int * pattern_weights,
const double * pattern_weights,
double branch_length,
const double * prop_invar,
double * const * freqs,
Expand Down Expand Up @@ -897,7 +897,7 @@ PLL_EXPORT int pll_core_likelihood_derivatives(unsigned int states,
case PLL_ATTRIB_AB_LEWIS:
{
// TODO: pattern_weight_sum should be stored somewhere!
unsigned int pattern_weight_sum = 0;
double pattern_weight_sum = 0;
for (n = 0; n < ef_sites; ++n)
pattern_weight_sum += pattern_weights[n];

Expand Down
10 changes: 6 additions & 4 deletions src/core_derivatives_avx.c
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Expand Up @@ -1616,7 +1616,7 @@ PLL_EXPORT int pll_core_likelihood_derivatives_avx(unsigned int states,
unsigned int states_padded,
unsigned int rate_cats,
unsigned int ef_sites,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * rate_weights,
const int * invariant,
const double * prop_invar,
Expand Down Expand Up @@ -1840,18 +1840,20 @@ PLL_EXPORT int pll_core_likelihood_derivatives_avx(unsigned int states,
_mm256_mul_pd(v_term2, v_recip0));

/* assumption: no zero weights */
if ((pattern_weights[n-3] | pattern_weights[n-2] |
pattern_weights[n-1] | pattern_weights[n]) == 1)
//if ((pattern_weights[n-3] | pattern_weights[n-2] |
// pattern_weights[n-1] | pattern_weights[n]) == 1)
if (pattern_weights[n-3] == 1.0 && pattern_weights[n-2] == 1.0 &&
pattern_weights[n-1] == 1.0 && pattern_weights[n] == 1.0)
{
/* all 4 weights are 1 -> no multiplication needed */
v_df = _mm256_sub_pd (v_df, v_deriv1);
v_ddf = _mm256_add_pd (v_ddf, v_deriv2);
}
else
{

__m256d v_patw = _mm256_setr_pd(pattern_weights[n-3], pattern_weights[n-2],
pattern_weights[n-1], pattern_weights[n]);

v_df = _mm256_sub_pd (v_df, _mm256_mul_pd(v_deriv1, v_patw));
v_ddf = _mm256_add_pd (v_ddf, _mm256_mul_pd(v_deriv2, v_patw));
}
Expand Down
8 changes: 5 additions & 3 deletions src/core_derivatives_avx2.c
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Expand Up @@ -1540,7 +1540,7 @@ int pll_core_likelihood_derivatives_avx2(unsigned int states,
unsigned int states_padded,
unsigned int rate_cats,
unsigned int ef_sites,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * rate_weights,
const int * invariant,
const double * prop_invar,
Expand Down Expand Up @@ -1764,8 +1764,10 @@ int pll_core_likelihood_derivatives_avx2(unsigned int states,
_mm256_mul_pd(v_term2, v_recip0));

/* assumption: no zero weights */
if ((pattern_weights[n-3] | pattern_weights[n-2] |
pattern_weights[n-1] | pattern_weights[n]) == 1)
//if ((pattern_weights[n-3] | pattern_weights[n-2] |
// pattern_weights[n-1] | pattern_weights[n]) == 1)
if (pattern_weights[n-3] == 1.0 && pattern_weights[n-2] == 1.0 &&
pattern_weights[n-1] == 1.0 && pattern_weights[n] == 1.0)
{
/* all 4 weights are 1 -> no multiplication needed */
v_df = _mm256_sub_pd (v_df, v_deriv1);
Expand Down
20 changes: 10 additions & 10 deletions src/core_likelihood.c
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Expand Up @@ -29,7 +29,7 @@ PLL_EXPORT double pll_core_root_loglikelihood(unsigned int states,
const unsigned int * scaler,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -216,7 +216,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_repeats_generic(unsigned int state
const unsigned int * scaler,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -292,7 +292,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_repeats(unsigned int states,
const unsigned int * scaler,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand All @@ -307,7 +307,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_repeats(unsigned int states,
const unsigned int * scaler,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -357,7 +357,7 @@ double pll_core_edge_loglikelihood_ti_4x4(unsigned int sites,
const double * pmatrix,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -589,7 +589,7 @@ double pll_core_edge_loglikelihood_ti(unsigned int states,
const double * pmatrix,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -932,7 +932,7 @@ double pll_core_edge_loglikelihood_repeats(unsigned int states,
const double * pmatrix,
double ** frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand All @@ -953,7 +953,7 @@ double pll_core_edge_loglikelihood_repeats(unsigned int states,
const double * pmatrix,
double ** frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -1026,7 +1026,7 @@ double pll_core_edge_loglikelihood_repeats_generic(unsigned int states,
const double * pmatrix,
double ** frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -1199,7 +1199,7 @@ double pll_core_edge_loglikelihood_ii(unsigned int states,
const double * pmatrix,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down
22 changes: 11 additions & 11 deletions src/core_likelihood_avx.c
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_avx(unsigned int states,
const unsigned int * scaler,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -118,7 +118,7 @@ PLL_EXPORT double pll_core_root_loglikelihood_repeats_avx(unsigned int states,
const unsigned int * scaler,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -209,7 +209,7 @@ double pll_core_root_loglikelihood_4x4_avx(unsigned int sites,
const unsigned int * scaler,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -291,7 +291,7 @@ double pll_core_edge_loglikelihood_ti_4x4_avx(unsigned int sites,
const double * pmatrix,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -537,7 +537,7 @@ double pll_core_edge_loglikelihood_ti_20x20_avx(unsigned int sites,
const double * pmatrix,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -782,7 +782,7 @@ double pll_core_edge_loglikelihood_ti_avx(unsigned int states,
const double * pmatrix,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -1031,7 +1031,7 @@ double pll_core_edge_loglikelihood_repeats_generic_avx(unsigned int states,
const double * pmatrix,
double ** frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -1278,7 +1278,7 @@ double pll_core_edge_loglikelihood_ii_avx(unsigned int states,
const double * pmatrix,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -1519,7 +1519,7 @@ double pll_core_edge_loglikelihood_ii_4x4_avx(unsigned int sites,
const double * pmatrix,
double * const * frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -1737,7 +1737,7 @@ double pll_core_edge_loglikelihood_repeats_4x4_avx(unsigned int states,
const double * pmatrix,
double ** frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down Expand Up @@ -1957,7 +1957,7 @@ double pll_core_edge_loglikelihood_repeatsbclv_4x4_avx(unsigned int states,
const double * pmatrix,
double ** frequencies,
const double * rate_weights,
const unsigned int * pattern_weights,
const double * pattern_weights,
const double * invar_proportion,
const int * invar_indices,
const unsigned int * freqs_indices,
Expand Down
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