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Hi, I have encountered a strange error on opening certain files. Emacs will completely freeze up (cpu 99%) when opening certain files. I'm not really sure what the difference between files that work and do not work, but I've attached the output from the debugger:
* substitute-command-keys("Quit")
c-forward-decl-or-cast-1(3098 arglist nil)
#f(compiled-function (match-pos inside-macro &optional toplev) #<bytecode -0xdbad6147da63c60>)(3098 nil t)
c-find-decl-spots(3129 "[[:alpha:]]" nil #f(compiled-function (match-pos inside-macro &optional toplev) #<bytecode -0xdbad6147da63c60>))
c-find-types-background(2021 3129)
c-type-finder-timer-func()
apply(c-type-finder-timer-func nil)
timer-event-handler([t 25032 1614 700213 nil c-type-finder-timer-func nil nil 0 nil])
I have also attached the file which caused this error:
functions {
#include absori.stan
#include tbabs.stan
#include powerlaw.stan
#include cstat.stan
#include partial_log_like.stan
}
data{
int N_grbs;
int N_ene;
int N_chan;
matrix[N_chan, N_ene] rsp[N_grbs];
vector[N_grbs] z; //redshift
vector[N_grbs] nH_mw;
vector[N_ene] precomputed_absorp[N_grbs];
vector[N_ene] host_precomputed_absorp[N_grbs];
vector[N_grbs] exposure_ratio;
vector[N_ene] ene_avg[N_grbs];
vector[N_ene] ene_width[N_grbs];
int n_chans_used[N_grbs];
vector[N_chan] counts[N_grbs];
vector[N_chan] bkg[N_grbs];
int mask[N_grbs,N_chan];
vector[N_grbs] exposure;
// absori input
real xi;
int atomicnumber[10];
real ion[10,26,10];
real sigma[10,26,721];
vector[721] spec;
vector[10] abundance;
matrix[10,26] sum_sigma_interp[N_grbs, N_ene];
}
transformed data{
int all_N[N_grbs];
int grainsize = 1;
//mw abs is fixed
vector[N_ene] mw_abs[N_grbs];
for (n in 1:N_grbs){
mw_abs[n] = absorption(nH_mw[n], precomputed_absorp[n]);
}
// precalculation of energy bounds
for (n in 1:N_grbs) {
all_N[n] = n;
}
}
parameters{
//vector<upper=0>[N_grbs] index;
real log_nH_host_mu_raw;
real<upper=0> host_alpha; // skew normal paramter
real<lower=0> log_nH_host_sigma;
vector[N_grbs] log_nH_host_raw;
real index_mu;
real<lower=0> index_sigma;
vector[N_grbs] index_raw;
real log_K_mu_raw;
real<lower=0> log_K_sigma;
vector[N_grbs] log_K_raw; // raw energy flux norm
// absori parameter
real log_n0_whim_raw;
real<upper=8> log_t_whim;
}
transformed parameters{
vector[N_grbs] index;
vector[N_grbs] log_K; // log eflux
vector[N_grbs] K;
vector[N_grbs] log_nH_host;
// vector[N_grbs] nH_host;
vector[N_grbs] nH_host_norm;
real log_n0_whim = log_n0_whim_raw -7;
real log_K_mu = log_K_mu_raw - 9;
// absori
real n0_whim = pow(10, log_n0_whim);
// free temp
matrix[10,26] num;
real t_whim=pow(10,log_t_whim);
num = calc_num(spec, t_whim, xi, atomicnumber, sigma, ion);
for (i in 1:10){
num[i] = abundance[i]*num[i];
}
// non centered parameterizartion
log_nH_host = log_nH_host_mu_raw + log_nH_host_raw * log_nH_host_sigma;
index = index_mu + index_raw * index_sigma;
log_K = log_K_mu + log_K_raw * log_K_sigma;
K = pow(10.,log_K);
nH_host_norm = pow(10.,log_nH_host);
}
model{
host_alpha ~ normal(-2,1);
index_raw ~ std_normal();
log_K_raw ~ std_normal();
log_nH_host_raw ~ std_normal();
//log_nH_host_mu_raw ~ skew_normal(0,1, host_alpha);
log_nH_host_raw ~ normal(0,1);
target += normal_lcdf(host_alpha * log_nH_host_raw | 0, 1);
log_nH_host_sigma ~ std_normal();
log_K_mu_raw ~ std_normal();
log_K_sigma ~ std_normal();
index_mu ~ normal(-2, .1);
index_sigma ~ std_normal();
//absori
log_n0_whim_raw ~ normal(0, 2);
log_t_whim ~ normal(6, 2);
target += reduce_sum(partial_log_like_all, all_N, grainsize, N_ene, N_chan, ene_avg, ene_width, mask, n_chans_used, mw_abs, K, index, n0_whim, num, sum_sigma_interp, nH_host_norm, host_precomputed_absorp, rsp, exposure, exposure_ratio, counts, bkg);
}
generated quantities {
}
GNU Emacs 29.0.50 (build 1, x86_64-apple-darwin21.1.0, NS appkit-2113.00 Version 12.0.1 (Build 21A559)) of 2021-11-19
Stan-mode is from the master branch.
Thanks!
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