Address reviews

Author: ErikQQY

HISTORY.md

@@ -1,5 +1,9 @@
 # AdvancedHMC Changelog
 
+## 0.9.0
+
+  - To compute the negative energy of a Hamiltonian `h` with parameter `θ` and momentum `r`, use `neg_energy(h, θ, r)` instead of `neg_energy(h, r, θ)`, which is now consistent with the common usage like `phasepoint(h, θ, r)`.
+
 ## 0.8.0
 
   - To make an MCMC transtion from phasepoint `z` using trajectory `τ`(or HMCKernel `κ`) under Hamiltonian `h`, use `transition(h, τ, z)` or `transition(rng, h, τ, z)`(if using HMCKernel, use `transition(h, κ, z)` or `transition(rng, h, κ, z)`).

Project.toml

@@ -1,6 +1,6 @@
 name = "AdvancedHMC"
 uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-version = "0.8.0"
+version = "0.9.0"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"

src/riemannian/hamiltonian.jl

@@ -74,7 +74,8 @@ function step(
         θ_full = copy(θ_init)
         term_1 = ∂H∂r(h, θ_init, r_half).gradient # unchanged across the loop
         for j in 1:(lf.n)
-            θ_full = θ_init + ϵ / 2 * (term_1 + ∂H∂r(h, θ_full, r_half).gradient)
+            grad_r = ∂H∂r(h, θ_full, r_half).gradient
+            θ_full = θ_init + ϵ / 2 * (term_1 + grad_r)
             # println("θ_full :", θ_full)
         end
         #! Eq (18) of Girolami & Calderhead (2011)

src/riemannian/integrator.jl

@@ -76,7 +76,8 @@ function step(
         θ_full = θ_init
         term_1 = ∂H∂r(h, θ_init, r_half).gradient # unchanged across the loop
         for j in 1:(lf.n)
-            θ_full = θ_init + ϵ / 2 * (term_1 + ∂H∂r(h, θ_full, r_half).gradient)
+            grad_r = ∂H∂r(h, θ_full, r_half).gradient
+            θ_full = θ_init + ϵ / 2 * (term_1 + grad_r)
         end
         # eq (18) of Girolami & Calderhead (2011)
         (; value, gradient) = ∂H∂θ(h, θ_full, r_half)