From d6f963c232039065ca532a777076093c947204b0 Mon Sep 17 00:00:00 2001
From: Sikorski <sikorski@zib.de>
Date: Fri, 20 Sep 2024 15:39:11 +0200
Subject: [PATCH] fix langevin_girsanov() typos

---
 src/simulators/openmm.jl | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/src/simulators/openmm.jl b/src/simulators/openmm.jl
index 2c7b1ee..1b89824 100644
--- a/src/simulators/openmm.jl
+++ b/src/simulators/openmm.jl
@@ -458,24 +458,26 @@ function langevin_girsanov(sim, q, steps, u)
     M = repeat(masses(sim), inner=3)
 
     # Maxwell-Boltzmann distribution
-    p = randn(length(M)) .* sqrt(M .* kB .* T)
+    p = randn(length(M)) .* sqrt.(M .* kB .* T)
 
     t2 = dt / 2
     a = @. t2 / M # eq 18
     d = @. exp(-ξ * dt) # eq 17
-    f = @. sqrt(kB * T * M * (1 - exp(-2 * γ * dt))) # eq 17
+    f = @. sqrt(kB * T * M * (1 - exp(-2 * ξ * dt))) # eq 17
 
     b = similar(p)
     η = similar(p)
     Δη = similar(p)
+    F = similar(p)
     g = 0
 
+
     for i in 1:steps
         randn!(η)
         @. q += a * p # A
 
         # girsanov part
-        F = u(q) # perturbation force ∇U_bias = -F
+        F .= u(q) # perturbation force ∇U_bias = -F
         @. Δη = (d + 1) / f + dt / 2 * F
         g += η' * Δη + Δη' * Δη / 2
         F .+= force(sim, q) # total force: -∇V - ∇U_bias
@@ -490,5 +492,9 @@ function langevin_girsanov(sim, q, steps, u)
     return q, exp(-g)
 end
 
+function batcheddot(x, y)
+    sum(a .* y, dims=1)
+end
+
 
 end #module
\ No newline at end of file