From 63c1ffd605c730c8d7c0b991d31f822834b62667 Mon Sep 17 00:00:00 2001
From: charlie sievers <charliesievers@charlies-MacBook-Pro.local>
Date: Mon, 7 Oct 2019 19:41:17 -0700
Subject: [PATCH 1/2] Clean up langevin gjf documentation, fixed potential
 langevin gjf bugs

---
 src/fix_langevin.cpp | 25 +++++++++++++++++--------
 1 file changed, 17 insertions(+), 8 deletions(-)

diff --git a/src/fix_langevin.cpp b/src/fix_langevin.cpp
index f805fddb4b..c12cdbaa26 100644
--- a/src/fix_langevin.cpp
+++ b/src/fix_langevin.cpp
@@ -240,7 +240,7 @@ void FixLangevin::init()
       if (strcmp(id,modify->fix[i]->id) == 0) before = 0;
       else if ((modify->fmask[i] && utils::strmatch(modify->fix[i]->style,"^nve")) && before) flag = 1;
     }
-    if (flag && comm->me == 0)
+    if (flag)
       error->all(FLERR,"Fix langevin gjf should come before fix nve");
   }
 
@@ -295,12 +295,12 @@ void FixLangevin::init()
       gfactor1[i] = -atom->mass[i] / t_period / force->ftm2v;
       if (gjfflag)
         gfactor2[i] = sqrt(atom->mass[i]) *
-                    sqrt(2.0*force->boltz/t_period/update->dt/force->mvv2e) /
-                    force->ftm2v;
+          sqrt(2.0*force->boltz/t_period/update->dt/force->mvv2e) /
+          force->ftm2v;
       else
         gfactor2[i] = sqrt(atom->mass[i]) *
-                    sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
-                    force->ftm2v;
+          sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
+          force->ftm2v;
       gfactor1[i] *= 1.0/ratio[i];
       gfactor2[i] *= 1.0/sqrt(ratio[i]);
     }
@@ -1007,12 +1007,21 @@ void FixLangevin::reset_dt()
 {
   if (atom->mass) {
     for (int i = 1; i <= atom->ntypes; i++) {
-      gfactor2[i] = sqrt(atom->mass[i]) *
-        sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
-        force->ftm2v;
+      if (gjfflag)
+        gfactor2[i] = sqrt(atom->mass[i]) *
+          sqrt(2.0*force->boltz/t_period/update->dt/force->mvv2e) /
+          force->ftm2v;
+      else
+        gfactor2[i] = sqrt(atom->mass[i]) *
+          sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) /
+          force->ftm2v;
       gfactor2[i] *= 1.0/sqrt(ratio[i]);
     }
   }
+  if (gjfflag) {
+    gjfa = (1.0-update->dt/2.0/t_period)/(1.0+update->dt/2.0/t_period);
+    gjfsib = sqrt(1.0+update->dt/2.0/t_period);
+  }
 }
 
 /* ---------------------------------------------------------------------- */

From 9b15f4e2dc4efb25730aff73e0d7ec453070e56c Mon Sep 17 00:00:00 2001
From: charlie sievers <charliesievers@campus-048-000.ucdavis.edu>
Date: Tue, 8 Oct 2019 12:47:30 -0700
Subject: [PATCH 2/2] Added the change to langevin gjf documentation

---
 doc/src/fix_langevin.txt | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/doc/src/fix_langevin.txt b/doc/src/fix_langevin.txt
index 07d8b274aa..49ecf96ff6 100644
--- a/doc/src/fix_langevin.txt
+++ b/doc/src/fix_langevin.txt
@@ -246,11 +246,11 @@ velocity given in "Gronbech-Jensen/Farago"_#Gronbech-Jensen; this velocity
 is shown to be systematically lower than the target temperature by a small
 amount, which grows quadratically with the timestep.
 The {gjf} option {vhalf} outputs the 2GJ half-step velocity given in
-"Gronbech Jensen/Gronbech-Jensen"_#2Gronbech-Jensen; this velocity is shown
-to not have any linear statistical errors for any stable time step.
+"Gronbech Jensen/Gronbech-Jensen"_#2Gronbech-Jensen; for linear systems,
+this velocity is shown to not have any statistical errors for any stable time step.
 An overview of statistically correct Boltzmann and Maxwell-Boltzmann
 sampling of true on-site and true half-step velocities is given in
-"Gronbech-Jensen_#1Gronbech-Jensen.
+"Gronbech-Jensen"_#1Gronbech-Jensen.
 Regardless of the choice of output velocity, the sampling of the configurational
 distribution of atom positions is the same, and linearly consistent with the
 target temperature.