repo.or.cz
/
gromacs.git
/
search
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
log
|
graphiclog1
|
graphiclog2
|
commit
|
commitdiff
|
tree
|
refs
|
edit
|
fork
first
·
prev
·
next
Change nbnxn grid reallocation
2018-05-22
B
erk Hess
Ch
a
ng
e
nbnxn grid real
l
o
c
a
t
i
on
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
Use std::vect
o
r in
n
b
n
xn_se
a
rch
_
t
commit
|
commitdiff
|
tree
2018-05-22
Berk Hess
U
se s
t
d::vect
o
r in nbnxn
_
grid_t
commit
|
commitdiff
|
tree
2018-05-18
B
e
rk He
s
s
Clean up in
nbnxn_grid
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Ber
k
H
ess
Split
off domdec distri
b
u
tion and cellsizes
commit
|
commitdiff
|
tree
2018-05-17
B
e
rk Hess
S
p
lit atom red
i
stributio
n
off
f
ro
m
domdec
.
cpp
commit
|
commitdiff
|
tree
2018-05-17
Berk He
s
s
Remov
e
comm
r
ec from set_d
d
box()
commit
|
commitdiff
|
tree
2018-05-15
Berk Hess
Clean up PME domain
c
ou
n
t pas
s
in
g
commit
|
commitdiff
|
tree
2018-05-03
Berk
H
ess
Enabl
e
S
I
MD ve
r
si
o
n of
updat
e
commit
|
commitdiff
|
tree
2018-04-27
Berk Hes
s
Remove
pu
l
l MPI code dupl
i
c
a
tion
commit
|
commitdiff
|
tree
2018-04-24
Berk He
s
s
Fix
in
d
exing issue in the p
u
ll code
commit
|
commitdiff
|
tree
2018-04-16
Berk Hess
Move nato
m
s_mol
o
ut of g
m
x_molblock_t
commit
|
commitdiff
|
tree
2018-04-09
Berk Hess
Co
n
v
e
r
t gmx_molblock_t to C++
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Convert gmx_mt
o
p_t
to
C++
commit
|
commitdiff
|
tree
2018-04-03
B
e
rk Hess
Change wa
r
n
i
n
p filenm to std::string
commit
|
commitdiff
|
tree
2018-04-03
Berk Hess
Do not calcula
t
e
C
OM for pull gr
o
up 0
commit
|
commitdiff
|
tree
2018-03-29
Berk Hess
Move file opening
o
ut
of
i
nit_pull()
commit
|
commitdiff
|
tree
2018-03-29
Berk H
e
ss
Mo
d
ul
a
rize pu
l
l_coord_work
_
t
commit
|
commitdiff
|
tree
2018-03-28
Berk
Hess
Remove mo
l
s from gmx_
m
top_t
commit
|
commitdiff
|
tree
2018-03-20
Berk Hess
Fix gmx
dump
A
WH formatting
i
ssue
commit
|
commitdiff
|
tree
2018-03-20
B
e
rk Hess
Disallo
w
single si
m
ulation
wit
h
multisim
commit
|
commitdiff
|
tree
2018-03-16
Berk He
s
s
Corre
c
t
PMF si
g
n error in
A
W
H
b
i
as sharin
g
commit
|
commitdiff
|
tree
2018-03-16
Be
r
k Hess
F
i
x recent mdrun
s
i
g
naling
b
ug
commit
|
commitdiff
|
tree
2018-03-15
Berk Hess
Fix virial
with external pull potentia
l
and MPI
commit
|
commitdiff
|
tree
2018-03-14
Berk Hess
Improve inter-simulation signaling
commit
|
commitdiff
|
tree
2018-03-14
Berk H
e
ss
Fix mdrun signa
l
ling with
AWH bias
sha
r
ing
commit
|
commitdiff
|
tree
2018-03-14
B
e
rk
Hess
Fix COM pulling
w
i
th extern
a
l
p
oten
t
ial with #ranks>32
commit
|
commitdiff
|
tree
2018-03-14
Be
r
k
Hess
Fix
p
u
l
l bug
with geom
e
try=dir
e
c
tion-
p
e
rio
d
ic
commit
|
commitdiff
|
tree
2018-03-13
Berk
H
ess
A
dd AWH fixes to release notes
commit
|
commitdiff
|
tree
2018-03-13
Berk He
s
s
Fix A
W
H ensemble check
p
ointing
commit
|
commitdiff
|
tree
2018-03-13
B
e
rk Hess
Fi
x
A
WH
d
econ
v
olution wh
e
n sharing a bi
a
s
commit
|
commitdiff
|
tree
2018-03-09
Berk Hess
Correct pdb2gmx
-
missing option
commit
|
commitdiff
|
tree
2018-03-07
Ber
k
He
s
s
Fix mem
o
r
y leak
i
n PME
commit
|
commitdiff
|
tree
2018-03-06
Berk He
s
s
C
o
nvert t_fi
l
e
nm t
o
C++
commit
|
commitdiff
|
tree
2018-03-06
Berk H
e
ss
M
a
ke multi-atom TPI rep
r
od
u
cible
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Wor
k
ar
o
un
d
gcc bug with
g
roup
kernel
t
ables
commit
|
commitdiff
|
tree
2018-03-05
Berk Hess
Leave nullptr opt in t_file
n
m
commit
|
commitdiff
|
tree
2018-03-02
Berk H
e
ss
F
ix c
p
p
c
heck warnin
g
commit
|
commitdiff
|
tree
2018-03-02
B
e
r
k Hess
Fix AWH bias-s
h
ar
i
ng with
parallel simulation
commit
|
commitdiff
|
tree
2018-03-01
Berk Hes
s
Detect AMD S
M
T
topology
commit
|
commitdiff
|
tree
2018-03-01
B
er
k
Hess
Fix mdru
n
multisim with
s
e
parate PME
rank
s
commit
|
commitdiff
|
tree
2018-02-23
Berk Hess
Fi
x
md
i
ntegra
t
o
r with Nose-Hoover coupl
i
n
g
commit
|
commitdiff
|
tree
2018-02-22
Berk Hess
S
implify mdrun tMPI th
r
ead sp
a
w
n
ing
commit
|
commitdiff
|
tree
2018-02-16
B
erk Hess
Co
r
rect
mult
i
sim MPI barrier
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Re
m
ove support
for tp
x
vers
i
o
n
before 58/gmx
4
.
0
commit
|
commitdiff
|
tree
2018-02-14
B
erk Hess
Fix range
b
ug in add_selecti
o
n_group
s
in tngio
.
cpp
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix
grompp net charge
ch
e
ck
commit
|
commitdiff
|
tree
2018-02-14
Berk Hess
Fix grompp
n
et char
g
e c
h
eck
commit
|
commitdiff
|
tree
2018-02-08
Berk
H
ess
Use SIMD bondeds without perturbed
i
nteracti
o
n
s
commit
|
commitdiff
|
tree
2018-02-08
Be
r
k Hess
Allow bonds with distance=0
commit
|
commitdiff
|
tree
2018-02-05
B
e
r
k
Hess
Set c
u
toff modifiers in
forcerec
commit
|
commitdiff
|
tree
2018-02-05
Berk Hess
Fix
ass
e
r
t
ion fa
i
lure in TPI
commit
|
commitdiff
|
tree
2018-01-30
Berk Hess
Removed unuse
d
flag
P
C
A_CA
N
_
RE
A
D_NODE
commit
|
commitdiff
|
tree
2018-01-18
B
erk Hess
Fix CO
M
M re
m
oval on part of the system
commit
|
commitdiff
|
tree
2018-01-18
Berk Hess
Add
check in grompp to avoid asser
t
io
n
f
a
ilur
e
commit
|
commitdiff
|
tree
2018-01-17
B
erk Hess
R
eplace stder
r
prints in filenm
.
c
pp by asserts
commit
|
commitdiff
|
tree
2018-01-17
Berk Hess
Re-enable GPU w
i
th wal
l
s and 1 e
n
ergy group
commit
|
commitdiff
|
tree
2018-01-16
B
e
rk Hess
Remove tumblin
g
ice-cub
e
wa
r
nin
g
w
i
t
h S
D
commit
|
commitdiff
|
tree
2018-01-16
Be
r
k Hess
Avoid mdrun echoing "
N
o option -multi"
commit
|
commitdiff
|
tree
2018-01-09
Berk H
e
ss
R
e
word C
P
U/GPU imbalance
n
otes
commit
|
commitdiff
|
tree
2018-01-09
Ber
k
He
s
s
Do not
turn on DLB at replica exchange
commit
|
commitdiff
|
tree
2018-01-08
Berk Hess
F
i
x triclinic
domain d
e
compositi
o
n bug
commit
|
commitdiff
|
tree
2017-12-19
Ber
k
Hess
Make acceleration
c
orrection
V
CM mode work
commit
|
commitdiff
|
tree
2017-12-19
Be
r
k Hess
Make oversu
b
s
cription warning consiste
n
t
commit
|
commitdiff
|
tree
2017-12-14
Berk Hess
Requ
i
re
-
ntmpi with setting -nto
m
p with GPUs
commit
|
commitdiff
|
tree
2017-12-12
Berk He
s
s
Che
c
k for
l
arge energy at
f
i
rst step
commit
|
commitdiff
|
tree
2017-12-12
Berk
Hess
A
vo
i
d yelling about
thread pinni
n
g
t
wi
c
e
commit
|
commitdiff
|
tree
2017-12-11
B
erk Hess
Add
grompp
note
for PR
pcouple + position restrain
t
s
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Remove SIMD warning for AMD Zen
commit
|
commitdiff
|
tree
2017-12-10
Berk Hess
Tone down note about
no
t
p
i
nning
t
hreads
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Correct
Shake test
tol
e
ra
n
c
es
commit
|
commitdiff
|
tree
2017-12-08
Berk Hess
Add
Viveca
L
indahl as contributor
commit
|
commitdiff
|
tree
2017-12-07
Be
r
k Hes
s
C
h
oose faster nbnx
n
SI
M
D
k
e
rnels on
A
MD Zen
commit
|
commitdiff
|
tree
2017-12-05
Berk Hess
Fi
x
DD exact continuation
b
ug
commit
|
commitdiff
|
tree
2017-12-04
B
erk Hess
Fix
pm
e
gathe
r
i
n
double with AVX(2)_128
commit
|
commitdiff
|
tree
2017-12-04
Berk H
e
ss
Mer
g
e
"Merge branch
relea
s
e-2016
into
r
eleas
e
-2018
.
.
.
commit
|
commitdiff
|
tree
2017-12-04
Berk
Hess
Fixed
initial te
m
peratur
e
re
p
ort
i
ng
commit
|
commitdiff
|
tree
2017-12-04
Berk H
e
ss
Updat
e
mdrun
s
ign
a
l h
e
lp text
commit
|
commitdiff
|
tree
2017-12-04
B
e
rk Hess
Only stop at ns
t
l
i
st steps with -reprod
commit
|
commitdiff
|
tree
2017-12-03
Berk Hes
s
Clear vsite v
e
locities for sim
p
l
e
i
n
te
g
rator
s
commit
|
commitdiff
|
tree
2017-12-03
B
e
rk H
e
ss
T
i
ght
e
n B-spline moduli single precision
t
e
s
t to
l
eran
c
e
.
.
.
commit
|
commitdiff
|
tree
2017-12-02
Berk H
e
s
s
Avoid
assertion failu
r
e in AWH
commit
|
commitdiff
|
tree
2017-11-29
Berk H
e
ss
Ch
a
ng
e
the GP
U
SMT cut-off to quadrati
c
commit
|
commitdiff
|
tree
2017-11-28
Be
r
k
Hess
Update d
o
cume
n
tion of Nose-H
o
over
out
p
ut
commit
|
commitdiff
|
tree
2017-11-28
B
e
rk Hess
Refact
o
r nbnxn exclusio
n
setting
commit
|
commitdiff
|
tree
2017-11-28
Berk H
e
ss
Extend grompp missing energy term
mes
s
age
commit
|
commitdiff
|
tree
2017-11-27
Be
r
k Hess
E
nable aut
o
threa
d
pinning
w
i
t
h
thread limiting
commit
|
commitdiff
|
tree
2017-11-27
Berk Hess
Fix
PME GPU wi
t
h walls
commit
|
commitdiff
|
tree
2017-11-25
B
e
rk Hes
s
Fix compi
l
er warning w
i
thout
MPI
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Disabled
C
UDA timings
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
Speed up nbnxn
buffer cle
a
ring
commit
|
commitdiff
|
tree
2017-11-24
Berk Hess
L
imit SMT wi
t
h PME o
n
GPU
commit
|
commitdiff
|
tree
2017-11-23
Berk Hess
Up
d
ate note
in manual on SD
commit
|
commitdiff
|
tree
2017-11-23
Berk H
e
ss
Correct PME GPU timing naming
commit
|
commitdiff
|
tree
2017-11-20
B
erk Hess
P
r
event P
M
E tuni
n
g excess
i
ve grid
scaling
commit
|
commitdiff
|
tree
2017-11-19
Ber
k
Hess
Add SIMD for AWH
commit
|
commitdiff
|
tree
2017-11-16
Berk
Hess
Also print 1x
1
p
air-list
set
u
p
to log
commit
|
commitdiff
|
tree
2017-11-10
Ber
k
Hess
F
ix genion charge summ
a
tion accuracy
commit
|
commitdiff
|
tree
2017-11-02
Berk Hess
Fix Ekin
at step 0
w
i
t
h COM removal
commit
|
commitdiff
|
tree
2017-11-02
B
erk Hess
Add missing Ewald corre
c
t
ion f
o
r pme-user
commit
|
commitdiff
|
tree
next