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
Fix grompp unbound atom check
2020-03-02
Berk He
s
s
Fix grompp unbound atom check
commit
|
commitdiff
|
tree
2020-03-02
Berk Hess
F
i
x
nrdf
with
p
artia
l
C
OMM remo
v
al
commit
|
commitdiff
|
tree
2020-03-02
Ber
k
H
ess
Fi
x
too
s
mall pairlist
buffer on Intel GPUs
commit
|
commitdiff
|
tree
2020-02-21
Berk Hess
Add
f
a
tal error when
m
ultisim runs
sharing
s
t
ate have
.
.
.
commit
|
commitdiff
|
tree
2020-02-05
Berk Hess
Act
u
all
y
fix PME f
o
rces with F
E
w
i
thout perturbed q/LJ
commit
|
commitdiff
|
tree
2020-02-04
Berk Hess
Actually fix P
M
E
forces with FE wit
h
out pert
u
r
bed q/LJ
commit
|
commitdiff
|
tree
2020-01-23
Berk Hess
Fix DD ran
k
count prime check
commit
|
commitdiff
|
tree
2020-01-22
B
e
r
k
Hess
Fix
ille
g
a
l
memory access in P
M
E c
o
m
m
un
i
cat
i
on
commit
|
commitdiff
|
tree
2020-01-22
Berk Hess
Clarify COMM
/
posres grom
p
p not
e
commit
|
commitdiff
|
tree
2020-01-17
Berk
He
s
s
Add c
h
e
c
k for sh
e
lls
a
nd GPU u
p
date
commit
|
commitdiff
|
tree
2020-01-16
B
e
rk Hess
C
o
rrect fixed redmine i
s
s
u
e id
from
3
297 to
32
9
6
commit
|
commitdiff
|
tree
2020-01-15
Ber
k
Hess
Fix multisim with para
l
lel
simu
l
ation
commit
|
commitdiff
|
tree
2019-12-19
Berk Hess
F
i
x mdrun a
p
pending
inv
a
lidating energ
y
files
commit
|
commitdiff
|
tree
2019-12-18
Berk Hess
Cha
n
ge
grompp decoupling SD
w
a
r
n
ing
t
o note
commit
|
commitdiff
|
tree
2019-12-17
Berk Hess
Add note for CO
M
remova
l
with positio
n
restrain
t
s
commit
|
commitdiff
|
tree
2019-12-02
Berk Hess
Add check for co
u
pled constr
a
ints for CUDA upda
t
e
commit
|
commitdiff
|
tree
2019-12-02
Be
r
k
H
ess
Ext
r
act LINCS CUDA
h
e
l
per functi
o
ns
commit
|
commitdiff
|
tree
2019-11-29
Ber
k
Hess
M
e
rg
e
"
M
erge branch r
e
le
a
se-2019 into r
e
lease-2020
.
.
.
commit
|
commitdiff
|
tree
2019-11-28
Ber
k
H
e
ss
Update doc
u
mena
t
i
on for NPT GPU
u
pd
a
te
commit
|
commitdiff
|
tree
2019-11-28
Ber
k
Hess
Remove assertion f
a
i
lu
r
e in AWH without in
i
t
i
a
l stage
commit
|
commitdiff
|
tree
2019-11-28
Berk Hess
Fix bug with GPU pr
e
ssu
r
e scaling at non T-scaling
.
.
.
commit
|
commitdiff
|
tree
2019-11-26
Berk Hess
Fix issues with
AWH with per
i
odic pu
l
ling
commit
|
commitdiff
|
tree
2019-11-20
B
e
rk Hess
Q
u
iet pdb2gmx an
d
use gmx_fata
l
commit
|
commitdiff
|
tree
2019-11-19
Berk Hess
Fix
b
onde
d
atom com
m
unication perfo
r
mance
commit
|
commitdiff
|
tree
2019-11-18
Ber
k
Hess
Fix intermol
e
c
ular
i
nteractions with DD
commit
|
commitdiff
|
tree
2019-11-07
Berk Hes
s
F
ix
.
gro large box writing
commit
|
commitdiff
|
tree
2019-11-06
Berk Hess
Deprec
a
te
d
s
c
-r-powe
r
=48
commit
|
commitdiff
|
tree
2019-11-01
Berk He
s
s
Add
haveEwaldSurfaceContribut
i
on to Sim
u
la
t
ionWorkloa
d
commit
|
commitdiff
|
tree
2019-10-31
Berk H
e
ss
Update GPU
u
pdat
e
r
e
strictions
commit
|
commitdiff
|
tree
2019-10-30
Berk
H
ess
Fix
w
alls with GPU
u
pdate
commit
|
commitdiff
|
tree
2019-10-29
Berk Hess
Add
m
drun GPU update
d
ocumentation
commit
|
commitdiff
|
tree
2019-10-29
Berk
H
ess
Fix Ewald d
i
pole correcti
o
n
with GPU update
commit
|
commitdiff
|
tree
2019-10-29
Berk
Hess
Disa
b
le pressure coup
l
ing with GPU update
commit
|
commitdiff
|
tree
2019-10-24
Berk Hess
Add boo
l
u
s
e
D
omainD
e
composition in mdrunner
commit
|
commitdiff
|
tree
2019-10-24
Be
r
k Hess
Add
g
mx_mtop_int
e
r
acti
o
n_count()
commit
|
commitdiff
|
tree
2019-10-24
Berk He
s
s
Fix in
i
tializers
in locality
.
h
commit
|
commitdiff
|
tree
2019-10-23
Ber
k
H
ess
Move local
i
ty
.
h f
r
om n
b
nxm to
m
d
types
commit
|
commitdiff
|
tree
2019-10-23
Berk
H
e
s
s
Use gmx::R
a
nge in
N
b
nxm griddi
n
g
func
t
ions
commit
|
commitdiff
|
tree
2019-10-23
Berk Hes
s
Fix ille
g
al memory acce
s
s in FE cal
c
ulations
commit
|
commitdiff
|
tree
2019-10-23
Berk Hess
Expand documentation for nbnxn_put_on_
g
rid()
commit
|
commitdiff
|
tree
2019-10-22
Berk
Hess
Require -e
i
for essent
i
al
dynami
c
s
commit
|
commitdiff
|
tree
2019-10-18
Berk He
s
s
Update
g
rompp cuto
f
f
-sch
e
me war
n
ings
commit
|
commitdiff
|
tree
2019-10-15
B
erk He
s
s
C
onst corre
c
tness for genhydro
commit
|
commitdiff
|
tree
2019-10-12
B
er
k
Hes
s
Add
cla
s
s F
i
xedC
a
p
a
c
ityVector
commit
|
commitdiff
|
tree
2019-10-09
B
e
rk Hess
I
n
crease spc mini
m
ization
t
est tol
e
r
ance
commit
|
commitdiff
|
tree
2019-10-09
Berk H
e
ss
Fix harmless
OpenMP wri
t
e race
commit
|
commitdiff
|
tree
2019-10-09
B
erk
H
ess
Fix GPU atom
d
ata init timer issue
commit
|
commitdiff
|
tree
2019-10-09
Berk Hess
F
ix
rando
m
energ
y
and virial with PME
on GPU on a PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-08
Berk He
s
s
Make nbn
x
m a proper module
commit
|
commitdiff
|
tree
2019-10-08
Berk Hes
s
S
i
mplify ewald_LRcorrec
t
ion(
)
call
s
ignature
commit
|
commitdiff
|
tree
2019-10-04
Berk Hess
Fix
r
a
nd
o
m e
n
ergy and virial with PM
E
on GPU on a PME
.
.
.
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Fix
G
P
U
at
o
m data
i
nit timer issue
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Use gmx::
R
ange for iZon
e
s in
p
air
s
earch
commit
|
commitdiff
|
tree
2019-10-03
Berk Hess
Fix settin
g
maxNu
m
Columns in Nbnxm::GridSet
commit
|
commitdiff
|
tree
2019-10-02
Berk H
e
ss
Fix harm
l
ess OpenMP wri
t
e race
commit
|
commitdiff
|
tree
2019-10-01
Ber
k
Hess
U
se gmx::Range in domd
e
c
commit
|
commitdiff
|
tree
2019-10-01
B
e
rk Hess
C
o
mp
l
etely remove charg
e
group
s
commit
|
commitdiff
|
tree
2019-10-01
Berk
Hess
Simplify DD exclusion counting
commit
|
commitdiff
|
tree
2019-10-01
Berk Hess
Always output
correct
k
inetic at la
s
t
step
commit
|
commitdiff
|
tree
2019-09-30
Berk Hess
Re
m
o
ve ch
a
rge
g
roup code from f
o
r
cere
c
commit
|
commitdiff
|
tree
2019-09-30
Berk
H
ess
Actu
a
lly f
i
x gmx wha
m
w
i
th angle g
e
ometries
commit
|
commitdiff
|
tree
2019-09-29
Berk H
e
ss
Increase ti3p5
minimizatio
n
t
es
t
tolerance
commit
|
commitdiff
|
tree
2019-09-28
Berk He
s
s
Fix C
G
minimiz
a
tion with DD
commit
|
commitdiff
|
tree
2019-09-27
Berk Hes
s
Extract gmx::R
a
nge
commit
|
commitdiff
|
tree
2019-09-27
Berk He
s
s
Fix
lo
c
at
i
on of
a
n
gle in vsite figure
commit
|
commitdiff
|
tree
2019-09-26
Berk
Hes
s
Made mdrun app
e
nd
i
ng wo
r
k again
commit
|
commitdiff
|
tree
2019-09-24
B
e
rk Hess
Remove obsolet
e
dd_ge
t
_ns_ranges()
commit
|
commitdiff
|
tree
2019-09-23
Berk Hess
Limit
Z
en nbnxm
kernel choice to Ze
n
1
commit
|
commitdiff
|
tree
2019-09-22
Ber
k
Hes
s
Re
m
ov
e
cgs_gl from
gmx_
d
omdec_comm_t
commit
|
commitdiff
|
tree
2019-09-21
B
erk Hess
F
i
x incorrect shift forces for CMAP
commit
|
commitdiff
|
tree
2019-09-20
Berk
Hess
Fix DD 1 pulse
c
hec
k
s
without D
L
B
commit
|
commitdiff
|
tree
2019-09-19
Berk
Hess
R
e
move bLocalCG from DD code
commit
|
commitdiff
|
tree
2019-09-19
Berk H
e
ss
Remove ob
s
olet
e
make_exc
l
usions_zone_cg
(
)
commit
|
commitdiff
|
tree
2019-09-19
Berk Hess
Re
m
ove charge gr
o
up data
f
rom
t
_
fo
r
cerec
commit
|
commitdiff
|
tree
2019-09-19
Berk
H
e
ss
Add
h
aveFreeEnergyWork to
D
omain
L
i
fetimeWorkload flags
commit
|
commitdiff
|
tree
2019-09-18
Berk
H
ess
Added free-energ
y
kernel performance
note
commit
|
commitdiff
|
tree
2019-09-18
Ber
k
Hess
Fix incorrect DD n
d
i
m
assertion
commit
|
commitdiff
|
tree
2019-09-17
Berk
H
ess
Remove spurio
u
s newline from log file
commit
|
commitdiff
|
tree
2019-09-17
Ber
k
H
ess
Fi
x
todos for update groups
commit
|
commitdiff
|
tree
2019-09-16
B
e
r
k Hess
Remov
e
obsolete md
p
o
ption
n
s-type
commit
|
commitdiff
|
tree
2019-09-16
Berk Hess
Add
v
irtu
a
l site type
2
FD
commit
|
commitdiff
|
tree
2019-09-16
B
e
rk Hes
s
Re
m
ove cut-off schemes from manual
commit
|
commitdiff
|
tree
2019-09-16
Berk
He
s
s
Add option
request 1D DD
w
i
th 1
p
u
lse
commit
|
commitdiff
|
tree
2019-09-13
Be
r
k H
e
ss
Fix nonbonded-bench compilati
o
n
issue
commit
|
commitdiff
|
tree
2019-09-13
Berk Hess
Add nb
n
xm
kernel benchmark t
o
ol
commit
|
commitdiff
|
tree
2019-09-12
Berk He
s
s
Updated
md
p
d
ocumenta
t
ion for g
r
ou
p
scheme
removal
commit
|
commitdiff
|
tree
2019-09-12
Be
r
k
H
ess
Fix maste
r
n
o
t compiling
commit
|
commitdiff
|
tree
2019-09-12
Be
r
k
Hess
Ena
b
le
T
P
I
w
i
th the Verlet cut-off scheme
commit
|
commitdiff
|
tree
2019-09-09
Berk Hess
R
e
move incorrect check with
r
f-zero
commit
|
commitdiff
|
tree
2019-09-09
B
e
rk Hess
E
x
tract Car
t
es
i
an
d
a
ta
from DDRankSetup
commit
|
commitdiff
|
tree
2019-09-09
Ber
k
Hess
Rename DDSetup to DDGridSetup
commit
|
commitdiff
|
tree
2019-09-09
Ber
k
Hes
s
Clean up PME rank variables
commit
|
commitdiff
|
tree
2019-09-09
Berk Hes
s
Refact
o
r
i
nit_domain_decomposition()
commit
|
commitdiff
|
tree
2019-09-06
Berk
H
e
ss
Ext
r
act ge
t
ting
o
f DDRankSetup
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
Add PP grid info
t
o DDRa
n
kSetup
commit
|
commitdiff
|
tree
2019-09-05
Berk Hess
E
x
tract
D
DRank
S
e
t
up from gmx_domdec_
c
omm_t
commit
|
commitdiff
|
tree
2019-09-05
Berk Hess
Split off gettin
g
of t
h
e D
D
setu
p
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Collect setting
s
fo
r
DD
in DDSettings
commit
|
commitdiff
|
tree
2019-09-04
Berk He
s
s
Extract getti
n
g
of DDSys
t
em
I
nfo
commit
|
commitdiff
|
tree
2019-09-04
Be
r
k Hess
Sim
p
lif
y
handling of DD bonde
d
dis
t
a
nces
commit
|
commitdiff
|
tree
next