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
Remove group scheme from deprecated release notes
2019-09-16
Kev
i
n B
o
yd
Rem
o
ve
g
roup scheme fro
m
deprecate
d
rele
a
se notes
commit
|
commitdiff
|
tree
2019-09-15
Pascal Merz
Int
r
o
d
uce the modula
r
sim
u
lato
r
commit
|
commitdiff
|
tree
2019-09-15
Peter Kass
o
n
Pa
t
ch gmxapi for Python
3
.
7
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrgang
Normalize usag
e
of GMXTO
O
LCHAINDIR in gm
x
a
p
i setup
.
py
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irr
g
a
ng
Do no
t
use groma
c
s-to
o
lchai
n
in darwin gm
x
api builds
.
commit
|
commitdiff
|
tree
2019-09-13
M
.
Eric Irrga
n
g
Upda
t
e
gmxapi setu
p
.
py
commit
|
commitdiff
|
tree
2019-09-12
Mark A
b
raham
D
i
sable repo
r
t-
m
ethod
s
en
d
-to-end test
commit
|
commitdiff
|
tree
2019-09-12
Szil
á
r
d Páll
Reorg
a
nize on
-
GPU
PME
f
orce reduction fla
g
handling
commit
|
commitdiff
|
tree
2019-09-12
Artem Zhmurov
Change PaddedVector to Pa
d
d
e
dHostVector for force CPU
.
.
.
commit
|
commitdiff
|
tree
2019-09-12
Christia
n
Blau
Add release not
e
for
density
f
i
tting
.
commit
|
commitdiff
|
tree
2019-09-12
Pascal Merz
U
pdate modul
a
r simulator tests
commit
|
commitdiff
|
tree
2019-09-12
Erik Lindah
l
Added
SIM
D
log2
and
pow
m
a
t
h fun
c
t
i
o
n
s
commit
|
commitdiff
|
tree
2019-09-12
Erik Lindah
l
Update SIMD m
a
th
tests and improve accu
r
acy
commit
|
commitdiff
|
tree
2019-09-11
Pau
l
Bauer
Re
m
o
ve -sub op
t
ion from
t
rjconv
commit
|
commitdiff
|
tree
2019-09-11
Artem Zhmu
r
ov
Fix for the post-submi
t
fa
i
l
u
re
commit
|
commitdiff
|
tree
2019-09-11
Artem
Z
hmurov
Decou
p
le
G
P
U
f
or
c
e buff
e
r m
a
na
g
ement
f
ro
m
buffe
r
ops
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irr
g
a
n
g
Use GROMACS CMake to
o
lchain file fo
r
gmxapi
P
ython
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
Paul Bauer
Basi
c
toolchain
to fac
i
lita
t
e GMXAPI buil
d
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Ir
r
gang
Add gm
x
api
.
modify_inp
u
t operation
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Irr
g
a
ng
Provide a gmxapi
.
read_tpr ope
r
atio
n
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eri
c
Irrg
a
ng
Update
g
mxapi
.
sim
u
lati
o
n
.
c
o
n
t
ex
t
details
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
Eric Ir
r
gang
Updat
e
gmxapi P
y
tho
n
package i
n
frastructure for new
.
.
.
commit
|
commitdiff
|
tree
2019-09-11
M
.
E
r
ic Irrg
a
ng
Norma
l
ize s
o
me t
e
st
i
n
g r
e
sourc
e
s for th
e
Pyt
h
on pac
k
ages
.
commit
|
commitdiff
|
tree
2019-09-11
Magnus Lu
n
dborg
Tidy
u
p
t
he FE
kernel
commit
|
commitdiff
|
tree
2019-09-10
Paul Bauer
Fix n
i
ghtly bu
i
ld
commit
|
commitdiff
|
tree
2019-09-10
Szilárd P
á
ll
Use thread-MPI in the gpucomm matri
x
commit
|
commitdiff
|
tree
2019-09-10
Pas
c
al
M
erz
Coordinate P
r
opagators
commit
|
commitdiff
|
tree
2019-09-10
Pascal Mer
z
St
a
t
e
PropagatorD
a
ta: Introduced const bo
x
a
c
cessor
.
.
.
commit
|
commitdiff
|
tree
2019-09-10
Pa
s
c
a
l Merz
A
d
d trivial
c
o
nst
q
ualifiers to she
l
lf
c
and En
e
r
g
yOut
p
u
t
commit
|
commitdiff
|
tree
2019-09-10
Pascal Merz
Constr
a
int e
l
ement for t
h
e
mod
u
lar simulat
o
r
commit
|
commitdiff
|
tree
2019-09-09
Szilár
d
Páll
Pass gmx::ForceFlag
s
t
o
CPU nb
n
xm dis
p
at
c
h
c
o
d
e
commit
|
commitdiff
|
tree
2019-09-09
S
z
i
lárd Páll
P
ass the new gmx:
:
F
orce
F
lags
t
o
the nbnxm module
commit
|
commitdiff
|
tree
2019-09-09
B
e
rk H
e
ss
Remove incorrect check with
r
f-zero
commit
|
commitdiff
|
tree
2019-09-09
P
a
scal Merz
Domain d
e
comp
o
sitio
n
a
n
d PME load b
a
lancing
f
or modul
a
r
.
.
.
commit
|
commitdiff
|
tree
2019-09-09
C
h
ristian Blau
Relative entropy as dens
i
t
y
s
imilar
i
ty measure
commit
|
commitdiff
|
tree
2019-09-09
Paul Bauer
Add gmx co
n
v
e
rt-trj
commit
|
commitdiff
|
tree
2019-09-09
Berk
Hess
Re
n
ame D
D
S
e
t
up to DDGridSetup
commit
|
commitdiff
|
tree
2019-09-09
B
erk
Hess
C
lean up
PME ra
n
k variables
commit
|
commitdiff
|
tree
2019-09-09
B
erk
H
ess
Refactor init_d
o
ma
i
n_dec
o
mposition()
commit
|
commitdiff
|
tree
2019-09-07
P
ascal Merz
Make pme_loadbal_do()
i
ndependent
o
f
t
_state
commit
|
commitdiff
|
tree
2019-09-07
Pascal Me
r
z
Fo
r
ceElement and ShellFCElement for the mo
d
ular s
i
m
u
lator
commit
|
commitdiff
|
tree
2019-09-06
Szi
l
árd
P
áll
Add gpuu
p
date
a
nd gpucomm OnDem
a
nd
t
okens
commit
|
commitdiff
|
tree
2019-09-06
B
e
r
k
H
ess
Extract getting of DDRankSetup
commit
|
commitdiff
|
tree
2019-09-06
Berk Hess
A
d
d PP grid info to DDRank
S
e
tup
commit
|
commitdiff
|
tree
2019-09-05
M
a
rk Abraham
Update mdrun test compar
i
son inf
r
astruct
u
re
commit
|
commitdiff
|
tree
2019-09-05
Pas
c
a
l
Merz
Ren
a
me Mi
c
roS
t
ate to StateP
r
opagatorData for m
o
du
l
ar
.
.
.
commit
|
commitdiff
|
tree
2019-09-05
C
hristian Blau
Add r
e
fe
r
ence density file
o
pti
o
n
t
o
de
n
sityfitting
commit
|
commitdiff
|
tree
2019-09-05
Berk H
e
ss
Spl
i
t off getting of the DD setup
commit
|
commitdiff
|
tree
2019-09-04
Szilárd Páll
Bump ARM HPC
t
o
o
l
cha
i
n
in
post-submit to v
1
9
.
3
commit
|
commitdiff
|
tree
2019-09-04
Szil
á
rd Páll
Ad
d
back a
c
lang-t
i
d
y
excep
t
ion
commit
|
commitdiff
|
tree
2019-09-04
Christian Blau
Read mrc file using file name
commit
|
commitdiff
|
tree
2019-09-04
B
e
rk Hess
Move update grouping to DDSystemInfo
commit
|
commitdiff
|
tree
2019-09-04
Magnus Lundborg
Inline fu
n
ctions of calculations o
f
FE i
n
teraction
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Be
r
k Hess
C
hange DD pm
e
f
o
rce buffer to st
d
::vec
t
o
r
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Initialize all m
e
mbers of g
m
x_domd
e
c
_
t
commit
|
commitdiff
|
tree
2019-09-03
M
.
E
ri
c
Irr
g
ang
Pytho
n
w
rapp
i
ng cod
e
for gmxapi md
r
un bindings
.
commit
|
commitdiff
|
tree
2019-09-03
Pascal Merz
Introduce e
n
ergy
ele
m
ent for mod
u
lar simulat
o
r
commit
|
commitdiff
|
tree
2019-09-03
M
ark Abraham
Simplify
energy-file compariso
n
s in tes
t
s
commit
|
commitdiff
|
tree
2019-09-03
Artem Zhmurov
Add
P
a
rrinell
o
-R
a
hman pressure
coupling to CUDA Leap
.
.
.
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
Onl
y
use fshift when
n
eeded
commit
|
commitdiff
|
tree
2019-09-01
Chr
i
s
tian Blau
Add checkp
o
in
t
ing for MdModules
commit
|
commitdiff
|
tree
2019-08-30
C
hristian B
l
au
Lo
c
a
lAtomS
e
t
c
o
nstruction wi
t
h v
e
ctors
o
f
gmx::i
n
dex
commit
|
commitdiff
|
tree
2019-08-30
M
.
Eric Irrgang
Import base co
d
e f
o
r Pyth
o
n-driven simulation from
.
.
.
commit
|
commitdiff
|
tree
2019-08-30
Magn
u
s Lundborg
Change
d
some vari
a
bles
from SCReal
to real i
n
FE kernel
.
commit
|
commitdiff
|
tree
2019-08-30
Christian Blau
Imple
m
en
t
ing the density fitting fo
r
ce p
r
ovid
e
r
commit
|
commitdiff
|
tree
2019-08-29
Ma
r
k Abraham
More quotes
commit
|
commitdiff
|
tree
2019-08-28
Pascal Mer
z
Intro
d
uce sig
n
allers for modula
r
integ
r
ator
commit
|
commitdiff
|
tree
2019-08-28
P
aul B
a
u
e
r
F
ix return
v
alue
commit
|
commitdiff
|
tree
2019-08-28
Mark
Abraham
F
i
x
integration issues
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
Introduce the main modular simulat
o
r in
t
erfa
c
es and
.
.
.
commit
|
commitdiff
|
tree
2019-08-28
Paul Bauer
Change tol
e
ran
c
e
f
or no
r
mal
m
od
e
tests
commit
|
commitdiff
|
tree
2019-08-28
Szilárd
Páll
A
d
d cla
n
g
-
t
i
dy
ni
g
htly test with SIM
D
+ Open
C
L
commit
|
commitdiff
|
tree
2019-08-28
Szilárd Páll
M
ove nonbonded GPU wait timing into th
e
GP
U
m
o
d
ule
commit
|
commitdiff
|
tree
2019-08-27
Mar
k
Abrah
a
m
Add integratio
n
tests for
e
xact restarts
commit
|
commitdiff
|
tree
2019-08-27
Ch
r
istian Blau
A
dd
d
e
n
sity fittin
g
p
a
ramet
e
rs
commit
|
commitdiff
|
tree
2019-08-27
Chr
i
stian
Blau
Access to GaussTransform3D da
t
a
commit
|
commitdiff
|
tree
2019-08-27
Chris
t
ian B
l
au
A
d
d index gr
o
up option to density
f
itting
commit
|
commitdiff
|
tree
2019-08-26
Paul Bauer
Rem
o
ve
section chec
k
ing ap
i
le
v
el
commit
|
commitdiff
|
tree
2019-08-26
Pa
u
l Bauer
Remov
e
installed
headers from CMake
commit
|
commitdiff
|
tree
2019-08-26
A
rtem Z
h
murov
Add temperature coupling
t
o CUDA Leap-Frog integrator
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric Irrgang
Move gmxapi
c
ompat TPR
t
ools to lib
g
mxapi
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
Er
i
c Irrgang
Re
d
uce
artifi
c
ial he
a
der dependenc
i
es
i
n r
e
strain
t
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Christian Bl
a
u
Activ
a
tio
n
o
f den
s
ity fit
t
ing and move of
modu
l
e
notification
s
commit
|
commitdiff
|
tree
2019-08-25
Szilárd
P
áll
clang-tidy 8 fixes for the GPU host
c
ode
-
path
commit
|
commitdiff
|
tree
2019-08-25
Szilá
r
d
Páll
Further fixes for clang-tidy c
l
ang version 8
commit
|
commitdiff
|
tree
2019-08-23
P
aul B
a
uer
Removes
c
h
ecker f
o
r i
n
st
a
lled files
commit
|
commitdiff
|
tree
2019-08-23
S
zilárd
Páll
F
ix c
l
ang
-
tidy
warnings
i
n the Ope
n
CL buil
d
commit
|
commitdiff
|
tree
2019-08-23
Ma
r
k Abraham
U
pdate
c
lang-ti
d
y to c
l
a
n
g ve
r
sion 8
commit
|
commitdiff
|
tree
2019-08-22
Mark
A
brah
a
m
M
e
rge branch release-
2
019
commit
|
commitdiff
|
tree
2019-08-22
Mark
Abraha
m
Impr
o
ve
clang-ana
l
yzer build t
i
me
commit
|
commitdiff
|
tree
2019-08-22
M
.
E
r
ic Irrgang
C++ cod
e
a
nd Pytho
n
b
i
n
din
g
s for T
P
R parameter read
.
.
.
commit
|
commitdiff
|
tree
2019-08-22
Berk Hes
s
Fix p
e
rturbed bond
e
d bug
commit
|
commitdiff
|
tree
2019-08-21
M
.
Eric Irrgang
E
n
a
b
le GMXAPI by default
.
commit
|
commitdiff
|
tree
2019-08-20
Ber
k
Hess
M
e
rg
e
two dihedral functions
commit
|
commitdiff
|
tree
2019-08-20
Berk
H
ess
Use
s
hiftForces in ForceOu
p
ut
s
commit
|
commitdiff
|
tree
2019-08-20
E
rik Lindahl
Avo
i
d usi
n
g GMX_SIMD macros to dete
c
t _mm_pau
s
e()
commit
|
commitdiff
|
tree
2019-08-20
Mark Abraham
Fix
iss
u
es for
c
la
n
g-analyzer-8
commit
|
commitdiff
|
tree
2019-08-20
Be
r
k Hes
s
Make bonded virial c
o
mputation co
n
di
t
ional
commit
|
commitdiff
|
tree
2019-08-19
Sz
i
lá
r
d
Páll
Switch
to ARM HPC too
l
chain v19
.
2 in post-submi
t
commit
|
commitdiff
|
tree
2019-08-19
Mark Abraham
Moderniz
e
t_mat
r
ix,
t_mapping, t_rgb
commit
|
commitdiff
|
tree
next