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Inline functions of calculations of FE interaction types.
2019-09-04
Magnus Lundborg
I
n
l
ine functions of calculati
o
n
s of FE in
t
era
c
tion
.
.
.
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
Ch
a
nge
D
D pme
f
orce buffer to std:
:
vec
t
o
r
commit
|
commitdiff
|
tree
2019-09-04
Berk Hess
I
n
itial
i
z
e all
members
of gm
x
_d
o
mde
c
_t
commit
|
commitdiff
|
tree
2019-09-03
M
.
Eric Irrgang
Python wrappin
g
code for gmxapi mdrun b
i
ndings
.
commit
|
commitdiff
|
tree
2019-09-03
Pascal Mer
z
Introdu
c
e
en
e
r
g
y elem
e
nt for m
o
dular simulator
commit
|
commitdiff
|
tree
2019-09-03
M
a
rk Abraham
S
implify energy-file comparis
o
ns in tests
commit
|
commitdiff
|
tree
2019-09-03
Artem Zh
m
urov
Add Parrinello-Rahman pressure coup
l
ing
t
o CUDA L
e
ap
.
.
.
commit
|
commitdiff
|
tree
2019-09-02
Berk Hess
Only use fshift when needed
commit
|
commitdiff
|
tree
2019-09-01
Christia
n
B
lau
Add checkpo
i
nting for MdModu
l
e
s
commit
|
commitdiff
|
tree
2019-08-30
Christian Blau
Local
A
tomSet construction with vectors of gmx::index
commit
|
commitdiff
|
tree
2019-08-30
M
.
Eric Irrgang
Im
p
ort ba
s
e
code
f
o
r Python-driven simula
t
ion from
.
.
.
commit
|
commitdiff
|
tree
2019-08-30
Ma
g
nus
Lundborg
Chan
g
e
d s
o
me variables from SCReal to real
i
n FE kern
e
l
.
commit
|
commitdiff
|
tree
2019-08-30
Christian
Blau
Impl
e
menting t
h
e
densit
y
fitti
n
g force provider
commit
|
commitdiff
|
tree
2019-08-29
Mark Abraham
More quotes
commit
|
commitdiff
|
tree
2019-08-28
Pascal Merz
I
n
tr
o
d
u
c
e
signal
l
e
r
s for mod
u
lar
i
nteg
r
ator
commit
|
commitdiff
|
tree
2019-08-28
Paul Baue
r
Fix
r
eturn value
commit
|
commitdiff
|
tree
2019-08-28
Mark Abraham
Fix integr
a
tion issues
commit
|
commitdiff
|
tree
2019-08-28
Pasca
l
Merz
Introduce th
e
m
a
i
n
m
odular simulat
o
r
interf
a
ces and
.
.
.
commit
|
commitdiff
|
tree
2019-08-28
Paul Baue
r
Chan
g
e toleranc
e
for normal mode
t
e
s
ts
commit
|
commitdiff
|
tree
2019-08-28
Szilá
r
d Páll
A
d
d
clang-tidy night
l
y test with SIMD +
O
penCL
commit
|
commitdiff
|
tree
2019-08-28
Szilárd Páll
Move non
b
onded
G
PU
wait timing into the GPU module
commit
|
commitdiff
|
tree
2019-08-27
M
a
r
k A
b
raham
Add
i
ntegration tests
f
or exact resta
r
ts
commit
|
commitdiff
|
tree
2019-08-27
Chri
s
t
ia
n
Blau
Add density fitting paramete
r
s
commit
|
commitdiff
|
tree
2019-08-27
Chr
i
sti
a
n Blau
Acce
s
s
to
G
au
s
sTrans
f
orm3
D
data
commit
|
commitdiff
|
tree
2019-08-27
Christian Blau
Add inde
x
group
option to
density fitting
commit
|
commitdiff
|
tree
2019-08-26
Paul Bauer
R
em
o
v
e
section checking
a
pi level
commit
|
commitdiff
|
tree
2019-08-26
Paul Bauer
Re
m
ove installed he
a
de
r
s from CMak
e
commit
|
commitdiff
|
tree
2019-08-26
Artem Zhmurov
Add
t
emperature coupling to
C
UDA Le
a
p-Frog integrator
commit
|
commitdiff
|
tree
2019-08-26
M
.
E
ric Irrgang
M
o
ve gmxapicompat TPR to
o
ls to libgmxa
p
i
.
commit
|
commitdiff
|
tree
2019-08-26
M
.
Eric Ir
r
gang
Reduc
e
artificial he
a
der dep
e
ndencies in restraint
.
.
.
commit
|
commitdiff
|
tree
2019-08-26
Christian Bl
a
u
Acti
v
atio
n
of density
f
itti
n
g and mov
e
of module notifications
commit
|
commitdiff
|
tree
2019-08-25
Szilárd
P
áll
clang-tid
y
8
fixes
f
o
r the GPU host
cod
e
-pat
h
commit
|
commitdiff
|
tree
2019-08-25
S
z
ilárd Páll
Further fixes for clang-tidy clang
v
e
r
sio
n
8
commit
|
commitdiff
|
tree
2019-08-23
Paul
Bauer
Remov
e
s checker for insta
l
l
e
d
files
commit
|
commitdiff
|
tree
2019-08-23
S
z
ilárd P
á
ll
Fix clan
g
-tidy warnings in the OpenCL build
commit
|
commitdiff
|
tree
2019-08-23
Mark Abraham
Update clang-tidy to c
l
ang version 8
commit
|
commitdiff
|
tree
2019-08-22
Mark Ab
r
aham
Merge bra
n
ch release-2019
commit
|
commitdiff
|
tree
2019-08-22
M
a
r
k Abraham
I
mprove clang
-
an
a
l
y
zer bu
i
ld t
i
me
commit
|
commitdiff
|
tree
2019-08-22
M
.
E
ric Irrg
a
ng
C
++ code and Python bi
n
d
i
ngs for TP
R
parameter r
e
ad
.
.
.
commit
|
commitdiff
|
tree
2019-08-22
B
erk Hess
Fix perturb
e
d b
o
nded bug
commit
|
commitdiff
|
tree
2019-08-21
M
.
E
ric Irrgang
E
nable GMXAPI
b
y
default
.
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Merge
two dihedra
l
functi
o
n
s
commit
|
commitdiff
|
tree
2019-08-20
Berk Hess
Use shiftFor
c
es in F
o
rceOuputs
commit
|
commitdiff
|
tree
2019-08-20
Erik Lind
a
hl
A
voi
d
usin
g
GMX_SIMD macr
o
s to detect _mm_pa
u
se()
commit
|
commitdiff
|
tree
2019-08-20
M
a
rk Ab
r
ah
a
m
Fix issues for cl
a
ng-analyzer-8
commit
|
commitdiff
|
tree
2019-08-20
B
e
rk Hes
s
Make bo
n
ded v
i
rial
computation conditio
n
a
l
commit
|
commitdiff
|
tree
2019-08-19
Szilá
r
d P
á
ll
S
w
itch to AR
M
HPC too
l
cha
i
n v19
.
2 in
p
ost-submit
commit
|
commitdiff
|
tree
2019-08-19
Mark Ab
r
aham
Moder
n
ize t_matrix, t_mapp
i
ng, t_rgb
commit
|
commitdiff
|
tree
2019-08-19
Mark Abraham
Modern
i
z
e t_psdata
commit
|
commitdiff
|
tree
2019-08-19
S
zilárd
Páll
W
o
r
k
a
round clang CUDA device
c
ode co
d
egen
bug
commit
|
commitdiff
|
tree
2019-08-16
Szilárd
P
áll
Fix sim_ut
i
l
.
cp
p
co
p
yrig
h
t header
commit
|
commitdiff
|
tree
2019-08-16
M
a
rk Abraham
U
p
d
a
te testing matrices and
f
ix warnings
commit
|
commitdiff
|
tree
2019-08-16
Mark Abra
h
am
Stop nbnx
m
/grid
.
h
depending on SI
M
D module
commit
|
commitdiff
|
tree
2019-08-15
S
z
ilárd Páll
Fix OpenCL gather reduc
t
i
on
commit
|
commitdiff
|
tree
2019-08-14
Christian Blau
Info class to
n
ame and generate t
h
e densityfitt
i
n
g
.
.
.
commit
|
commitdiff
|
tree
2019-08-14
Mar
k
Abraham
F
i
x vv integrat
o
rs
commit
|
commitdiff
|
tree
2019-08-14
M
.
Er
i
c Irrg
a
ng
Add
i
n
it
i
al
.
clang-forma
t
f
ile
.
commit
|
commitdiff
|
tree
2019-08-13
Mark A
b
raham
Fix icc 1
9
c
od
e
gen iss
u
e
commit
|
commitdiff
|
tree
2019-08-12
M
.
Er
i
c Irrgang
Introduc
e
C
ontext requir
e
ment
.
commit
|
commitdiff
|
tree
2019-08-12
Mark Abraham
Q
uiet
wa
r
ning
commit
|
commitdiff
|
tree
2019-08-12
Mark Abraham
F
ix o
c
l_k
e
rnel
t
ar
g
e
t
commit
|
commitdiff
|
tree
2019-08-12
Pascal Mer
z
Use new
s
etenv function
f
or ene
r
g
y
output tes
t
commit
|
commitdiff
|
tree
2019-08-12
M
.
E
ric Irrgang
Separa
t
e ou
t
some ab
s
tract base cl
a
sses
.
commit
|
commitdiff
|
tree
2019-08-09
A
rte
m
Zh
m
uro
v
Prepare Update and
Con
s
trai
n
t
s f
o
r Domain De
c
o
m
p
osition
commit
|
commitdiff
|
tree
2019-08-09
Artem Zhmu
r
ov
R
e
f
a
ctor
i
ng o
f
the SETTL
E
tests
commit
|
commitdiff
|
tree
2019-08-09
Be
r
k Hess
SI
M
D acc
e
leratio
n
for
F_FOURD
I
HS a
n
d F_PIDIHS
commit
|
commitdiff
|
tree
2019-08-08
M
a
rk Abraham
Fix estimate of the size of a j list
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eri
c
Irrg
a
ng
A
d
d
g
m
xapi_
p
y
t
est custom
t
arget to CMake `che
c
k` tar
g
et
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Irrg
a
ng
Allow gmxap
i
Pytho
n
package tests to be ru
n
from GROMACS
.
.
.
commit
|
commitdiff
|
tree
2019-08-08
Chri
s
tian Bla
u
H
ar
m
onize mrc
d
e
n
s
i
ty forma
t
e
x
tents with rest of
code
.
commit
|
commitdiff
|
tree
2019-08-08
M
.
Eric Irrgang
Reenable gtest
_
mai
n
tar
g
et
.
commit
|
commitdiff
|
tree
2019-08-08
Mark Abraha
m
S
top
t
estin
g
ICC o
n
Window
s
commit
|
commitdiff
|
tree
2019-08-08
Artem
Zhmur
o
v
Refact
o
r
L
eap-Frog
t
e
sts and conne
c
t them to CPU version
commit
|
commitdiff
|
tree
2019-08-07
M
.
Eric Ir
r
gang
Use
gmock
a
n
d gtest targets
f
rom g
o
ogletest-release
.
.
.
commit
|
commitdiff
|
tree
2019-08-05
Pascal Mer
z
Move owne
r
s
h
i
p of kinet
i
c
e
nergy o
b
je
c
t
t
o ISimulator
commit
|
commitdiff
|
tree
2019-08-05
Pas
c
a
l Merz
Add
e
d
S
imulator compar
i
s
o
n test
commit
|
commitdiff
|
tree
2019-08-05
Mark Abrah
a
m
R
emove
l
ibgromacs_ge
n
erated contributions from
F
indCUDA
.
.
.
commit
|
commitdiff
|
tree
2019-08-02
yongwangCPH
Solve issu
e
with demux
.
pl
commit
|
commitdiff
|
tree
2019-08-01
Berk
H
ess
Re
m
ove a point
e
r in
t
_
forcerec
commit
|
commitdiff
|
tree
2019-08-01
Berk Hess
F
ix n
b
nxm GP
U
memory reservatio
n
issue
commit
|
commitdiff
|
tree
2019-08-01
Mark
Abraham
M
a
nage compiler flags and
s
ome include opti
o
ns
per
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Mark A
b
ra
h
a
m
I
mp
r
ove use of object libraries in
l
ibg
r
o
macs
commit
|
commitdiff
|
tree
2019-08-01
Mark Abraham
Merge "Merge release-2019 into
mas
t
er"
commit
|
commitdiff
|
tree
2019-07-31
Berk Hess
Add
g
r
o
mpp warning w
i
th use of GROMOS FF
commit
|
commitdiff
|
tree
2019-07-31
Artem Zhmurov
Intr
o
d
uce function
t
hat che
c
ks if the computations
.
.
.
commit
|
commitdiff
|
tree
2019-07-31
Szilárd
P
áll
Fixe
s
fo
r
F
buffer ops
change
commit
|
commitdiff
|
tree
2019-07-31
Berk
Hess
Remov
e
n
e
e
d for GROMOS FF
i
n test
commit
|
commitdiff
|
tree
2019-07-31
Pascal Merz
Rename Si
m
ulator to LegacySimulator
commit
|
commitdiff
|
tree
2019-07-31
Szi
l
á
r
d Páll
Move cycle counting
into
t
he
G
PU bo
n
ded mod
u
le
commit
|
commitdiff
|
tree
2019-07-31
Sz
i
l
árd
P
á
ll
R
eport when development fea
t
ure flag
s
are us
e
d
commit
|
commitdiff
|
tree
2019-07-31
Szilárd Pá
l
l
M
o
ve end of
s
tep GPU task launche
s
to a f
u
ncti
o
n
commit
|
commitdiff
|
tree
2019-07-30
Paul Bauer
Add
wrapper
f
or o
u
tpu
t
adapte
r
method
s
commit
|
commitdiff
|
tree
2019-07-28
Berk
He
s
s
Convert Ewald correc
t
ion tables
t
o
C
+
+
commit
|
commitdiff
|
tree
2019-07-26
Berk Hess
Add default i
n
iti
a
lizatio
n
t
o
interaction_c
o
nst
_
t
commit
|
commitdiff
|
tree
2019-07-26
Christia
n
B
lau
Fix fai
l
ing check-sou
r
ce
t
a
rget on pyt
h
on3
.
6
commit
|
commitdiff
|
tree
2019-07-25
B
e
rk Hess
Split
c
a
n
D
e
t
ectG
p
us()
commit
|
commitdiff
|
tree
2019-07-25
Szi
l
árd Páll
O
nly sto
p
the C
U
DA profiler i
f
the
r
e are
devic
e
s
commit
|
commitdiff
|
tree
2019-07-24
P
a
u
l B
a
u
er
F
ix dox
y
gen in coord
i
ante
i
o
files
commit
|
commitdiff
|
tree
2019-07-24
Paul Bauer
Add
o
u
t
p
uta
d
a
pters (3/3)
commit
|
commitdiff
|
tree
2019-07-24
M
.
Eric Irrg
a
n
g
Fix gm
x
api noteboo
k
image an
d
sample_rest
r
aint
docker
.
.
.
commit
|
commitdiff
|
tree
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