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Improved some logic in do_force
2019-08-22
Mark
Abraham
F
i
x re
l
eas
e
m
atrix
commit
|
commitdiff
|
tree
2019-08-21
Mark Abra
h
am
Improve organiz
a
t
io
n
of LI
N
CS
r
epor
t
i
n
g
commit
|
commitdiff
|
tree
2019-08-20
Mar
k
Abraham
A
p
ply clang-tidy-8 rea
d
ability-uppercase-literal-suffix
commit
|
commitdiff
|
tree
2019-08-20
Mark Abraham
Use
poten
t
i
a
l-shift as default
m
odifier
commit
|
commitdiff
|
tree
2019-08-20
Mark Abra
h
am
R
educe cosi
n
e acceleration quantity properly
commit
|
commitdiff
|
tree
2019-08-20
Ma
r
k
Abra
h
am
Fix issues for clang-analyzer-
8
commit
|
commitdiff
|
tree
2019-08-19
Mark Ab
r
aha
m
Moderni
z
e t_m
a
tri
x
, t_map
p
ing, t_rgb
commit
|
commitdiff
|
tree
2019-08-19
Mark Abraham
M
o
derni
z
e t
_
psdata
commit
|
commitdiff
|
tree
2019-08-16
Mark Abraham
Update t
e
s
ting
m
atrices a
n
d
fix warn
i
ngs
commit
|
commitdiff
|
tree
2019-08-16
M
ark A
b
raham
Move keyvalu
e
t
r
eewri
t
e
r c
o
de
commit
|
commitdiff
|
tree
2019-08-16
Mark Abraham
Stop nbnxm/gri
d
.
h
dep
e
nding
o
n SIMD module
commit
|
commitdiff
|
tree
2019-08-15
Mark Abraham
Remove
r
un
-
time
c
heck fro
m
calc_shifts
commit
|
commitdiff
|
tree
2019-08-14
Mark Ab
r
aham
Fix v
v
int
e
grators
commit
|
commitdiff
|
tree
2019-08-13
M
ark Abraham
R
emo
v
e workaround
f
o
r
buggy cmake
commit
|
commitdiff
|
tree
2019-08-13
Ma
r
k Abraham
Fi
x
icc 19 cod
e
gen issue
commit
|
commitdiff
|
tree
2019-08-12
Mark Abraham
Quiet wa
r
n
ing
commit
|
commitdiff
|
tree
2019-08-12
Mark Abraham
Fix
o
c
l_
k
ernel target
commit
|
commitdiff
|
tree
2019-08-08
Mark Abra
h
am
Fix estimate of the si
z
e of
a
j
list
commit
|
commitdiff
|
tree
2019-08-08
Mark A
b
raham
Initial
i
ze gmx_ekindat
a
_t
a
n
d t_
v
cm properly
commit
|
commitdiff
|
tree
2019-08-08
Mark A
b
r
aha
m
Stop
t
esting ICC on
Windo
w
s
commit
|
commitdiff
|
tree
2019-08-06
M
ar
k
Abrah
a
m
Fix for
M
SVC
+
CU
D
A
commit
|
commitdiff
|
tree
2019-08-05
Mark Abraham
Add
quote
commit
|
commitdiff
|
tree
2019-08-05
Mar
k
Abrah
a
m
Remove libgromacs_g
e
n
e
r
ated
contributions from F
i
ndCUDA
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Mark Abraham
M
a
nage comp
i
ler fl
a
gs and some inclu
d
e
o
p
tions p
e
r
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
M
ark
Abraham
I
m
prove use
of object
l
i
bra
r
i
e
s
i
n libgromacs
commit
|
commitdiff
|
tree
2019-08-01
M
ark Abr
a
ha
m
Merg
e
"Merge release
-
2019 into master"
commit
|
commitdiff
|
tree
2019-07-24
Mar
k
Ab
r
aham
R
e
mo
v
e tests of make_u
n
ique
commit
|
commitdiff
|
tree
2019-07-23
Mark Abra
h
am
Update
d
evelop
e
r guid
e
commit
|
commitdiff
|
tree
2019-07-16
Mar
k
Abraham
A
dd gpubufferops test matrix
commit
|
commitdiff
|
tree
2019-07-11
Mark Abr
a
ham
Fix pre-sub
m
it build matr
i
x
a
n
d descr
i
ption
commit
|
commitdiff
|
tree
2019-07-08
Mark Abraham
Fix hwlo
c
and sphinx
detection
commit
|
commitdiff
|
tree
2019-07-08
Mark Ab
r
a
h
am
T
e
st
s
pecific hwloc versions
commit
|
commitdiff
|
tree
2019-07-05
Mark Abra
h
a
m
Imp
r
ove tests of index block constr
u
c
t
ion
commit
|
commitdiff
|
tree
2019-07-05
Mark Abraham
Moderniz
e
F
i
ndHwlo
c
.
cmake
commit
|
commitdiff
|
tree
2019-07-04
M
a
r
k Abraham
Fu
r
the
r
clang-t
i
dy-7 fix
commit
|
commitdiff
|
tree
2019-07-04
Ma
r
k Abraham
F
i
x clang-tidy-7 i
s
sues
commit
|
commitdiff
|
tree
2019-07-03
Mark Abraham
R
eorder opti
o
n
s
commit
|
commitdiff
|
tree
2019-07-02
Mark Abraham
Clarify wordin
g
o
f
r
e
l
ease n
o
tes
commit
|
commitdiff
|
tree
2019-06-18
Mark Abrah
a
m
M
o
v
e
code han
d
ling m
d
run -gpu_id to taskassignme
n
t
.
.
.
commit
|
commitdiff
|
tree
2019-06-12
Mark Abr
a
ham
F
i
x pygments detec
t
ion for
s
phinx f
o
r docs build
commit
|
commitdiff
|
tree
2019-06-11
Mark A
b
raham
Use RAII appro
a
ches f
o
r hardware
information detect
i
on
commit
|
commitdiff
|
tree
2019-06-11
Mark Abr
a
ham
Cl
e
an
up multisi
m
, communicati
o
n,
a
nd REMD code
commit
|
commitdiff
|
tree
2019-06-11
Mark Abra
h
am
Initialize
a
ll of gm
x
_domd
e
c_com
m
_
t
commit
|
commitdiff
|
tree
2019-05-24
Mark A
b
raham
Reorder code
before thre
a
d-MPI spawns thre
a
ds
commit
|
commitdiff
|
tree
2019-05-23
Mark Ab
r
aham
Teach ArrayRe
f
WithPadding to
m
a
ke a const fla
v
o
ur
commit
|
commitdiff
|
tree
2019-05-23
M
a
r
k Abraham
Revert "Fixed dvdlam
b
da for
S
HAKE
+
FE"
commit
|
commitdiff
|
tree
2019-05-22
M
a
r
k Ab
r
ah
a
m
R
e
write starting behavior
commit
|
commitdiff
|
tree
2019-05-22
Mark Abraham
Introduce tri-stat
e
enums for res
t
arts
commit
|
commitdiff
|
tree
2019-05-22
Mark Abr
a
ham
Move function
a
lity
to mdrunutil
i
ty
commit
|
commitdiff
|
tree
2019-05-20
M
ark Ab
r
aham
F
i
x equation typo
commit
|
commitdiff
|
tree
2019-05-14
M
ark Abraham
Update
infrastructu
r
e needed
for
r
e
s
tart rewrite
commit
|
commitdiff
|
tree
2019-05-08
Mark Abraham
P
rovide h
o
ok
f
or fo
r
ks of GROM
A
CS
t
o describe them
s
elves
commit
|
commitdiff
|
tree
2019-05-07
M
a
r
k
Abraham
P
rovi
d
e better help for
u
s
i
ng libc++
commit
|
commitdiff
|
tree
2019-05-07
Mark Abraham
Add an ex
a
m
ple o
f
using an MPI wrapper compile
r
commit
|
commitdiff
|
tree
2019-05-06
Mark Abra
h
am
Imp
r
ove
h
ow mdrun -noapp
e
nd name
s
outp
u
t fi
l
es
commit
|
commitdiff
|
tree
2019-05-03
Mar
k
Abraham
More tests
for
how mdrun -cpi
r
estarts
h
and
l
e files
commit
|
commitdiff
|
tree
2019-05-02
M
ark A
b
r
a
ham
Enha
n
ce
path s
e
ar
c
h fu
n
c
t
ions
commit
|
commitdiff
|
tree
2019-04-30
Ma
r
k Abra
h
a
m
Test the
outpu
t
of "gmx md
r
un he
l
p"
commit
|
commitdiff
|
tree
2019-04-25
Mark Abraham
Update
styl
e
guide about
c
lass en
u
m
s
commit
|
commitdiff
|
tree
2019-04-23
Ma
r
k Abraham
Clarify
pushing of interac
t
i
o
n
types
commit
|
commitdiff
|
tree
2019-04-23
Mark Abrah
a
m
U
pd
a
ted clang -Wevery
t
h
i
n
g ch
e
cks to clang-7
commit
|
commitdiff
|
tree
2019-04-18
Mark Abra
h
a
m
Cr
e
ate gmx::compat::optional
commit
|
commitdiff
|
tree
2019-04-18
Mark Abraha
m
M
o
ve pull wo
r
k
struct out of inpu
t
rec
commit
|
commitdiff
|
tree
2019-04-18
Mark Abraham
Impro
v
e s
w
ap
c
oords
s
ession lifetim
e
managem
e
nt
commit
|
commitdiff
|
tree
2019-04-17
Mark
A
bra
h
am
Fi
x
post-s
u
bmit
commit
|
commitdiff
|
tree
2019-04-16
Mark Abraham
Rem
o
ved mdrun -
g
c
o
m
commit
|
commitdiff
|
tree
2019-04-13
Mark Ab
r
aham
F
ix self-c
o
ns
i
stency te
s
t
s of hw
l
oc data structures
commit
|
commitdiff
|
tree
2019-04-12
M
ar
k
Abraham
I
m
prove w
a
rning messages
a
bout
d
uplicate
d
e
f
init
i
ons
commit
|
commitdiff
|
tree
2019-04-10
Mar
k
Abrah
a
m
Start
m
a
kin
g
IMD and swap mod
e
l IMDModu
l
e
commit
|
commitdiff
|
tree
2019-04-10
M
ark Abraham
R
e
u
se rvecs_differ
in InteractiveM
D
module
commit
|
commitdiff
|
tree
2019-04-10
Mark Abr
a
ham
M
a
ke Im
d
Se
s
sion
i
nto
a
Pimpl-ed class wi
t
h factory
.
.
.
commit
|
commitdiff
|
tree
2019-04-10
Ma
r
k
Abraham
Refor
m
IMD module
commit
|
commitdiff
|
tree
2019-04-09
Mar
k
Ab
r
aham
Fix
t
ypo in AVX512
detecti
o
n
c
ode
commit
|
commitdiff
|
tree
2019-04-03
Mar
k
Abra
h
am
Initial deac
t
ivat
i
on of gro
u
p scheme
.
commit
|
commitdiff
|
tree
2019-04-01
M
ark Abraha
m
Move MDModules ini
t
ialization ea
r
lier
commit
|
commitdiff
|
tree
2019-04-01
Mark Abraham
M
o
ve ene
r
d
ata ownership to md
r
unner
commit
|
commitdiff
|
tree
2019-03-28
Mark Abrah
a
m
Move DomdecO
p
tions
into its own header
commit
|
commitdiff
|
tree
2019-03-25
Mark Abraha
m
Support
A
rr
a
yRef
o
f
EnumerationArray
commit
|
commitdiff
|
tree
2019-03-25
M
ark
A
brah
a
m
Convert gmx dump to m
o
dule
commit
|
commitdiff
|
tree
2019-03-20
Mark Abraham
C
l
ean up
mdrun help description
commit
|
commitdiff
|
tree
2019-03-20
Ma
r
k
A
b
r
aham
Improve
m
imic module
commit
|
commitdiff
|
tree
2019-03-19
Mar
k
Abraha
m
A
d
d support fo
r
s
e
r
i
ali
z
ing 32-bi
t
integers
commit
|
commitdiff
|
tree
2019-03-19
M
a
rk Abraham
Fix c
l
ang wa
r
n
ing
commit
|
commitdiff
|
tree
2019-03-19
Mark Ab
r
aham
U
pd
a
te ElectricFi
e
ld module
commit
|
commitdiff
|
tree
2019-03-19
Mark Ab
r
aham
Prevented FFT
W
build
e
rrors with c
l
an
g
and AVX-512
commit
|
commitdiff
|
tree
2019-03-13
Mark Abraham
Provid
e
reminder
o
f
w
h
ich nvcc is in us
e
commit
|
commitdiff
|
tree
2019-03-12
Mark Abraham
Fix memory leak
commit
|
commitdiff
|
tree
2019-03-07
Mark A
b
r
aham
Eliminate md
l
ib/md
r
un
.
h
commit
|
commitdiff
|
tree
2019-03-07
Mar
k
A
br
a
ham
Remove ine
f
fec
t
iv
e
co
d
e fo
r
writing more
T
ER fiel
d
s
.
.
.
commit
|
commitdiff
|
tree
2019-03-07
Mark A
b
raham
New tests for p
d
b
2
g
mx and editcon
f
commit
|
commitdiff
|
tree
2019-03-06
Mark A
b
ra
h
am
Clean
up use o
f
loop
indices
commit
|
commitdiff
|
tree
2019-03-06
Mark Abraham
Rever
t
"E
l
iminate mdli
b
/mdrun
.
h"
commit
|
commitdiff
|
tree
2019-03-06
Mark Abraha
m
E
liminate
m
dl
i
b/
m
dr
u
n
.
h
commit
|
commitdiff
|
tree
2019-03-06
Mark Abraham
Minor mode
r
nization
in gmx_dum
p
commit
|
commitdiff
|
tree
2019-03-05
Mark
Abr
a
h
am
Make pdb2
g
mx
tests run
in Jenkins
commit
|
commitdiff
|
tree
2019-03-02
Ma
r
k Abraham
Merge branch rel
e
ase-2019
commit
|
commitdiff
|
tree
2019-03-02
Mark Abra
h
am
Remove
defu
n
ct mdrun
options
commit
|
commitdiff
|
tree
2019-02-27
Mark Abra
h
a
m
Keep niche CMa
k
e v
a
r
i
ables
as a
d
van
c
ed
commit
|
commitdiff
|
tree
2019-02-27
Mark
A
b
raham
Remove m
i
no
r
broken functi
o
na
l
ity in gmx
b
ar
commit
|
commitdiff
|
tree
2019-02-26
M
ark Ab
r
aham
Ad
d
n
ew
l
ine to trjconv noti
c
e to users
commit
|
commitdiff
|
tree
next