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Merge branch release-2019
2019-08-22
M
ark
A
br
a
ham
Mer
g
e
b
ranch rel
e
ase-2019
commit
|
commitdiff
|
tree
2019-08-22
Mark Abraham
Improve cl
a
ng-a
n
alyzer
b
ui
l
d
t
ime
commit
|
commitdiff
|
tree
2019-08-22
Mark
A
braham
Fi
x
r
e
lease matrix
commit
|
commitdiff
|
tree
2019-08-21
Mark
A
braham
Improve
organizatio
n
of LINC
S
re
p
o
r
ting
commit
|
commitdiff
|
tree
2019-08-20
Mark Abrah
a
m
Ap
p
ly cla
n
g-ti
d
y-8 readabi
l
ity-uppercas
e
-
l
iteral-suffi
x
commit
|
commitdiff
|
tree
2019-08-20
Mark Abraham
Use potential-shift
a
s default
m
o
difier
commit
|
commitdiff
|
tree
2019-08-20
Mark Abraham
Reduce
c
osine accele
r
a
t
i
on quantity pr
o
perly
commit
|
commitdiff
|
tree
2019-08-20
M
a
r
k
A
b
rah
a
m
Fix issues for cla
n
g
-analy
z
er-8
commit
|
commitdiff
|
tree
2019-08-19
Mark Abraham
Modernize
t_
m
atrix, t_
m
apping, t_rgb
commit
|
commitdiff
|
tree
2019-08-19
M
a
rk Ab
r
aham
M
odernize t_ps
d
ata
commit
|
commitdiff
|
tree
2019-08-16
Mark Abraham
U
p
d
a
te
t
esting m
a
trices and fix warning
s
commit
|
commitdiff
|
tree
2019-08-16
Ma
r
k
Abraha
m
Move keyva
l
uetreewriter code
commit
|
commitdiff
|
tree
2019-08-16
Mark Abraham
Stop nbn
x
m/grid
.
h depen
d
ing on SIMD mod
u
le
commit
|
commitdiff
|
tree
2019-08-15
Mark Ab
r
aha
m
Remove run-
t
ime check
f
r
o
m calc_shift
s
commit
|
commitdiff
|
tree
2019-08-14
Mark
A
braham
Fi
x
v
v
integra
t
ors
commit
|
commitdiff
|
tree
2019-08-13
Mark Abraha
m
Remove w
o
rkaroun
d
for buggy cm
a
ke
commit
|
commitdiff
|
tree
2019-08-13
Mark Abraham
Fi
x
i
c
c
1
9
codegen issue
commit
|
commitdiff
|
tree
2019-08-12
Mark Abraham
Qu
i
et warning
commit
|
commitdiff
|
tree
2019-08-12
M
ark Abraham
Fix o
c
l_
k
e
r
n
e
l target
commit
|
commitdiff
|
tree
2019-08-08
Mark Abra
h
am
Fix estimate of the
size of a j list
commit
|
commitdiff
|
tree
2019-08-08
Mark Ab
r
aham
Ini
t
i
alize gmx_ekindata_t and t_vcm prope
r
ly
commit
|
commitdiff
|
tree
2019-08-08
Mark Abraham
Stop tes
t
ing ICC on Windows
commit
|
commitdiff
|
tree
2019-08-06
Mark Abraham
Fix for MSVC+C
U
DA
commit
|
commitdiff
|
tree
2019-08-05
Mark Abra
h
am
Add quote
commit
|
commitdiff
|
tree
2019-08-05
M
a
rk A
b
raham
R
e
m
o
ve
li
b
g
r
omacs_
g
enerated
contribut
i
ons from FindCUDA
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Mark Ab
r
aham
Man
a
ge co
m
pil
e
r fla
g
s
a
nd som
e
incl
u
de
options per
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
M
a
rk
A
braham
Improve use
o
f
o
b
j
ect libraries in libgromacs
commit
|
commitdiff
|
tree
2019-08-01
Ma
r
k Abra
h
am
Merge "Merge re
l
ease-2
0
1
9
i
n
to m
a
ster"
commit
|
commitdiff
|
tree
2019-07-24
M
a
rk A
b
rah
a
m
R
emove tests of make_un
i
que
commit
|
commitdiff
|
tree
2019-07-23
M
a
r
k Ab
r
aham
U
p
date dev
e
loper
g
uide
commit
|
commitdiff
|
tree
2019-07-16
Ma
r
k Abra
h
am
Add gpu
b
uf
f
e
r
ops te
s
t matri
x
commit
|
commitdiff
|
tree
2019-07-11
Mark Abraham
F
i
x pre-submit build matrix
a
nd des
c
ription
commit
|
commitdiff
|
tree
2019-07-08
Mark
A
b
raham
Fix hwloc
a
nd sphinx detection
commit
|
commitdiff
|
tree
2019-07-08
M
a
r
k
Abraham
Te
s
t spec
i
fic hwloc
v
e
rsions
commit
|
commitdiff
|
tree
2019-07-05
Ma
r
k A
b
r
aha
m
Impr
o
v
e tests of index
block constructio
n
commit
|
commitdiff
|
tree
2019-07-05
Mark Abraham
Mo
d
e
rn
i
ze FindHwloc
.
cma
k
e
commit
|
commitdiff
|
tree
2019-07-04
Mark Abraha
m
Further
c
lang-tidy-7 fix
commit
|
commitdiff
|
tree
2019-07-04
M
a
rk Abraham
Fi
x
clang-ti
d
y
-7 issu
e
s
commit
|
commitdiff
|
tree
2019-07-03
Mark Abraham
Reo
r
der optio
n
s
commit
|
commitdiff
|
tree
2019-07-02
Mark A
b
raham
C
l
arify
w
o
rd
i
ng of re
l
ease note
s
commit
|
commitdiff
|
tree
2019-06-18
Mark Abra
h
am
Move code h
a
ndling m
d
run -gpu_id to tas
k
assignment
.
.
.
commit
|
commitdiff
|
tree
2019-06-12
Mark Abraham
F
ix
p
y
g
m
ents detection for sphi
n
x for
d
ocs build
commit
|
commitdiff
|
tree
2019-06-11
Mark
A
braham
Use RAI
I
approaches for hardware informatio
n
detection
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraham
Clea
n
up m
u
lt
i
s
i
m, communication, and
REMD code
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraham
Initiali
z
e
al
l
of
g
mx_
d
omde
c
_
c
omm_t
commit
|
commitdiff
|
tree
2019-05-24
Mark Ab
r
aham
Reorder code
befo
r
e thread-MP
I
spawns threads
commit
|
commitdiff
|
tree
2019-05-23
Mark Abraham
Teach Ar
r
ayRefWithP
a
dding
t
o make a
const flavo
u
r
commit
|
commitdiff
|
tree
2019-05-23
M
ark
A
b
r
aham
Revert "Fixed dvdlambd
a
f
o
r SHAKE + FE
"
commit
|
commitdiff
|
tree
2019-05-22
M
ark Abraham
Rewri
t
e s
t
a
r
ting
behavio
r
commit
|
commitdiff
|
tree
2019-05-22
Mark Abraham
Introduc
e
tri-sta
t
e
enums for restarts
commit
|
commitdiff
|
tree
2019-05-22
Mark Abraham
Move functional
i
ty to mdrunu
t
ilit
y
commit
|
commitdiff
|
tree
2019-05-20
Mark A
b
ra
h
a
m
Fix e
q
uat
i
on typo
commit
|
commitdiff
|
tree
2019-05-14
Mark Abraham
Upda
t
e i
n
frastructure n
e
ede
d
for re
s
t
a
rt rewrite
commit
|
commitdiff
|
tree
2019-05-08
M
ark
Abraham
Provide hook for forks
o
f
G
ROMACS to describe themselves
commit
|
commitdiff
|
tree
2019-05-07
Mark Abraha
m
Provide better help for usin
g
li
b
c++
commit
|
commitdiff
|
tree
2019-05-07
M
ar
k
Ab
r
aha
m
A
d
d
an example of
using an MP
I
wrapper com
p
i
ler
commit
|
commitdiff
|
tree
2019-05-06
Ma
r
k A
b
raham
Improve how
mdru
n
-
n
oa
p
pend names output files
commit
|
commitdiff
|
tree
2019-05-03
M
a
rk Abrah
a
m
More tests fo
r
how mdrun
-cpi restarts handle f
i
les
commit
|
commitdiff
|
tree
2019-05-02
M
a
rk Abraham
Enha
n
ce path search fun
c
tion
s
commit
|
commitdiff
|
tree
2019-04-30
Mark Ab
r
a
ham
Tes
t
the
o
ut
p
ut of "gmx mdrun help
"
commit
|
commitdiff
|
tree
2019-04-25
M
a
rk Abraham
Upda
t
e style
guide about
class e
n
u
m
s
commit
|
commitdiff
|
tree
2019-04-23
Mark Abraham
Clar
i
fy pushing o
f
inter
a
ct
i
on types
commit
|
commitdiff
|
tree
2019-04-23
Mark A
b
raha
m
Updat
e
d clang -Weverything che
c
k
s
to
clang-7
commit
|
commitdiff
|
tree
2019-04-18
Mark Abraham
Create gmx::compat:
:
opti
o
nal
commit
|
commitdiff
|
tree
2019-04-18
Ma
r
k Ab
r
aham
Move p
u
ll w
o
rk struct out of inputrec
commit
|
commitdiff
|
tree
2019-04-18
M
ark Abraham
Improve swapc
o
o
rds session lifetime management
commit
|
commitdiff
|
tree
2019-04-17
Ma
r
k Abraham
Fi
x
po
s
t-submit
commit
|
commitdiff
|
tree
2019-04-16
Mark A
b
raham
R
e
m
o
ve
d
mdrun -gcom
commit
|
commitdiff
|
tree
2019-04-13
Mark Abrah
a
m
Fix sel
f
-
c
o
nsis
t
e
n
c
y
tests of hwl
o
c data structures
commit
|
commitdiff
|
tree
2019-04-12
Mark Abraha
m
Improve warning messag
e
s
about duplicate
definiti
o
ns
commit
|
commitdiff
|
tree
2019-04-10
Mark Abra
h
a
m
Start making I
M
D and swap mode
l
IMD
M
odule
commit
|
commitdiff
|
tree
2019-04-10
Mark
A
b
r
a
ham
Reuse
r
vecs_differ in I
n
terac
t
iveMD
module
commit
|
commitdiff
|
tree
2019-04-10
Mark Abra
h
a
m
Make ImdSession into
a Pim
p
l-ed class
wit
h
factory
.
.
.
commit
|
commitdiff
|
tree
2019-04-10
Mar
k
A
braha
m
R
e
form
IMD m
o
dule
commit
|
commitdiff
|
tree
2019-04-09
Mark
A
braham
Fix
typo
i
n
A
V
X51
2
d
e
t
ection code
commit
|
commitdiff
|
tree
2019-04-03
Mark Abraha
m
Initia
l
deactivat
i
on of
group
s
cheme
.
commit
|
commitdiff
|
tree
2019-04-01
Mark Abr
a
ham
Mo
v
e
MDModules initiali
z
ation earlier
commit
|
commitdiff
|
tree
2019-04-01
Mark Abrah
a
m
M
o
v
e enerdata
o
wnership t
o
md
r
unn
e
r
commit
|
commitdiff
|
tree
2019-03-28
Mark
A
b
raham
Mo
v
e Domdec
O
p
tions into its own header
commit
|
commitdiff
|
tree
2019-03-25
Mark
Abraha
m
Su
p
port ArrayRef of Enume
r
at
i
o
nArray
commit
|
commitdiff
|
tree
2019-03-25
Mark
A
brah
a
m
Conv
e
rt gmx dump
to module
commit
|
commitdiff
|
tree
2019-03-20
M
a
rk
Abraha
m
C
l
ean u
p
mdrun help descri
p
tion
commit
|
commitdiff
|
tree
2019-03-20
Mark A
b
r
aham
Im
p
rov
e
mimic
modu
l
e
commit
|
commitdiff
|
tree
2019-03-19
Mark Abraham
Add suppo
r
t fo
r
serializing 32-bit
i
nteg
e
rs
commit
|
commitdiff
|
tree
2019-03-19
Mark Abraham
Fix
c
lang w
a
rning
commit
|
commitdiff
|
tree
2019-03-19
Ma
r
k Abraham
Upd
a
te ElectricFie
l
d module
commit
|
commitdiff
|
tree
2019-03-19
M
ark Abraham
Prevented
F
FTW build errors with clang
a
nd AVX-512
commit
|
commitdiff
|
tree
2019-03-13
Mark Abraham
Provide rem
i
n
der of wh
i
c
h
nvcc i
s
i
n use
commit
|
commitdiff
|
tree
2019-03-12
Mar
k
Abraham
Fix
m
e
mory
l
eak
commit
|
commitdiff
|
tree
2019-03-07
Mark
A
b
rah
a
m
Eliminate mdlib/
m
drun
.
h
commit
|
commitdiff
|
tree
2019-03-07
Mark Abraha
m
Remove ineffectiv
e
code for writing more TE
R
fields
.
.
.
commit
|
commitdiff
|
tree
2019-03-07
Mark
A
braham
N
ew test
s
for pd
b
2gmx and editconf
commit
|
commitdiff
|
tree
2019-03-06
Mark Abraham
Clean up use
of
l
oop
i
n
d
ice
s
commit
|
commitdiff
|
tree
2019-03-06
M
ark Abraham
Revert "Eliminate mdlib/mdrun
.
h"
commit
|
commitdiff
|
tree
2019-03-06
M
a
r
k
Abraham
Eliminate m
d
lib/mdrun
.
h
commit
|
commitdiff
|
tree
2019-03-06
Mark Abra
h
am
Mi
n
o
r
m
o
derniz
a
tion
i
n gmx_dump
commit
|
commitdiff
|
tree
2019-03-05
M
ark
Abraha
m
Make pdb2gmx tests run i
n
Jenkins
commit
|
commitdiff
|
tree
2019-03-02
M
ark Abraham
Merge branch re
l
ease-2019
commit
|
commitdiff
|
tree
2019-03-02
Mark Abraham
Remov
e
defunct mdrun opti
o
ns
commit
|
commitdiff
|
tree
2019-02-27
Mar
k
Abra
h
am
Keep niche CMake
v
ari
a
bles as adv
a
n
ced
commit
|
commitdiff
|
tree
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