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Use potential-shift as default modifier
2019-08-20
Mark Abraham
Us
e
potential-
s
hi
f
t as default modi
f
ier
commit
|
commitdiff
|
tree
2019-08-20
Mark Abraham
Reduce cosine acceleration
qu
a
n
t
i
t
y properly
commit
|
commitdiff
|
tree
2019-08-20
Mark Abraham
Fix
i
s
sues
f
or
c
lang-analy
z
er-8
commit
|
commitdiff
|
tree
2019-08-19
Mark A
b
r
aham
Modernize t_matrix, t_ma
p
ping, t_rgb
commit
|
commitdiff
|
tree
2019-08-19
M
a
r
k
Abraha
m
Moderniz
e
t_psdata
commit
|
commitdiff
|
tree
2019-08-16
M
a
rk Abraham
Update testin
g
ma
t
ric
e
s and fix
w
ar
n
ings
commit
|
commitdiff
|
tree
2019-08-16
Mark Ab
r
aham
Move
key
v
al
u
etreewriter code
commit
|
commitdiff
|
tree
2019-08-16
Mark Abraham
Stop nbnxm/grid
.
h depending o
n
SIMD modul
e
commit
|
commitdiff
|
tree
2019-08-15
Mark
A
b
r
aham
Remove run-time check from calc_shif
t
s
commit
|
commitdiff
|
tree
2019-08-14
Mark Abra
h
a
m
F
ix
v
v i
n
teg
r
at
o
rs
commit
|
commitdiff
|
tree
2019-08-13
Mark
Abrah
a
m
Remove
w
or
k
around for bugg
y
cmake
commit
|
commitdiff
|
tree
2019-08-13
Mark Abraham
Fix icc 19 codegen
i
ssue
commit
|
commitdiff
|
tree
2019-08-12
Ma
r
k Abra
h
am
Qui
e
t
warning
commit
|
commitdiff
|
tree
2019-08-12
Mar
k
Abraha
m
Fix
oc
l
_ke
r
nel ta
r
get
commit
|
commitdiff
|
tree
2019-08-08
Mark
Abraha
m
Fix estimate of the
size of a
j list
commit
|
commitdiff
|
tree
2019-08-08
Mark Abr
a
ham
Initializ
e
gmx_ekind
a
ta_t and t
_
v
cm prope
r
ly
commit
|
commitdiff
|
tree
2019-08-08
Mar
k
A
b
r
aham
Stop testing ICC o
n
Win
d
o
w
s
commit
|
commitdiff
|
tree
2019-08-05
M
ark Abraham
A
d
d
qu
o
te
commit
|
commitdiff
|
tree
2019-08-05
Mark A
b
raha
m
Remove libgromacs_generated
c
ontributions
from Fi
n
dCUDA
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
M
a
rk
Abr
a
ham
Manag
e
compiler f
l
ags and some include optio
n
s per
.
.
.
commit
|
commitdiff
|
tree
2019-08-01
Mar
k
Abra
h
a
m
I
m
p
rove use of object l
i
braries in
libgromacs
commit
|
commitdiff
|
tree
2019-08-01
Mark Abraham
Merge
"
M
e
rge rele
a
se-2019 into master"
commit
|
commitdiff
|
tree
2019-07-24
Mark
Abraham
Re
m
ove tests of make_unique
commit
|
commitdiff
|
tree
2019-07-23
Mark Abraham
Update developer g
u
i
d
e
commit
|
commitdiff
|
tree
2019-07-16
Mark Abraham
Add gpubuffer
o
ps test matrix
commit
|
commitdiff
|
tree
2019-07-11
Mark
A
bra
h
am
Fi
x
pre-submit b
u
ild
m
a
t
rix and d
e
sc
r
iption
commit
|
commitdiff
|
tree
2019-07-08
Mark Ab
r
aham
Fix hwloc
and sphi
n
x detecti
o
n
commit
|
commitdiff
|
tree
2019-07-08
Ma
r
k Abr
a
h
am
Test sp
e
cif
i
c
h
wloc versions
commit
|
commitdiff
|
tree
2019-07-05
Mark Abr
a
h
am
Improve tests of
i
nde
x
block construction
commit
|
commitdiff
|
tree
2019-07-05
M
ark Abraha
m
Mode
r
niz
e
F
i
ndHwloc
.
cmake
commit
|
commitdiff
|
tree
2019-07-04
Mar
k
A
braham
Further clang-tidy-7
f
ix
commit
|
commitdiff
|
tree
2019-07-04
Ma
r
k Abra
h
am
Fi
x
clang-tid
y
-
7 issues
commit
|
commitdiff
|
tree
2019-07-03
Mark Abraham
Reorder option
s
commit
|
commitdiff
|
tree
2019-07-02
M
a
r
k
Abraham
Clarif
y
w
o
rding of release notes
commit
|
commitdiff
|
tree
2019-06-18
Mar
k
Abraham
Move code h
a
ndling mdrun
-gpu_id to
ta
s
kassig
n
me
n
t
.
.
.
commit
|
commitdiff
|
tree
2019-06-12
M
ark
A
b
r
aham
F
i
x pygments detection for sphinx for docs build
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraham
Use RAII approaches for
h
ardw
a
re information detection
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraha
m
Clean up mul
t
i
s
im, communi
c
a
t
ion, and REMD code
commit
|
commitdiff
|
tree
2019-06-11
Ma
r
k Abraham
Init
i
a
lize all o
f
gmx_domdec_comm_t
commit
|
commitdiff
|
tree
2019-05-24
Mark Ab
r
ah
a
m
R
eorder
code before
t
hread-MPI spawns threads
commit
|
commitdiff
|
tree
2019-05-23
M
a
rk Abraham
Teach
A
rray
R
efWith
P
adding to make a const fla
v
o
ur
commit
|
commitdiff
|
tree
2019-05-23
Mark Abra
h
am
R
e
vert "Fixed dvdlambd
a
for SHAKE + FE"
commit
|
commitdiff
|
tree
2019-05-22
M
a
rk Abraham
R
e
wri
t
e
starti
n
g b
e
havior
commit
|
commitdiff
|
tree
2019-05-22
Mark
Abraham
I
ntrodu
c
e tri-state
enums for restart
s
commit
|
commitdiff
|
tree
2019-05-22
Mar
k
Abra
h
am
Move functionality to m
d
r
unu
t
il
i
ty
commit
|
commitdiff
|
tree
2019-05-20
Mark
A
braham
Fi
x
e
quation typo
commit
|
commitdiff
|
tree
2019-05-14
Mark Abraham
U
p
date infrastructure nee
d
e
d f
o
r restart rewrite
commit
|
commitdiff
|
tree
2019-05-08
Mark Abr
a
ham
Provide
h
ook for fo
r
ks of GROMACS
t
o
describ
e
themselve
s
commit
|
commitdiff
|
tree
2019-05-07
Mark Abraham
P
rovid
e
better he
l
p f
o
r us
i
n
g
l
i
bc++
commit
|
commitdiff
|
tree
2019-05-07
Mark Ab
r
a
h
am
Add an exam
p
l
e
of using
an MPI wr
a
pper
compi
l
e
r
commit
|
commitdiff
|
tree
2019-05-06
M
a
r
k Abraham
Imp
r
ove ho
w
mdru
n
-noapp
e
nd n
a
mes o
u
tput
f
il
e
s
commit
|
commitdiff
|
tree
2019-05-03
Ma
r
k Abraham
Mo
r
e tests for
how mdrun
-cpi restart
s
handle
f
i
l
es
commit
|
commitdiff
|
tree
2019-05-02
Mark Ab
r
aham
Enhance path
search funct
i
on
s
commit
|
commitdiff
|
tree
2019-04-30
Mark Abraham
Tes
t
t
he out
p
ut of "
g
mx mdrun help"
commit
|
commitdiff
|
tree
2019-04-25
Ma
r
k Abraham
U
p
date style guide
about
c
l
a
ss
enums
commit
|
commitdiff
|
tree
2019-04-23
Mark
A
brah
a
m
Cla
r
i
f
y pushing of intera
c
tion ty
p
es
commit
|
commitdiff
|
tree
2019-04-23
Mark Abraham
Updated clang -Weve
r
ything check
s
to c
l
ang-7
commit
|
commitdiff
|
tree
2019-04-18
Mark
Abr
a
ham
Cre
a
te gmx::compat::optional
commit
|
commitdiff
|
tree
2019-04-18
Mark A
b
raham
Move pull w
o
rk
s
truct out of inputrec
commit
|
commitdiff
|
tree
2019-04-18
Mark Abraham
Improve swapcoor
d
s ses
s
i
o
n lifetime manage
m
ent
commit
|
commitdiff
|
tree
2019-04-17
Mark Abraha
m
Fix pos
t
-submit
commit
|
commitdiff
|
tree
2019-04-16
Mark Abrah
a
m
Removed mdrun
-gcom
commit
|
commitdiff
|
tree
2019-04-13
Mark Abra
h
am
Fi
x
self-consiste
n
cy tes
t
s of hwloc data structu
r
es
commit
|
commitdiff
|
tree
2019-04-12
M
ark Abraham
Impr
o
ve w
a
rning messa
g
es
a
bout
d
uplicate def
i
nitio
n
s
commit
|
commitdiff
|
tree
2019-04-10
Mark
A
braha
m
Start making IMD and sw
a
p model
I
MDModule
commit
|
commitdiff
|
tree
2019-04-10
Mark
A
b
raham
R
e
use
rvec
s
_differ in Interactiv
e
MD module
commit
|
commitdiff
|
tree
2019-04-10
Mark
Ab
r
ah
a
m
M
a
ke ImdSession into a Pimpl-ed class with
f
actor
y
.
.
.
commit
|
commitdiff
|
tree
2019-04-10
Mark Abra
h
am
Reform IMD m
o
dule
commit
|
commitdiff
|
tree
2019-04-09
Mark Abraham
Fix typo in AVX512
detection code
commit
|
commitdiff
|
tree
2019-04-03
M
a
rk Ab
r
a
ham
Initial deactivation
of group scheme
.
commit
|
commitdiff
|
tree
2019-04-01
M
a
rk Abraham
Move
MDModules i
n
itializa
t
ion earlier
commit
|
commitdiff
|
tree
2019-04-01
Mark
Abr
a
ham
Move
enerdata o
w
n
ership to mdrunner
commit
|
commitdiff
|
tree
2019-03-28
Mark
Abra
h
am
Mov
e
DomdecOptions in
t
o i
t
s own header
commit
|
commitdiff
|
tree
2019-03-25
M
ark
A
braham
Support ArrayRef of Enumer
a
tionArray
commit
|
commitdiff
|
tree
2019-03-25
Mark Abraham
Conv
e
rt gmx du
m
p t
o
module
commit
|
commitdiff
|
tree
2019-03-20
Mark Abraham
C
lea
n
up mdrun help descript
i
on
commit
|
commitdiff
|
tree
2019-03-20
Mar
k
A
b
rah
a
m
Im
p
r
ove mimi
c
module
commit
|
commitdiff
|
tree
2019-03-19
Mark Abraham
Add support fo
r
seri
a
lizing 32-bit i
n
tegers
commit
|
commitdiff
|
tree
2019-03-19
Mark Abraham
Fix clang warning
commit
|
commitdiff
|
tree
2019-03-19
Ma
r
k
Abraham
U
p
date ElectricFiel
d
module
commit
|
commitdiff
|
tree
2019-03-19
Ma
r
k Abrah
a
m
Prevented FFTW build errors with c
l
ang and AVX-
5
12
commit
|
commitdiff
|
tree
2019-03-13
M
a
rk Abraham
Provide re
m
in
d
er o
f
which nvcc
is in use
commit
|
commitdiff
|
tree
2019-03-12
M
a
r
k Ab
r
a
h
a
m
Fi
x
me
m
o
r
y
leak
commit
|
commitdiff
|
tree
2019-03-07
Mark Abraham
Eliminate mdlib/mdrun
.
h
commit
|
commitdiff
|
tree
2019-03-07
Mark Abraham
Rem
o
v
e
ineffective code for w
r
it
i
n
g m
o
re T
E
R fields
.
.
.
commit
|
commitdiff
|
tree
2019-03-07
M
a
rk Abraham
Ne
w
t
e
sts fo
r
pd
b
2gmx and editconf
commit
|
commitdiff
|
tree
2019-03-06
M
a
rk
A
br
a
ham
Cl
e
an up us
e
o
f loo
p
ind
i
ces
commit
|
commitdiff
|
tree
2019-03-06
M
ark Abraham
Revert "
E
lim
i
n
a
te mdlib
/
mdrun
.
h"
commit
|
commitdiff
|
tree
2019-03-06
Mark A
b
ra
h
am
E
l
iminate md
l
i
b
/mdrun
.
h
commit
|
commitdiff
|
tree
2019-03-06
Mark Abraham
Mino
r
mode
r
nization in gmx_dump
commit
|
commitdiff
|
tree
2019-03-05
Mark Abr
a
h
a
m
Make pdb2gmx te
s
ts ru
n
in Jenkins
commit
|
commitdiff
|
tree
2019-03-02
Ma
r
k
Abraham
Merge
branch release-2019
commit
|
commitdiff
|
tree
2019-03-02
M
a
rk
A
b
r
ah
a
m
Remove d
e
func
t
m
dru
n
op
t
ions
commit
|
commitdiff
|
tree
2019-02-27
Mark Abraham
Keep niche CMa
k
e va
r
i
a
bles
a
s advan
c
ed
commit
|
commitdiff
|
tree
2019-02-27
Mark Ab
r
aham
Remove minor
b
roken functionality in gm
x
bar
commit
|
commitdiff
|
tree
2019-02-26
Mark Abraham
A
dd new line to trjconv
n
otice t
o
users
commit
|
commitdiff
|
tree
2019-02-25
Mark Abraham
Move
c
o
d
e o
u
t
o
f
sim_
u
til
.
c
p
p
commit
|
commitdiff
|
tree
2019-02-25
M
a
rk Abraham
De-dup
l
icate gmx_tmpna
m
an
d
gmx_fopen_temporary
commit
|
commitdiff
|
tree
2019-02-15
Mar
k
Abra
h
am
Improve
d
diagnostics
wh
e
n PME
c
annot run on GPUs
commit
|
commitdiff
|
tree
2019-02-14
M
ark Ab
r
aha
m
Fix use of selections r
e
ferring
to
i
ndex groups
commit
|
commitdiff
|
tree
next