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Use random water removal in gmx solvate
2019-06-18
Mark Abraha
m
Move code han
d
lin
g
mdrun -gpu_id to ta
s
k
assignm
e
nt
.
.
.
commit
|
commitdiff
|
tree
2019-06-12
Mark Abra
h
am
Fix py
g
me
n
ts d
e
tection for sphinx for doc
s
build
commit
|
commitdiff
|
tree
2019-06-11
Mark Abraham
Use R
A
II approaches for
h
ardware
info
r
mation det
e
ction
commit
|
commitdiff
|
tree
2019-06-11
Mark Abr
a
ham
Clean up multisim, c
o
mmun
i
cat
i
o
n
, and
R
EMD code
commit
|
commitdiff
|
tree
2019-05-24
Ma
r
k
A
braham
Reorder c
o
de
before
thread-MPI spawns threads
commit
|
commitdiff
|
tree
2019-05-23
Mark A
b
raham
Teach ArrayRefWithPadding t
o
make
a const flavour
commit
|
commitdiff
|
tree
2019-05-22
Mark
Abra
h
am
Rewr
i
te s
t
arting behavior
commit
|
commitdiff
|
tree
2019-05-22
Mark
Abraha
m
In
t
rod
u
ce tri-state enu
m
s
for restarts
commit
|
commitdiff
|
tree
2019-05-22
Mark Abraham
Move
f
u
n
ct
i
onality to mdrun
u
ti
l
ity
commit
|
commitdiff
|
tree
2019-05-14
Mark Abraham
U
pdate in
f
rastru
c
ture need
e
d
for restart rewrite
commit
|
commitdiff
|
tree
2019-05-08
Mark
Abrah
a
m
P
r
ovide
h
ook for for
k
s of GRO
M
ACS to
d
escribe t
h
emsel
v
e
s
commit
|
commitdiff
|
tree
2019-05-07
Mark Abr
a
h
a
m
P
r
ovide better
help for u
s
ing lib
c
++
commit
|
commitdiff
|
tree
2019-05-06
M
a
rk
A
b
raham
I
mprove how
m
d
run -noappen
d
names ou
t
put files
commit
|
commitdiff
|
tree
2019-05-03
Mark Abraham
M
o
re tes
t
s for how mdrun
-
c
pi restarts handle files
commit
|
commitdiff
|
tree
2019-05-02
Mark Ab
r
aham
Enhance path search functions
commit
|
commitdiff
|
tree
2019-04-30
Mar
k
Abraham
Test the outpu
t
o
f "gmx mdrun help"
commit
|
commitdiff
|
tree
2019-04-25
M
a
rk Abraham
U
p
date s
t
yle gu
i
de ab
o
ut class enums
commit
|
commitdiff
|
tree
2019-04-23
Mark Abraham
Clarif
y
pushing of intera
c
tion types
commit
|
commitdiff
|
tree
2019-04-23
M
ark Abraham
Updated cla
n
g -Weverything ch
e
c
k
s to clang-
7
commit
|
commitdiff
|
tree
2019-04-18
M
a
rk
Abr
a
ham
Create gmx::compa
t
::op
t
ional
commit
|
commitdiff
|
tree
2019-04-18
Mark Ab
r
ah
a
m
Move pull wo
r
k
struct out
o
f inputrec
commit
|
commitdiff
|
tree
2019-04-18
Mar
k
Abraham
Improve s
w
a
p
coords session lifetime management
commit
|
commitdiff
|
tree
2019-04-17
Mar
k
Abr
a
ham
F
i
x post-submit
commit
|
commitdiff
|
tree
2019-04-16
Mark Abraham
Removed mdru
n
-g
c
om
commit
|
commitdiff
|
tree
2019-04-10
Mark Abra
h
a
m
Start making
IMD and swap model I
M
D
M
odule
commit
|
commitdiff
|
tree
2019-04-10
Mark Abr
a
h
am
R
e
us
e
rv
e
cs_d
i
ffer in
I
n
te
r
ac
t
i
v
eMD
module
commit
|
commitdiff
|
tree
2019-04-10
Mark Abraham
M
ake ImdSession int
o
a Pimp
l
-ed class with fa
c
tory
.
.
.
commit
|
commitdiff
|
tree
2019-04-10
Ma
r
k Abraham
R
eform IMD module
commit
|
commitdiff
|
tree
2019-04-03
Ma
r
k
A
brah
a
m
I
n
itial deactivation
o
f
g
r
o
up s
c
hem
e
.
commit
|
commitdiff
|
tree
2019-04-01
Mark Ab
r
a
ham
Move M
D
Modules initialization earlier
commit
|
commitdiff
|
tree
2019-04-01
Mark Abraham
Move e
n
er
d
a
t
a owners
h
ip
t
o
m
drunner
commit
|
commitdiff
|
tree
2019-03-28
Ma
r
k
Abraham
Move DomdecOptions i
n
to its own h
e
ader
commit
|
commitdiff
|
tree
2019-03-25
Mark Ab
r
a
h
a
m
Support ArrayRe
f
o
f
EnumerationArray
commit
|
commitdiff
|
tree
2019-03-25
M
a
rk
Abraham
C
onvert gmx dump to m
o
dule
commit
|
commitdiff
|
tree
2019-03-20
Mark Abra
h
am
Cle
a
n up
m
drun help d
e
s
c
r
i
p
tion
commit
|
commitdiff
|
tree
2019-03-20
M
ark
A
brah
a
m
Improve mi
m
ic mod
u
le
commit
|
commitdiff
|
tree
2019-03-19
Mark
A
braham
Add support fo
r
serializing 32-bit integers
commit
|
commitdiff
|
tree
2019-03-19
M
a
rk Ab
r
aham
F
i
x clang
w
arning
commit
|
commitdiff
|
tree
2019-03-19
Mark
A
braha
m
U
p
date ElectricField
module
commit
|
commitdiff
|
tree
2019-03-12
Mark Abraham
Fix
m
emory
l
eak
commit
|
commitdiff
|
tree
2019-03-07
Mark Abraham
Elimina
t
e mdlib/md
r
un
.
h
commit
|
commitdiff
|
tree
2019-03-07
Mark Abraham
Remov
e
in
e
ffective code for w
r
iting mo
r
e TER fields
.
.
.
commit
|
commitdiff
|
tree
2019-03-07
Mark Abraham
N
ew tests for pdb2gmx
and
editconf
commit
|
commitdiff
|
tree
2019-03-06
M
ark Abraham
Clean up use of loop indice
s
commit
|
commitdiff
|
tree
2019-03-06
Mark Abraham
Revert
"Elimin
a
te md
l
ib/md
r
un
.
h"
commit
|
commitdiff
|
tree
2019-03-06
Ma
r
k Abraham
Eliminate mdlib/mdrun
.
h
commit
|
commitdiff
|
tree
2019-03-06
Mark Abrah
a
m
M
i
n
o
r moderniza
t
ion in gmx
_
dump
commit
|
commitdiff
|
tree
2019-03-05
Mark Abraham
Make pdb2g
m
x tests
r
un in J
e
nkins
commit
|
commitdiff
|
tree
2019-03-02
M
a
rk A
b
raham
M
e
rge br
a
nch r
e
lease-201
9
commit
|
commitdiff
|
tree
2019-03-02
Mark
A
braham
Remove d
e
f
u
nct mdrun opti
o
ns
commit
|
commitdiff
|
tree
2019-02-27
Mark Abraha
m
Keep niche
C
Make v
a
riabl
e
s as advanced
commit
|
commitdiff
|
tree
2019-02-27
Ma
r
k Abr
a
ham
Re
m
ov
e
mino
r
br
o
ken funct
i
onality
in g
m
x bar
commit
|
commitdiff
|
tree
2019-02-26
Mar
k
Abra
h
am
A
d
d new line to t
r
jco
n
v notice to
u
sers
commit
|
commitdiff
|
tree
2019-02-25
Mark Abraha
m
Mov
e
code out of sim_util
.
cpp
commit
|
commitdiff
|
tree
2019-02-25
Mar
k
Abraham
De-du
p
licate gmx_
t
mpnam and gmx_fopen_temp
o
ra
r
y
commit
|
commitdiff
|
tree
2019-02-15
Ma
r
k
Abr
a
ham
Im
p
roved diagnostics when PME
c
annot
run
on GPUs
commit
|
commitdiff
|
tree
2019-02-14
Mark Ab
r
a
ham
Fix use of s
e
lectio
n
s referr
i
ng to in
d
ex groups
commit
|
commitdiff
|
tree
2019-02-14
Mark Abraham
Re
v
ert
changes to impl
e
menta
t
ion of inse
r
t-molecules
.
.
.
commit
|
commitdiff
|
tree
2019-02-13
Mark Abraha
m
I
m
proved elect
r
i
c-f
i
eld docs
commit
|
commitdiff
|
tree
2019-02-13
Mark Abrah
a
m
Mak
e
EnergyOut
p
ut wrapper class
commit
|
commitdiff
|
tree
2019-02-13
Mark Abraham
Reduce coupling to padded
v
e
c
tor
.
h
commit
|
commitdiff
|
tree
2019-02-12
Mark
A
braham
Quie
t
clang warning
commit
|
commitdiff
|
tree
2019-02-12
Mark Abraham
Remove gmx::
R
egex
commit
|
commitdiff
|
tree
2019-02-08
Mark Abraham
Fix
Intel com
p
iler
w
arning
commit
|
commitdiff
|
tree
2019-02-08
Mark
Abraha
m
Remov
e
copy_energy from e
n
ergy-w
r
it
i
ng
s
te
p
s
commit
|
commitdiff
|
tree
2019-02-08
Ma
r
k Ab
r
aham
Reform energy output tests
commit
|
commitdiff
|
tree
2019-02-04
Mark Abraham
Remove SIMD supp
o
rt from group s
c
heme
commit
|
commitdiff
|
tree
2019-01-30
Mark Abraham
M
e
r
ge remote branch rel
e
ase-2018 int
o
release-2019
commit
|
commitdiff
|
tree
2019-01-30
Mark Abraham
Fix rele
a
se not
e
s issue links
commit
|
commitdiff
|
tree
2019-01-30
Ma
r
k Abra
h
a
m
Fix release notes issue links
commit
|
commitdiff
|
tree
2019-01-28
Mark Abraham
Stop
t
rying to check nvcc on Windows
commit
|
commitdiff
|
tree
2019-01-28
M
a
r
k Abrah
a
m
Bump C
U
DA requi
r
e
m
e
nt to 9
.
0
commit
|
commitdiff
|
tree
2019-01-25
Mark
A
brah
a
m
Require clang 3
.
6
commit
|
commitdiff
|
tree
2019-01-25
M
a
rk Abraham
Fix pos
t
-s
u
bm
i
t build
commit
|
commitdiff
|
tree
2019-01-25
Ma
r
k
Abraham
Unify regex implementation
commit
|
commitdiff
|
tree
2019-01-25
Mark Abra
h
a
m
Bump requir
e
d gcc com
p
il
e
r to
5
.
1
commit
|
commitdiff
|
tree
2019-01-25
M
a
rk Abraham
Use
n
a
ti
v
e cmake C++11 support
commit
|
commitdiff
|
tree
2019-01-22
Mark Abraham
Remove init_md a
n
d
improve init_e
m
commit
|
commitdiff
|
tree
2019-01-21
Mark Abr
a
ham
Clean up initial
i
z
e_la
m
bdas
commit
|
commitdiff
|
tree
2019-01-21
Mark Abraham
Fi
x
t
r
jconv -n
d
ec
commit
|
commitdiff
|
tree
2019-01-18
Ma
r
k Abraham
Disa
b
led in
t
ernal clF
F
T when using MSVC with O
p
enC
L
commit
|
commitdiff
|
tree
2019-01-18
Mark Abraham
I
mprove nvcc error report
i
ng
commit
|
commitdiff
|
tree
2019-01-18
Mark Abraha
m
Rem
o
ve
ctest s
e
c
t
ion call
e
d
s
imple
commit
|
commitdiff
|
tree
2019-01-16
Mark Abraham
Migrate t
e
st configuration
o
ff
bs_mac
commit
|
commitdiff
|
tree
2019-01-16
Mark
Abraham
R
e
move several unnec
e
ssary things
commit
|
commitdiff
|
tree
2019-01-15
Mark
Abra
h
am
Revert
e
d standard Extern
a
lProject
f
or FFTW downlo
a
d
commit
|
commitdiff
|
tree
2019-01-14
Mark Abraham
Improve portability
of PME on GPU code
commit
|
commitdiff
|
tree
2019-01-14
Mark Abraham
Re
m
ove ctest sect
i
o
n
called kernel
commit
|
commitdiff
|
tree
2019-01-14
Mark Ab
r
ah
a
m
M
i
g
ra
t
e TPI
testing to Verlet s
c
heme
commit
|
commitdiff
|
tree
2019-01-13
Mark Abraham
Improve
u
se of gmx
p
reprocess headers
commit
|
commitdiff
|
tree
2019-01-11
Mar
k
A
b
rah
a
m
Use e
n
um cla
s
s for gromp
p
d
ire
c
tives
commit
|
commitdiff
|
tree
2019-01-11
Mark Abraham
Fix t
y
p
o
i
n re
l
ease no
t
es
commit
|
commitdiff
|
tree
2019-01-11
Mark Abraham
A
d
d
h
elper fun
c
tionality for s
a
fer
e
n
u
merations
commit
|
commitdiff
|
tree
2019-01-10
Mark
A
braham
A
dd mor
e
checks for division
b
y zero
commit
|
commitdiff
|
tree
2019-01-10
Mark Abraham
Ad
d
m
o
re che
c
ks for
d
i
visi
o
n
by zer
o
commit
|
commitdiff
|
tree
2019-01-09
Mark Abra
h
am
Fix e
i
oNam
e
s
commit
|
commitdiff
|
tree
2019-01-08
Mark Abraha
m
F
ix
t
rjconv -nde
c
commit
|
commitdiff
|
tree
2019-01-08
M
a
rk
Abraha
m
S
i
m
plify reporting o
f
GPU selection
commit
|
commitdiff
|
tree
2019-01-07
Mark Abraham
Finish removing
g
r
oup-schem
e
all-vs-all sup
p
ort
commit
|
commitdiff
|
tree
2019-01-02
Mark A
b
raham
Merge branc
h
r
ele
a
se-2019
commit
|
commitdiff
|
tree
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