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Start making IMD and swap model IMDModule
2019-04-10
Mark Ab
r
aham
Start making IMD and swap
m
odel IMDModule
commit
|
commitdiff
|
tree
2019-04-10
M
a
rk Abraham
Reuse rv
e
c
s_differ
in Int
e
ractiveMD module
commit
|
commitdiff
|
tree
2019-04-10
Mark Abr
a
ham
Make ImdSession into a
P
impl-ed
class wit
h
factory
.
.
.
commit
|
commitdiff
|
tree
2019-04-10
Mark A
b
raham
Ref
o
rm IMD m
o
dule
commit
|
commitdiff
|
tree
2019-04-03
Mark Abraham
Initial deact
i
vation of gr
o
up
s
cheme
.
commit
|
commitdiff
|
tree
2019-04-01
M
a
rk Abraham
Move
M
D
Modu
l
e
s in
i
tiali
z
ation
e
a
r
lie
r
commit
|
commitdiff
|
tree
2019-04-01
M
a
r
k
Abraham
Move enerda
t
a ow
n
ership to m
d
runner
commit
|
commitdiff
|
tree
2019-03-28
Mark Abraham
Move Do
m
decOptions
into its ow
n
head
e
r
commit
|
commitdiff
|
tree
2019-03-25
Mark Abraham
Supp
o
r
t
ArrayRef of
E
numeratio
n
A
rray
commit
|
commitdiff
|
tree
2019-03-25
M
ar
k
Abraham
Convert gmx dump
t
o module
commit
|
commitdiff
|
tree
2019-03-20
M
ark
Abrah
a
m
C
l
ean up mdrun h
e
lp descrip
t
ion
commit
|
commitdiff
|
tree
2019-03-20
Mark Abraham
Imp
r
o
v
e mi
m
i
c
mo
d
ule
commit
|
commitdiff
|
tree
2019-03-19
Mar
k
Abraham
Add suppo
r
t fo
r
serializing 3
2
-bit integ
e
rs
commit
|
commitdiff
|
tree
2019-03-19
Mark A
b
raham
Fix clang warning
commit
|
commitdiff
|
tree
2019-03-19
M
ark
Abraham
Update Electr
i
cField module
commit
|
commitdiff
|
tree
2019-03-12
Mark Abr
a
ham
Fix memory le
a
k
commit
|
commitdiff
|
tree
2019-03-07
Mark Abraha
m
Eliminate
m
dlib/mdrun
.
h
commit
|
commitdiff
|
tree
2019-03-07
Mark
A
brah
a
m
Remove
i
neffective code for writing more
TER fields
.
.
.
commit
|
commitdiff
|
tree
2019-03-07
M
a
rk Ab
r
aham
New tests for p
d
b
2gmx and edi
t
conf
commit
|
commitdiff
|
tree
2019-03-06
M
a
rk Abraham
Clean up use of
l
o
op indices
commit
|
commitdiff
|
tree
2019-03-06
Mark
Abrah
a
m
Revert "Eliminate mdlib/mdrun
.
h"
commit
|
commitdiff
|
tree
2019-03-06
Mark Abraham
E
liminate
mdlib/md
r
un
.
h
commit
|
commitdiff
|
tree
2019-03-06
M
a
r
k
A
b
raham
Mino
r
modernization in gmx_dump
commit
|
commitdiff
|
tree
2019-03-05
Ma
r
k A
b
r
aham
Make pdb2gmx tests run i
n
Jenk
i
ns
commit
|
commitdiff
|
tree
2019-03-02
Mark Abra
h
am
Merge bra
n
c
h release-2019
commit
|
commitdiff
|
tree
2019-03-02
Mar
k
A
braham
Remove defunct
m
dru
n
options
commit
|
commitdiff
|
tree
2019-02-27
M
ark Abraham
Kee
p
n
i
che CMake
v
ariables as advanced
commit
|
commitdiff
|
tree
2019-02-27
Mark
A
brah
a
m
Remove minor broken functionalit
y
in g
m
x b
a
r
commit
|
commitdiff
|
tree
2019-02-26
Mark Abr
a
ham
Add new line to trjconv noti
c
e to users
commit
|
commitdiff
|
tree
2019-02-25
Mark Abraham
Mov
e
code out of sim_util
.
cpp
commit
|
commitdiff
|
tree
2019-02-25
M
a
rk Abrah
a
m
De-d
u
pl
i
cat
e
gmx_tmpnam
a
nd g
m
x_fopen_te
m
porary
commit
|
commitdiff
|
tree
2019-02-15
Mark Abraham
I
mproved diagnosti
c
s
when P
M
E can
n
ot run on GPUs
commit
|
commitdiff
|
tree
2019-02-14
Mark A
b
raham
Fix us
e
of selections referring to index
g
roups
commit
|
commitdiff
|
tree
2019-02-14
Mar
k
Abraham
Revert
c
hang
e
s to imp
l
eme
n
tation o
f
insert-
m
ol
e
cules
.
.
.
commit
|
commitdiff
|
tree
2019-02-13
Mark Abr
a
h
a
m
Improved electric-fie
l
d docs
commit
|
commitdiff
|
tree
2019-02-13
Mark Abraham
Make
EnergyO
u
tput w
r
apper class
commit
|
commitdiff
|
tree
2019-02-13
Mark Abra
h
am
Reduce coupling
t
o
padde
d
ve
c
tor
.
h
commit
|
commitdiff
|
tree
2019-02-12
Mark Abr
a
ham
Quiet
cl
a
ng war
n
ing
commit
|
commitdiff
|
tree
2019-02-12
Mar
k
A
braham
Remove gmx::
R
egex
commit
|
commitdiff
|
tree
2019-02-08
Mark Ab
r
aham
Fix
I
ntel compiler
w
arning
commit
|
commitdiff
|
tree
2019-02-08
Mark Abraham
R
e
move copy_energ
y
f
r
om ener
g
y-writing steps
commit
|
commitdiff
|
tree
2019-02-08
M
ark Ab
r
aham
Reform ener
g
y outpu
t
tests
commit
|
commitdiff
|
tree
2019-02-04
Mark Abraham
Remove SIMD support fr
o
m
group scheme
commit
|
commitdiff
|
tree
2019-01-30
Mark Abr
a
ham
Merg
e
remote branch r
e
lease-2018 into release
-
201
9
commit
|
commitdiff
|
tree
2019-01-30
M
ark A
b
raham
Fix release n
o
tes issue l
i
nks
commit
|
commitdiff
|
tree
2019-01-30
Mark Abraha
m
Fix
r
elease no
t
es
i
ssue l
i
nks
commit
|
commitdiff
|
tree
2019-01-28
Mark Abraham
Stop
t
r
ying to ch
e
c
k
nvcc on
Windows
commit
|
commitdiff
|
tree
2019-01-28
Mark Abr
a
ha
m
Bump CUDA requireme
n
t to 9
.
0
commit
|
commitdiff
|
tree
2019-01-25
Mark Abraham
Req
u
ire cla
n
g
3
.
6
commit
|
commitdiff
|
tree
2019-01-25
Mark Ab
r
aham
Fix post-submit b
u
i
ld
commit
|
commitdiff
|
tree
2019-01-25
Mark Ab
r
aham
Un
i
f
y regex implementation
commit
|
commitdiff
|
tree
2019-01-25
Mark Abraham
Bump required gcc
compile
r
to 5
.
1
commit
|
commitdiff
|
tree
2019-01-25
Mark Ab
r
aham
Use nativ
e
cma
k
e C++11 support
commit
|
commitdiff
|
tree
2019-01-22
Mark Abraham
Remove i
n
i
t_
m
d and
i
mprove
i
nit_em
commit
|
commitdiff
|
tree
2019-01-21
Mark Abraham
Clean up
i
niti
a
l
i
ze_
l
ambdas
commit
|
commitdiff
|
tree
2019-01-21
Mark Abra
h
am
F
ix trjconv
-ndec
commit
|
commitdiff
|
tree
2019-01-18
M
ark Abraham
Disabled internal clFFT
when using MSVC w
i
th OpenCL
commit
|
commitdiff
|
tree
2019-01-18
Mark Abraham
I
m
p
rove nvcc err
o
r repo
r
ting
commit
|
commitdiff
|
tree
2019-01-18
M
a
rk Abraham
Remove ct
e
st section
called simpl
e
commit
|
commitdiff
|
tree
2019-01-16
Mark
Abraham
M
i
g
rate tes
t
c
o
n
f
iguration off
b
s_mac
commit
|
commitdiff
|
tree
2019-01-16
Mark Ab
r
aham
Remo
v
e several unnecessary things
commit
|
commitdiff
|
tree
2019-01-15
Mark Abraha
m
R
everted standard Externa
l
Project for FFTW download
commit
|
commitdiff
|
tree
2019-01-14
Mark Abraham
Improve portability o
f
P
ME on GPU code
commit
|
commitdiff
|
tree
2019-01-14
Mar
k
Abraham
R
emove ct
e
s
t
section call
e
d kernel
commit
|
commitdiff
|
tree
2019-01-14
Mark Ab
r
aham
Migr
a
te
TPI te
s
t
i
n
g t
o
Verle
t
scheme
commit
|
commitdiff
|
tree
2019-01-13
Mark Abraham
Improve u
s
e of gmxpre
p
roce
s
s headers
commit
|
commitdiff
|
tree
2019-01-11
Mark Abraham
Use
e
n
um
c
la
s
s
for g
r
ompp directive
s
commit
|
commitdiff
|
tree
2019-01-11
Mark A
b
r
ah
a
m
F
ix
typo in r
e
leas
e
note
s
commit
|
commitdiff
|
tree
2019-01-11
M
a
r
k Abraham
Add helper functi
o
n
a
l
ity for safer enumeration
s
commit
|
commitdiff
|
tree
2019-01-10
Mark Abraham
Ad
d
more checks f
o
r
div
i
sion by zer
o
commit
|
commitdiff
|
tree
2019-01-10
Mark
A
b
raham
A
d
d
more checks for division
b
y zero
commit
|
commitdiff
|
tree
2019-01-09
Mark Abraha
m
Fix eioNames
commit
|
commitdiff
|
tree
2019-01-08
Mar
k
Abrah
a
m
F
i
x trjconv -ndec
commit
|
commitdiff
|
tree
2019-01-08
Mark Abraham
Simplify reporting of GPU
s
election
commit
|
commitdiff
|
tree
2019-01-07
M
a
rk
Abraham
Fin
i
s
h
removing group-sc
h
eme all-vs-all
s
upport
commit
|
commitdiff
|
tree
2019-01-02
Mark Abra
h
am
Merge bran
c
h
r
e
lease-2
0
19
commit
|
commitdiff
|
tree
2018-12-22
M
ark Abraham
Fix
u
nused parameter warning
commit
|
commitdiff
|
tree
2018-12-10
Mark A
b
raham
M
ake on
l
y md
r
un
repor
t
process ID
commit
|
commitdiff
|
tree
2018-12-09
M
ark Abrah
a
m
Fi
x
P
OW
E
R8 and POW
E
R
9
b
u
i
ld
commit
|
commitdiff
|
tree
2018-12-03
Mark Abraha
m
Move res
p
onsibility for PM
E
reduction to i
t
s mod
u
le
commit
|
commitdiff
|
tree
2018-11-29
M
a
r
k
Ab
r
aham
Removed
errono
u
s
ma
n
u
a
l varia
b
le
h
a
ndling
commit
|
commitdiff
|
tree
2018-11-28
M
ar
k
Abraham
Introdu
c
e GpuBonded
commit
|
commitdiff
|
tree
2018-11-26
Mark Abraham
C
lean
u
p initi
a
l log output
commit
|
commitdiff
|
tree
2018-11-22
Ma
r
k Abraham
Introdu
c
e PpForceWorkload
commit
|
commitdiff
|
tree
2018-11-22
M
a
rk Abraham
Me
r
ge
"Merge br
a
n
c
h 'rele
a
se-2
0
19'
"
commit
|
commitdiff
|
tree
2018-11-20
Ma
r
k Abraham
Partial revert of "Fix ine
f
ficient shell minimization"
commit
|
commitdiff
|
tree
2018-11-20
Mark Abr
a
ham
Merge
"Merge releas
e
-2
0
1
9
into master"
commit
|
commitdiff
|
tree
2018-11-19
Mark
Abraham
Fix
inefficient shell mini
m
i
zation
commit
|
commitdiff
|
tree
2018-11-15
M
a
r
k
A
braham
Fix checkpoin
t
re
s
tart of
t
pr wi
t
h
infinite step cou
n
t
commit
|
commitdiff
|
tree
2018-11-15
M
a
r
k
Abraham
Relax ar
b
itrary
t
oler
a
nce on rerun test
commit
|
commitdiff
|
tree
2018-11-14
Mark Abraham
Fix
O
p
enCL
m
drun from installed path
commit
|
commitdiff
|
tree
2018-11-14
M
ark Abraham
M
ore warning suppressi
o
ns
f
or
Q
M
M
M code
commit
|
commitdiff
|
tree
2018-11-09
Mark
A
braham
D
i
s
abled FPE
c
hecking
for non-
r
e
l
eas
e
builds
commit
|
commitdiff
|
tree
2018-11-08
M
a
rk Abraham
Pragma wa
r
ning suppr
e
s
s
i
n
s
f
or i
c
c+windo
w
s
commit
|
commitdiff
|
tree
2018-11-07
Mark Abraham
S
u
ppress clang wa
r
nings abou
t
QMMM
code
commit
|
commitdiff
|
tree
2018-11-05
Mark Abr
a
h
am
Make PME OpenCL
e
nable
d
only f
o
r
AMD dev
i
ces
commit
|
commitdiff
|
tree
2018-11-05
Mark A
b
raham
R
emove source file with no content
commit
|
commitdiff
|
tree
2018-11-02
M
ark Abraham
Quiet unused variable war
n
ing
s
commit
|
commitdiff
|
tree
2018-11-01
M
ark Ab
r
ah
a
m
Stop using
hwlo
c
on ol
d
A
RM sl
a
ve
commit
|
commitdiff
|
tree
2018-11-01
Mark Abraham
Disable cc
a
che by default
commit
|
commitdiff
|
tree
next