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Updates to documentation
2016-06-07
Mark Abraham
Update
s
to d
o
cumentation
commit
|
commitdiff
|
tree
2016-06-02
Mark
A
braham
Fix
co
m
patibility with older CMake
commit
|
commitdiff
|
tree
2016-05-31
Mar
k
Abraham
Fix refere
n
c
e
to vmdio
.
c t
o
be vmdio
.
cpp
commit
|
commitdiff
|
tree
2016-05-31
Mark Abraham
Sec
o
nd 2
0
16
beta
r
el
e
ase
commit
|
commitdiff
|
tree
2016-05-29
Mark Abraha
m
Sim
p
lified a
n
d updated
OpenCL compi
l
ation
commit
|
commitdiff
|
tree
2016-05-26
Mark
A
brah
a
m
N
e
w quote
commit
|
commitdiff
|
tree
2016-05-12
Ma
r
k Abraham
M
e
r
ge
b
ranch
rel
e
ase-5-1
in
t
o
re
l
ease-2016
commit
|
commitdiff
|
tree
2016-05-12
Mark Abraham
GROM
A
CS
2016 beta1 re
l
e
ase
commit
|
commitdiff
|
tree
2016-05-10
Mark Abr
a
ham
Bump cl
a
ng static analy
z
er to
v
ers
i
on 3
.
8
commit
|
commitdiff
|
tree
2016-05-10
Mark
Abra
h
am
M
in
o
r update to sphinx dependen
c
y
commit
|
commitdiff
|
tree
2016-05-10
Mark Abrah
a
m
Facilitate
l
i
nki
n
g wit
h
libcx
x
commit
|
commitdiff
|
tree
2016-05-08
M
ar
k
Abraham
Fi
x
es for clang 3
.
7
o
n
Powe
r
PC
commit
|
commitdiff
|
tree
2016-05-08
Mark Abraham
Fi
x
constants,
units and
c
onversi
o
n
fac
t
ors
commit
|
commitdiff
|
tree
2016-04-27
Ma
r
k Abraham
Me
r
ge
branch r
e
le
a
se-5-1
commit
|
commitdiff
|
tree
2016-04-19
Mark Abraham
Replac
e
libxm
l
2
w
ith
tinyxml2 for
u
se in test c
o
de
commit
|
commitdiff
|
tree
2016-04-19
M
a
r
k
Abraham
Fix parse_digits_from_string
commit
|
commitdiff
|
tree
2016-04-19
M
a
rk Abr
a
ham
F
i
x
md
p
lab
e
l
g
eneration
commit
|
commitdiff
|
tree
2016-04-18
Mark Ab
r
aha
m
Reduce comp
i
lation
coupling of SIMD module
commit
|
commitdiff
|
tree
2016-04-14
Mark Abraham
Merg
e
br
a
nc
h
release
-
5
-
1
commit
|
commitdiff
|
tree
2016-04-01
M
ark Abra
h
am
Revert to
treating -1 as "ge
n
erate a se
e
d"
i
n
.
mdp
commit
|
commitdiff
|
tree
2016-03-31
Mark Abraham
Add te
s
t
a
nd i
m
proved doc
s
for
c
ustom checkSe
q
u
e
nce
commit
|
commitdiff
|
tree
2016-03-30
Mark Abr
a
ham
Clea
n
up vsite cod
e
commit
|
commitdiff
|
tree
2016-03-19
Ma
r
k
Abraham
Add more const correctness
commit
|
commitdiff
|
tree
2016-03-19
Mark Abraham
Fi
x
warning f
r
om
G
CC 6
commit
|
commitdiff
|
tree
2016-03-19
Ma
r
k Abrah
a
m
I
m
prove
d
some m
d
run
i
nte
g
ration tests
commit
|
commitdiff
|
tree
2016-03-18
Mark
Abr
a
ham
Warn
a
bo
u
t OpenMPI 1
.
8
.
6
commit
|
commitdiff
|
tree
2016-03-18
Mark Abraham
Fix typo in Fourie
r
dihe
d
ral equation
commit
|
commitdiff
|
tree
2016-03-15
M
ark Abraham
M
e
rge bran
c
h rele
a
se-5-0 into relea
s
e-5-1
commit
|
commitdiff
|
tree
2016-03-12
Ma
r
k
Abraham
Update
u
se
of isnan in linear
a
l
g
ebra
commit
|
commitdiff
|
tree
2016-03-12
Mark Abraham
F
i
nd hw
l
oc quietly
i
f
i
t's alr
e
ady b
e
en
found
commit
|
commitdiff
|
tree
2016-03-11
Mark Abrah
a
m
A
d
d infrastructure
f
or tests
t
o comp
a
re mdrun
s
commit
|
commitdiff
|
tree
2016-03-11
M
a
rk Abrah
a
m
Merge branc
h
re
l
ease
-
5-0 into relea
s
e-5
-
1
commit
|
commitdiff
|
tree
2016-03-10
Mar
k
A
b
raham
Require
2
0
15 versio
n
for MSVC
commit
|
commitdiff
|
tree
2016-03-05
M
ark Abraham
Add
SETTLE unit t
e
sts
commit
|
commitdiff
|
tree
2016-02-26
Mark Abr
a
h
am
S
e
parated
te
s
t o
f
CDA
T
A en
d
tag h
a
ndlin
g
fr
o
m others
commit
|
commitdiff
|
tree
2016-02-23
M
ark
Abra
h
am
R
e
p
l
ac
e
cppchec
k
suppression in
checkpoint co
d
e
commit
|
commitdiff
|
tree
2016-02-22
M
a
rk Abraham
Move init of specia
l
ize
d
dynamical algor
i
thms
t
o do_md
commit
|
commitdiff
|
tree
2016-02-21
Mark Abraham
Sep
a
rate table construct
i
o
n
commit
|
commitdiff
|
tree
2016-02-19
Mark Abr
a
ham
Merge b
r
anch relea
s
e-5-1
commit
|
commitdiff
|
tree
2016-02-19
Mark Abraham
Make both ftp and http links for source download
commit
|
commitdiff
|
tree
2016-02-18
Mark Abraham
Updated reference m
a
nual t
e
x
t about PME tuning
commit
|
commitdiff
|
tree
2016-02-16
Mark Abraham
M
e
rge br
a
nch
r
e
lease-5-0 into release-5-1
commit
|
commitdiff
|
tree
2016-02-14
Mar
k
Abraham
Re-generate
d
e
ps fo
r
figure 4
.
8
commit
|
commitdiff
|
tree
2016-02-10
M
a
rk Ab
r
aham
Re-remove
*_
s
tochd_state function declara
t
ions
commit
|
commitdiff
|
tree
2016-02-10
Mark Abra
h
am
Im
p
r
oved
u
pdate_coords h
a
nd
l
i
ng
of xprime
commit
|
commitdiff
|
tree
2016-02-10
Mark Abraham
Fi
x
issues to
updat
e
cppche
c
k sup
p
ort to 1
.
7
2
commit
|
commitdiff
|
tree
2016-02-08
Mark A
b
raha
m
Merge branch releas
e
-5-0 into releas
e
-5-1
commit
|
commitdiff
|
tree
2016-02-06
Mark Abraham
Merg
e
branc
h
r
e
l
ease-5-1
commit
|
commitdiff
|
tree
2016-02-03
Mark
Ab
r
a
ham
Bumped patch nu
m
ber to prepare
f
or future 5
.
1
.
3
r
e
le
a
se
commit
|
commitdiff
|
tree
2016-02-03
Mark Abraham
Version 5
.
1
.
2
commit
|
commitdiff
|
tree
2016-02-03
M
ark
Ab
r
aham
Fix grompp n
o
t warning whe
n
.
mdp va
l
ues have w
r
ong
.
.
.
commit
|
commitdiff
|
tree
2016-02-03
M
ark
Abraham
Merge rele
a
se-5-0
i
nto relea
s
e-5-1
commit
|
commitdiff
|
tree
2016-02-03
M
a
r
k Abraham
Fix dEkin/dl h
a
ndling
with m
u
l
t
ipl
e
ran
k
s
commit
|
commitdiff
|
tree
2016-01-28
Mar
k
Abraha
m
Merge branc
h
releas
e
-
5
-
1
commit
|
commitdiff
|
tree
2016-01-28
Mark Abrah
a
m
Fix use o
f
__APPLE__ in Op
e
n
CL code
commit
|
commitdiff
|
tree
2016-01-28
Ma
r
k Abraham
Add OpenCL source file types to copyright checker
commit
|
commitdiff
|
tree
2016-01-28
Mar
k
Abr
a
h
am
Avoid F
P
e
x
ception
commit
|
commitdiff
|
tree
2016-01-27
Ma
r
k
A
br
a
ham
Merge bran
c
h r
e
le
a
se-5-1
commit
|
commitdiff
|
tree
2016-01-27
Mark
Abraham
R
e
m
o
ve bNot
L
astF
r
ame
commit
|
commitdiff
|
tree
2016-01-27
M
a
rk
A
braham
Add suggestions for
u
pdati
n
g binut
i
ls
commit
|
commitdiff
|
tree
2016-01-26
Mark Abraham
Fix
d
e
f
a
ul
t
for GMX
_
USE_NVML
commit
|
commitdiff
|
tree
2016-01-25
Mark Abra
h
a
m
Mer
g
e branch release-5-1
commit
|
commitdiff
|
tree
2016-01-24
Mark Ab
r
aham
F
i
x
duplicate LaTeX eq
u
a
t
ion label
commit
|
commitdiff
|
tree
2016-01-24
Mark Abr
a
ham
U
p
date r
e
ferenc
e
s to HTML and online
documentatio
n
commit
|
commitdiff
|
tree
2016-01-14
Mark
A
braham
Permi
t
cus
t
omized t
e
sting of g
r
ompp and mdru
n
commit
|
commitdiff
|
tree
2016-01-13
Mark Abraham
Allowe
d
NVM
L
s
u
ppor
t
to be toggled
commit
|
commitdiff
|
tree
2016-01-12
Mark Abraham
Merge branch release-5-0 into release-5-1
commit
|
commitdiff
|
tree
2016-01-11
M
ark Abraham
Imp
r
oved
u
p
date_coord
s
commit
|
commitdiff
|
tree
2016-01-08
Mark Abraham
I
m
prove
tpr
heade
r
v
e
rsion
handl
i
ng
commit
|
commitdiff
|
tree
2016-01-08
Mark Abraham
Mer
g
e
b
r
anch release-5-1
commit
|
commitdiff
|
tree
2016-01-07
Mark
A
braham
Fix so
m
e mdrun head
e
r dependenc
i
es
commit
|
commitdiff
|
tree
2016-01-07
Mark Abrah
a
m
Avo
i
d more C++ bind
i
n
gs for MPI
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
Document
how potential-sw
i
t
c
h wor
k
s
commit
|
commitdiff
|
tree
2016-01-07
Ma
r
k A
b
r
aham
Stop using
UNDE
F
I
N
E
D
as
n
ame of a symbol
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
R
emo
v
e fields used o
n
ly for S
D
2
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
Backp
o
rt m
d
-vv
fixes
commit
|
commitdiff
|
tree
2016-01-07
Mark Abraham
Remove
S
D
2 integrato
r
commit
|
commitdiff
|
tree
2016-01-06
Mark Abraham
Fix spurious gcc warning
commit
|
commitdiff
|
tree
2016-01-05
Mark Abraham
Fix logic
f
or DD missin
g
-interacti
o
ns ch
e
ck
commit
|
commitdiff
|
tree
2016-01-05
Mark
Abra
h
am
Use
E
X
PECT_TR
U
E and E
X
PECT_FALSE in
new SIMD t
e
sts
commit
|
commitdiff
|
tree
2016-01-04
Mark Abraham
Change GMX_DOU
B
L
E
t
o be al
w
ays defined
commit
|
commitdiff
|
tree
2015-12-28
Mark Abraham
Create inv
e
rtmatrix
.
h
commit
|
commitdiff
|
tree
2015-12-28
Ma
r
k Abraham
M
e
rge b
r
a
nch release-5-1
commit
|
commitdiff
|
tree
2015-12-27
Mark Ab
r
aham
Fix so
m
e Op
e
n
C
L issues
commit
|
commitdiff
|
tree
2015-12-24
Mark
Abraham
Move
d
responsibility for f_g
l
obal
commit
|
commitdiff
|
tree
2015-12-24
Mark
A
braham
Shel
l
c
ode cleanup
commit
|
commitdiff
|
tree
2015-12-17
Mar
k
Abraham
S
implified
e
nergy-summ
a
ti
o
n code
commit
|
commitdiff
|
tree
2015-12-12
M
ark
A
brah
a
m
Broke up
c
opyrigh
t
.
*
commit
|
commitdiff
|
tree
2015-12-12
M
ark A
b
raham
Require Nos
e
-Hoo
v
e
r with MTTK
commit
|
commitdiff
|
tree
2015-12-11
Mark Ab
r
a
h
am
S
t
op global communicati
o
n depe
n
ding on integrator
commit
|
commitdiff
|
tree
2015-12-10
Mark Ab
r
a
h
am
Merge branch 'ori
g
in
/
re
l
ease
-
5-1'
commit
|
commitdiff
|
tree
2015-12-09
Mark
A
bra
h
am
Upd
a
te
u
se of preprocessor i
n
managing
G
PU sup
p
ort
commit
|
commitdiff
|
tree
2015-12-08
Mark Abr
a
ham
M
erge branch 're
l
ease-5-0'
in
t
o release-5-1
commit
|
commitdiff
|
tree
2015-12-08
Mark Abraham
F
ix
Trott
e
r in
t
e
grati
o
n
commit
|
commitdiff
|
tree
2015-12-03
Ma
r
k
A
braham
Remove mdrun -compact
commit
|
commitdiff
|
tree
2015-12-02
Mark Abraham
Remove twin-ra
n
ge scheme
commit
|
commitdiff
|
tree
2015-11-30
Mark Abraham
R
e
factor ha
r
dware inf
o
rm
a
tion management
commit
|
commitdiff
|
tree
2015-11-25
Mark A
b
r
a
ham
Fix logic
of
dd_print_
m
iss
i
ng_int
e
ractions ex
i
t
commit
|
commitdiff
|
tree
2015-11-24
M
a
rk Abr
a
ham
Fi
x
error in multi-sim
c
ommu
n
ication
commit
|
commitdiff
|
tree
2015-11-23
Mark Abraham
U
p
d
a
te and ex
p
a
n
d pre-sub
m
it commi
t
matrix
commit
|
commitdiff
|
tree
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