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Some overview content for Doxygen documentation.
2013-10-28
Mark Abraham
Create
f
ileio module
commit
|
commitdiff
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tree
2013-10-26
Mark Ab
r
a
h
am
Encapsulate gmx_wallclock_accounting_t into new
t
iming
.
.
.
commit
|
commitdiff
|
tree
2013-10-26
M
a
rk
Abr
a
h
am
Clea
n
ed u
p
r
un time me
a
sureme
n
t
commit
|
commitdiff
|
tree
2013-10-26
Mark
A
b
raham
A
d
d
ed documentati
o
n for
gmx_runtime
_
t st
r
uct
commit
|
commitdiff
|
tree
2013-10-23
Mark
Ab
r
aham
Merge branch rele
a
se-4
-
6 into master
commit
|
commitdiff
|
tree
2013-10-20
Mark Abraham
R
emove html t
a
rget from and excessive PDFs for m
a
nual
commit
|
commitdiff
|
tree
2013-10-18
Mark Abraham
BlueGene/Q Verlet
c
u
t-off sc
h
e
m
e kernels
commit
|
commitdiff
|
tree
2013-10-18
Mar
k
A
braham
Ca
l
l ato
m
i
c
s from TestAtomic
.
c
commit
|
commitdiff
|
tree
2013-10-17
Mark
A
braham
M
o
v
e
mdrun trajecto
r
y writing
i
nto wrapp
e
r function
commit
|
commitdiff
|
tree
2013-10-17
Mark
A
braham
Fix typo
in g_membed do
c
um
e
ntation
commit
|
commitdiff
|
tree
2013-10-16
Mark Abraham
Move manu
a
l repo i
n
to code repo, a
n
d m
a
ke
i
t build
commit
|
commitdiff
|
tree
2013-10-10
Mark
A
braha
m
Introduced MPI initi
a
l
i
zation c
o
unter
commit
|
commitdiff
|
tree
2013-10-08
M
a
rk Abraham
Remove some un
u
sed variables
from MD loop
commit
|
commitdiff
|
tree
2013-10-06
Mark
Abraham
F
i
xed
t
rig
g
ering
o
f CPU accelera
t
io
n
-
scheme de
t
ecti
o
n
commit
|
commitdiff
|
tree
2013-10-04
Mark Abraham
Further consolida
t
i
o
n of commrec initialization
commit
|
commitdiff
|
tree
2013-10-04
Mark Abraham
M
o
re consolidation o
f
M
P
I initi
a
lization
commit
|
commitdiff
|
tree
2013-10-01
Mark Ab
r
aham
Bro
k
e so
m
e
useless depend
e
ncies
commit
|
commitdiff
|
tree
2013-10-01
Mark
A
b
r
aham
Split
M
PI ini
t
iali
z
a
tion fr
o
m t_commrec constru
c
tion
commit
|
commitdiff
|
tree
2013-10-01
M
a
rk Abraham
Silenc
e
clang wa
r
n
i
n
gs
commit
|
commitdiff
|
tree
2013-09-26
Ma
r
k
A
b
r
aham
Un-d
u
pli
c
ate gmx_get
t
ime c
o
de
commit
|
commitdiff
|
tree
2013-09-26
Ma
r
k A
b
raha
m
Merge branch releas
e
-
4-6
commit
|
commitdiff
|
tree
2013-09-26
Mark Abraham
Remo
v
e m
d
run
-i
o
n
ize fe
a
ture
commit
|
commitdiff
|
tree
2013-09-26
M
ark Abraha
m
Remove General Cou
p
li
n
g
T
heory
s
tuff
commit
|
commitdiff
|
tree
2013-09-20
Mark
Abrah
a
m
Remove
r
e
peat sfree(state->nosehoover_xi)
commit
|
commitdiff
|
tree
2013-09-20
M
a
rk
Abraham
M
e
r
g
e
branch 'release-4-6'
commit
|
commitdiff
|
tree
2013-09-20
Mark Abraham
D
e
scribed
anoth
e
r way g_tun
e
_pm
e
m
igh
t
reasona
b
ly fail
commit
|
commitdiff
|
tree
2013-09-20
Mar
k
Abraham
Fix total ti
m
e me
a
s
urement with separate
P
ME nodes
commit
|
commitdiff
|
tree
2013-09-19
Mark A
b
r
a
h
am
F
i
xed readi
n
g histo
r
y
_t fro
m
ch
e
ckpoint
commit
|
commitdiff
|
tree
2013-09-19
Ma
r
k Abraham
Fixed
g_tune_pme
a
ssum
p
t
io
n
t
hat MPI
is
a
vaila
b
le
commit
|
commitdiff
|
tree
2013-09-18
Mark
Ab
r
aham
R
e
move fo
r
cefield-
s
can feature
commit
|
commitdiff
|
tree
2013-08-25
Mark Abr
a
ham
Split up Verlet SIMD kern
e
ls for faster compila
t
ion
commit
|
commitdiff
|
tree
2013-08-25
Mark Abraham
Fix detec
t
ion and
s
uggestio
n
i
n g
m
x_cpuid fo
r
IBM QPX
commit
|
commitdiff
|
tree
2013-08-25
M
ark Ab
r
ah
a
m
Fixes
for B
l
uegen
e
/Q
commit
|
commitdiff
|
tree
2013-08-25
M
a
rk Abra
h
am
Consolidated NBNxN
SIMD ker
n
el u
t
ility rou
t
ines
commit
|
commitdiff
|
tree
2013-08-25
Mark Abraham
Fix mi
n
or
wallcycle out
p
ut issues
commit
|
commitdiff
|
tree
2013-08-25
Mark Abrah
a
m
Fixed
G
M
X
_DD_D
U
MP
_
GRI
D
commit
|
commitdiff
|
tree
2013-08-20
Mark Abraham
Remove
Ope
n
MM
commit
|
commitdiff
|
tree
2013-08-15
Mark Abraham
P
r
oductive
afternoon of meetings
.
.
.
more quotes!
commit
|
commitdiff
|
tree
2013-08-09
M
a
rk Abra
h
a
m
Reordered FFTW
f
atal
e
r
r
or; avoids using
unset v
a
r
iables
commit
|
commitdiff
|
tree
2013-08-05
Mark Abraham
Fixed reference SIMD code to w
o
rk
w
i
t
h
MSVC
commit
|
commitdiff
|
tree
2013-08-01
Mark Abraham
Refac
t
o
red preparation
o
f b
u
f
f
er
for NB
N
xN table loads
commit
|
commitdiff
|
tree
2013-08-01
M
a
rk Abra
h
a
m
Fi
x
ed example c
o
de function
nam
e
commit
|
commitdiff
|
tree
2013-07-30
Ma
r
k Ab
r
aham
Removed
u
n
u
sed v
a
riab
l
e
s
commit
|
commitdiff
|
tree
2013-07-26
Mark Abraham
M
e
rge branch
r
e
lease-4
-
6
i
nt
o
master
commit
|
commitdiff
|
tree
2013-07-25
Mark
A
brah
a
m
Clarif
i
ed
l
ogi
c
in
g_wham
commit
|
commitdiff
|
tree
2013-07-25
Mar
k
A
b
r
aham
F
i
n
d mkl
.
h
on more icc versions
commit
|
commitdiff
|
tree
2013-07-25
Ma
r
k Abr
a
ham
Upd
a
te management of linear algebra librarie
s
commit
|
commitdiff
|
tree
2013-07-24
Mark Abraha
m
Add five new quotes
commit
|
commitdiff
|
tree
2013-07-24
Mar
k
Abraham
Remove
d
buggy -seppot output
commit
|
commitdiff
|
tree
2013-07-24
Mark Abraham
Merge
branch
r
elea
s
e-4-6 i
n
to maste
r
commit
|
commitdiff
|
tree
2013-07-18
Mar
k
Abraham
Fixed pdb2gmx -vsite
h
y
d
rogen -
o
c
onf
.
pdb
commit
|
commitdiff
|
tree
2013-07-14
Mark Abrah
a
m
Fixed possible der
e
f
e
r
e
n
c
e of
null pointer
commit
|
commitdiff
|
tree
2013-07-11
Mar
k
A
b
raham
Fix
e
d
typo
s
in #include g
u
ard #def
i
nes
commit
|
commitdiff
|
tree
2013-07-09
M
ark Abraham
Remove orphan CMake file
commit
|
commitdiff
|
tree
2013-07-07
M
ark Abraham
Fixed m
i
nor
a
d
m
in issues
commit
|
commitdiff
|
tree
2013-07-05
Mark Abraham
B
u
mp vers
i
on after 4
.
6
.
3 release
commit
|
commitdiff
|
tree
2013-07-01
Mark Ab
r
aha
m
C
o
rrecte
d
de
f
in
i
tion
o
f E
E
L_USE
R
commit
|
commitdiff
|
tree
2013-06-25
Mark Abr
a
ham
Fixed #inclu
d
e of header for
atomics on
K-comput
e
r
commit
|
commitdiff
|
tree
2013-06-13
M
a
rk
A
braham
Remove unu
s
ed varia
b
les
commit
|
commitdiff
|
tree
2013-05-30
M
ark Abraham
Merge "Merge branch 'release-
4
-
6'"
commit
|
commitdiff
|
tree
2013-05-30
Mark Abraham
New patch
r
ele
a
se 4
.
6
.
2
commit
|
commitdiff
|
tree
2013-05-30
Ma
r
k Abraha
m
Work
aro
u
n
d
for correct t
r
eatmen
t
o
f al
l
-vs-all
commit
|
commitdiff
|
tree
2013-05-25
Mark A
b
raham
Make F
F
T
detec
t
ion q
u
iet
e
r
when
n
oth
i
ng is changing
commit
|
commitdiff
|
tree
2013-05-22
Mark
Abraham
Cla
r
ify g_gyrate -
h
commit
|
commitdiff
|
tree
2013-05-22
Ma
r
k A
b
raham
F
i
x
g
_chi -omeg
a
commit
|
commitdiff
|
tree
2013-05-21
Mark
A
braham
Upd
a
ted gro
m
pp cut-off and PME-Switch ch
e
c
k
s
commit
|
commitdiff
|
tree
2013-05-21
Mark Ab
r
aham
Hack co
m
piler flags to silence warnings on gc
c
4
.
8
commit
|
commitdiff
|
tree
2013-05-17
Ma
r
k A
b
raham
Intr
o
duce fata
l
e
r
r
o
r
for G
B
with FE
commit
|
commitdiff
|
tree
2013-05-10
Mark A
b
raham
M
e
rge "Fixes
"
Func
t
i
o
n type U-B not
i
m
pleme
n
ted in
.
.
.
commit
|
commitdiff
|
tree
2013-05-10
Mark Abraha
m
Mer
g
e "im
p
rove build with OpenMM,
s
ti
l
l n
o
t
100%
f
i
xed
.
.
.
commit
|
commitdiff
|
tree
2013-05-10
Mark Abraham
Mer
g
e
"
fixing re
r
un
w
i
th fr
e
e energy +
.
x
t
c or
.
gro
.
.
.
commit
|
commitdiff
|
tree
2013-05-07
Mark
A
braha
m
Fix extant r
e
f
e
r
e
nces to former G
P
L lic
e
n
s
ing
commit
|
commitdiff
|
tree
2013-05-02
Mark Abraham
Mer
g
e "Improve master-sp
e
cific CMake be
h
avior
.
"
commit
|
commitdiff
|
tree
2013-04-29
M
ark Abraham
Merge "Update lin
k
ing to MKL and document same"
i
nt
o
.
.
.
commit
|
commitdiff
|
tree
2013-04-29
Mark Abraham
M
e
r
ge
"
g
eneral SI
M
D
acceleration for ang
l
es+di
h
edra
l
s
.
.
.
commit
|
commitdiff
|
tree
2013-04-29
Mark Abrah
a
m
Merge "PME load balancing now c
h
ecks fo
r
P
M
E
grid rest
r
i
c
tio
.
.
.
commit
|
commitdiff
|
tree
2013-04-29
Mark
A
braham
M
e
rge "Fix
i
ng
a
problem with dh/dl 1-4 int
e
ractio
n
s
.
.
.
commit
|
commitdiff
|
tree
2013-04-26
Ma
r
k Abr
a
ham
Merge "CUDA PME kernels with analy
t
i
cal Ewa
l
d correction
.
.
.
commit
|
commitdiff
|
tree
2013-04-26
Mark Abrah
a
m
Merge "improved
load
b
a
l
ancin
g
with Ver
l
et cut-off
.
.
.
commit
|
commitdiff
|
tree
2013-04-26
Mark Abraham
Update lin
k
ing
t
o
MKL and doc
u
ment s
a
me
commit
|
commitdiff
|
tree
2013-04-25
Mar
k
Abraham
Merge "Merge
branch 'rele
a
se-4
-
5
-patches'" into re
l
eas
e
-4-6
commit
|
commitdiff
|
tree
2013-04-22
Mark
Abraham
Merge "Use git sna
p
sh
o
ts of the te
s
ts
i
f are on git
.
.
.
commit
|
commitdiff
|
tree
2013-04-19
Ma
r
k Abraham
v-resca
l
e works w
i
th tau-
t
>= 0
commit
|
commitdiff
|
tree
2013-04-12
M
a
rk
Abraham
Merge "removed x86 spe
c
if
i
cs f
r
om
n
bnx
n
SI
M
D ker
n
el
s
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
Ma
r
k
A
brah
a
m
Merge "correct
e
d
lo
g
file wal
l
time brea
k
down"
i
n
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-04-12
M
a
rk
Abraham
Merge "m
a
d
e
P
ME w
o
rk w
i
t
h
a
mix of 1 an
d
more threads
.
.
.
commit
|
commitdiff
|
tree
2013-03-12
M
a
rk
Ab
r
aham
Merge "fix bro
k
en
things
i
n
mkhtml" into releas
e
-4-
6
commit
|
commitdiff
|
tree
2013-03-11
Mark Abr
a
ham
A
d
ded install guide sec
t
ion for BL
A
S/
L
APACK
commit
|
commitdiff
|
tree
2013-03-11
Mark Abraham
Merge "Fi
x
es linkage wit
h
FFTW + M
K
L for BLAS/L
A
PACK
.
.
.
commit
|
commitdiff
|
tree
2013-03-05
Mark Abraham
N
ew patch release 4
.
6
.
1
commit
|
commitdiff
|
tree
2013-03-05
Mark A
b
rah
a
m
Fix
au
t
omated
reg
r
e
s
sion testing GMXLIB
v
a
l
u
e
commit
|
commitdiff
|
tree
2013-03-05
Mark A
b
rah
a
m
Fix regressiontests
a
utomate
d
down
l
oad
commit
|
commitdiff
|
tree
2013-03-05
Mark Abraham
Update shell completions
commit
|
commitdiff
|
tree
2013-03-05
Mark Abraha
m
U
pd
a
te outdated admin things
commit
|
commitdiff
|
tree
2013-03-05
Mark Abraham
Up
d
a
ted ins
t
all guide
commit
|
commitdiff
|
tree
2013-03-05
Ma
r
k
A
braham
Warn if X11 was n
o
t fo
u
nd an
d
t
h
e u
s
er wanted it
commit
|
commitdiff
|
tree
2013-03-05
Mark Abraham
fix broken things in mkhtml
commit
|
commitdiff
|
tree
2013-02-26
Mark A
b
raham
U
n
c
r
ust
i
fied cod
e
changes since 4
.
6
commit
|
commitdiff
|
tree
2013-02-20
Mark Abrah
a
m
M
erge release-4-5-pat
c
hes i
n
to relea
s
e-4-6
commit
|
commitdiff
|
tree
2013-02-18
Mark
A
braham
Fix C
M
a
ke
namespace
p
ol
l
ution
commit
|
commitdiff
|
tree
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