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Removed unused host-side allocation code
2017-03-04
David
v
an
d
er
S
po
e
l
Removes
r
ogu
e
printing
t
o xvg
f
i
l
e in g
m
x
mindi
s
t
commit
|
commitdiff
|
tree
2017-02-27
David van der Spoel
Fixes bug in gmx solvate
w
ith -
s
hell tha
t
yi
e
lded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
David va
n
der Spoel
Fixes
SEGV in gmx
o
rder
.
commit
|
commitdiff
|
tree
2016-09-27
David
van de
r
Spo
e
l
Fixed script xplo
r
2gmx
.
p
l
t
o
work with GMX
D
ATA
commit
|
commitdiff
|
tree
2016-08-03
David van der
S
poel
Three new quo
t
e
s
.
commit
|
commitdiff
|
tree
2016-07-31
Dav
i
d
van der Sp
o
el
Merge "Merge br
a
nch release-5-1 into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
David van d
e
r Spoel
Fixes incorrect charg
e
s in OPLS/AA-L for H
I
SD
and HISE
commit
|
commitdiff
|
tree
2016-07-08
David van der Spoel
M
erge "Merge b
r
anch r
e
lease-5-1 into release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
David van
d
er Spoel
Introduce fatal erro
r
f
o
r t
o
o few frames in gmx
d
o
s
.
commit
|
commitdiff
|
tree
2016-06-27
David van der Spoel
M
ade
g
mx dos work again
.
commit
|
commitdiff
|
tree
2016-06-22
D
a
vi
d
va
n
der Spoel
R
emoved spurious r_ij in force for Morse pot
e
ntial
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
David v
a
n der
Spoel
Mo
d
ify lm
f
it library
t
o avoid clashe
s
with other versions
.
commit
|
commitdiff
|
tree
2016-03-23
David van der Spoel
Re
m
o
v
ed srenew
that was making array sma
l
ler incor
r
ectly
.
commit
|
commitdiff
|
tree
2016-03-18
David van der Sp
o
el
Fixed division by zero in p
o
l
a
r
i
ze
.
commit
|
commitdiff
|
tree
2016-01-20
D
av
i
d van der Spo
e
l
Co
u
ple of
new quotes
commit
|
commitdiff
|
tree
2016-01-07
D
avid van der Spoel
Made no
r
mal modes work with shell
s
and vs
i
t
es
commit
|
commitdiff
|
tree
2015-11-24
David van der Sp
o
e
l
Fixes n
e
wly
i
ntroduced bug in
make_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David van d
e
r
Spo
e
l
Moved domdec s
t
r
u
ctures ou
t
of
c
ommr
e
c
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
David van der Spo
e
l
Cleanups in
l
egacyhe
a
der
/
types/commrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David
van de
r
Spoel
Mer
g
ed legacyhea
d
e
r
s/types/qmmmrec
.
h into mdli
b
/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
D
a
vid van de
r
S
p
o
e
l
Merge
d
g
e
nborn
.
h from legacyhea
d
e
rs/
t
ype
s
into mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
van d
e
r Spo
e
l
Moved leg
a
c
yheaders/types/group
.
h
to
m
dtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David
v
an
der Spoel
Merged legacyheaders/type
s
/ns
.
h
and nblist
.
h to mdty
p
es
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David
van der Spoel
C
o
mbine enums
.
h and names*
.
commit
|
commitdiff
|
tree
2015-11-20
David
van der Spoel
M
erged legacyheader
s
/n
r
nb
.
h
and types/nrnb
.
h to gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
David v
a
n de
r
Sp
o
el
Moved mdatom
.
h from legac
y
header/types to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
David van der
S
p
oel
Moved le
g
acyheaders/types/ene
r
g
y
.
h to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-15
David van
d
er Spoel
Merged legacyheaders/t
y
pes/i
n
putrec
.
h in
t
o m
d
t
y
pe
s
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David
va
n
der Spoel
Merged
l
e
g
acyheaders
/
t
ypes/state
.
h in
t
o
mdtypes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
David van de
r
Spoel
Re
p
laced atom
_
i
d by in
t
.
commit
|
commitdiff
|
tree
2015-11-13
David v
a
n der Spoel
Moved gen
b
orn
.
h
t
o
mdlib
commit
|
commitdiff
|
tree
2015-11-12
D
a
vid van
d
e
r Spoel
M
oved txtdump
.
* to fil
e
io
.
commit
|
commitdiff
|
tree
2015-11-12
Davi
d
v
a
n der Sp
o
e
l
M
ove
d
cop
y
rite
.
*
to fil
e
io from gmx
l
ib
and legacyhe
a
ders
.
commit
|
commitdiff
|
tree
2015-11-11
Da
v
i
d
v
an
d
er Sp
o
el
Moved inputrec
.
* from gmxlib an
d
legac
y
headers to m
d
types
.
commit
|
commitdiff
|
tree
2015-11-10
David van der Spoel
Removed le
g
acyheaders/typ
e
defs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David van der Sp
o
el
M
ov
e
d df_history util
i
ty routines
fro
m
typed
e
fs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
Davi
d
van der Spoel
R
ep
l
a
ced
NOTS
E
T from
typedefs
.
h by local solutions
.
commit
|
commitdiff
|
tree
2015-10-23
David
v
a
n
der Spoel
Remov
e
d en
e
rg
y
histor
y
code
f
r
om typedefs to a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
D
a
vid van
der Spoel
Mo
v
e
d pbc/cut-off r
e
l
a
t
ed utili
t
i
es from ty
p
edefs
to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
D
a
vi
d
van
d
e
r
Spoel
Fre
e
d mem
o
ry
i
n l
e
gacy statistic
s
r
o
ut
i
nes
.
commit
|
commitdiff
|
tree
2015-10-03
David
van der Spoel
Removed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van
d
e
r S
p
oel
Re
m
oved simple
.
h fro
m
nb_kerne
l
_sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
David van de
r
Spoel
Removed si
m
ple
.
h from nb_kernel_sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
Dav
i
d van der Spo
e
l
R
e
mo
v
ed si
m
pl
e
.
h fro
m
nb_kernel_c and nb_kernel_sp
a
rc64_h
p
c
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David
van der Spoel
Removed inc
l
ude s
i
m
ple
.
h from nb_kerne
l
_avx_128_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
Da
v
i
d
van
d
er Spo
e
l
Rem
o
ved simple
.
h
from nb_kernel_avx_256_X
X
commit
|
commitdiff
|
tree
2015-10-02
D
avid van de
r
Spoe
l
Remo
v
e
d
outpu
t
_env_t, now using gmx_o
u
tp
u
t_env
_
t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
David van der S
p
oel
Remove
d
type
s
/nrnb
.
h fr
o
m typedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David va
n
de
r
Spoel
Removed types/nblis
t
.
h
and
t
ype
s
/nsgrid
.
h
f
r
om t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
David v
a
n der Spoel
Removed types/mdatom
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David va
n
der Spoel
R
e
moved
types/inputrec
.
h
from typedefs
.
h and r
e
lete
d
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
Davi
d
va
n
der Spoel
Fixes bug in the computation of Coefficient of Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David van der S
p
oel
Removed types/forcerec
.
h
from type
d
ef
s
.
h
commit
|
commitdiff
|
tree
2015-09-25
Davi
d
van der Spoel
Removed inc
l
ude o
f
types/ifun
c
.
h fr
o
m ty
p
e
defs
.
h
commit
|
commitdiff
|
tree
2015-09-22
Dav
i
d v
a
n der Spoel
Removed four includes from legac
y
he
a
ders/
t
ypedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
Dav
i
d van
der Spoel
Remove
d
legacyheaders/types/commrec_fwd
.
h from typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David v
a
n der Spoel
Moved content from mdrun
.
h to separate headers
.
commit
|
commitdiff
|
tree
2015-09-10
D
a
vid
v
an der Sp
o
el
Removed <sys/ty
p
es
.
h> and "t
y
pes/
c
o
n
str
.
h" from typedefs
commit
|
commitdiff
|
tree
2015-09-09
Davi
d
van der Spoe
l
Removed fileio/trx
.
h f
r
om ty
p
edefs
.
h
commit
|
commitdiff
|
tree
2015-09-08
Dav
i
d v
a
n
der Spoel
Mo
v
ed f
u
nctions operating on for
c
e
r
ec to se
p
arate header
.
commit
|
commitdiff
|
tree
2015-08-28
David
v
a
n
d
e
r
Spoel
Ad
d
ed
e
nergy (edr
)
file type
to O
p
tio
n
s headers
.
commit
|
commitdiff
|
tree
2015-08-28
Davi
d
van de
r
Spoel
A
d
ded additional
constru
c
tor to StringStr
e
a
m
clas
s
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David van der Sp
o
el
Made
output from dump
i
ng
n
eig
h
tborlists easier to r
e
a
d
.
commit
|
commitdiff
|
tree
2015-07-31
David v
a
n der
S
poel
Change ini
t
ial
p
a
ramete
r
s for testing
expfit
.
commit
|
commitdiff
|
tree
2015-07-29
David van der Spoe
l
Code f
o
r checki
n
g xvg files in
t
estuti
l
s
.
commit
|
commitdiff
|
tree
2015-04-17
Dav
i
d va
n
der S
p
oel
U
p
dated exponential fitting
to make it robust
.
commit
|
commitdiff
|
tree
2015-04-09
David
va
n
de
r
S
poel
Clari
f
ied comme
n
ts
for
t
ime-depe
n
dent elec
t
ric
fields
.
commit
|
commitdiff
|
tree
2015-04-08
David van
der Spoel
F
ixe
d
in
c
o
rrect output of gb_al
g
orith as
sa_algori
t
hm
.
commit
|
commitdiff
|
tree
2015-03-02
David van der S
p
oel
Updated documentation
f
o
r elect
r
ic fiel
d
s
.
commit
|
commitdiff
|
tree
2014-12-13
David van
d
er Sp
o
e
l
Four n
e
w quotes
f
rom around the world
.
commit
|
commitdiff
|
tree
2014-11-28
David van
d
e
r
Spoel
Fixes recen
t
ly introduced bug
in gm
x
analyze
.
commit
|
commitdiff
|
tree
2014-11-24
David
v
an de
r
Spoe
l
Added
warnings for ewal
d
-
g
eom
e
try
and surface-e
p
silon
commit
|
commitdiff
|
tree
2014-10-28
Da
v
id
v
a
n de
r
Spoel
E
ven
m
ore
refreshing quotes
.
commit
|
commitdiff
|
tree
2014-10-14
David van der Spoel
Reorg
a
niz
i
ng
analysis
o
f correlation
f
unct
i
ons
.
commit
|
commitdiff
|
tree
2014-09-23
David van der
S
p
o
el
F
i
xes potential bug
in neighborsearchin
g
.
commit
|
commitdiff
|
tree
2014-09-17
David v
a
n der Spoel
Merge release-5
-
0 into ma
s
t
er
commit
|
commitdiff
|
tree
2014-09-10
D
avid van
d
er Spoel
R
e
mo
v
e
.
t
pa,
.
tpb,
.
tpx
,
.
trj f
i
les
.
Part of #150
0
.
commit
|
commitdiff
|
tree
2014-08-30
David van der S
p
oel
Fixes
issue with vsiten and verlet buffers
.
commit
|
commitdiff
|
tree
2014-07-05
David van der Spoel
Fix
e
d inconsistency i
n
blocka handling
.
commit
|
commitdiff
|
tree
2014-06-29
David van der Spoel
Fixes #1532, SEGV in
g
_current
.
commit
|
commitdiff
|
tree
2014-06-25
Da
v
id van der Spoel
Added check for domain
d
eco
m
positio
n
and
s
hells
.
commit
|
commitdiff
|
tree
2014-06-24
D
avid van
d
e
r
Spoel
Added check
i
n
grompp for shells and inputr
e
c issue
s
.
commit
|
commitdiff
|
tree
2014-06-22
D
avid
v
a
n der Spoel
Implemented fatal error
for nstca
l
cenergy!=1 with sh
e
lls
.
commit
|
commitdiff
|
tree
2014-06-13
David van der Spoe
l
F
i
x memory
-
usage
error
i
n g_chi
commit
|
commitdiff
|
tree
2014-06-11
David van der Spo
e
l
F
i
xes bug where -e and -dt flag
s
did not
work
any
m
o
re
.
commit
|
commitdiff
|
tree
2014-06-07
Dav
i
d van d
e
r Spoel
Merg
e
"M
e
rg
e
release-5-0 into maste
r
"
commit
|
commitdiff
|
tree
2014-06-07
D
avid van
d
er Spoel
M
erge re
l
ease-5-0 into master
commit
|
commitdiff
|
tree
2014-06-02
Da
v
i
d van
d
er Spo
e
l
Fixed w
r
ong journal refer
e
nc
e
in man
u
al
commit
|
commitdiff
|
tree
2014-05-31
David v
a
n
d
er
S
p
oel
Permit
trjconv to read a
n
d
write v
e
locities with TNG
.
.
.
commit
|
commitdiff
|
tree
2014-05-16
Da
v
id
van der Spoel
Fixes a comp
l
icat
e
d bug i
n
g_anaeig
.
commit
|
commitdiff
|
tree
2014-05-15
D
avid van der Spo
e
l
Added cmake profiling
suppo
r
t
commit
|
commitdiff
|
tree
2014-04-02
David van der
S
poel
R
e
m
oved possibility of
c
ompiling wi
t
h GSL
.
commit
|
commitdiff
|
tree
2014-03-31
David van der
Spoel
F
ixed compilat
i
on iss
u
e in fgrid
.
cpp du
e
to int/e
n
um
commit
|
commitdiff
|
tree
2014-03-06
David
v
an der Spoel
S
i
x new q
u
otes from classic literature
.
commit
|
commitdiff
|
tree
2014-02-11
Davi
d
v
a
n der Spoel
Fix
e
d another vmdio issue
.
commit
|
commitdiff
|
tree
2014-02-10
David van der Spo
e
l
Move
d
conditional c
m
ake code f
o
r vmd
i
o
.
commit
|
commitdiff
|
tree
2014-01-28
David van d
e
r Spo
e
l
Mo
v
ed random
n
umber
generat
o
r
code to separate di
r
.
commit
|
commitdiff
|
tree
2014-01-18
Dav
i
d van
d
er Spoel
This patch moves the statist
i
cs library to its own
.
.
.
commit
|
commitdiff
|
tree
2014-01-17
David v
a
n der
Sp
o
el
This patch moves p
r
eprocessing
h
e
a
d
ers to gmxpreproces
s
commit
|
commitdiff
|
tree
2014-01-15
D
a
vid van der Spoel
Thi
s
pat
c
h m
o
v
es t
h
e nr
a
ma
.
[c
h
] to
the
gmxana dir
.
commit
|
commitdiff
|
tree
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