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Use std::vector in nbnxn_search_t
2018-03-21
D
avid va
n
der Spoel
R
enamed entropy
.
* to thermoch
e
mistry
.
*
commit
|
commitdiff
|
tree
2018-03-16
D
a
v
id v
a
n
d
er
S
p
o
e
l
Split off entropy
c
alcu
l
ation
t
o separate file
.
commit
|
commitdiff
|
tree
2017-12-28
D
avi
d
van der Spoel
Fixes and
u
p
d
ates f
o
r xplor2
g
ml
.
pl and atom_nom
.
tb
l
commit
|
commitdiff
|
tree
2017-11-06
Da
v
id van
d
er Spoel
Fixed
check fo
r
water in
g
en_vsite
.
cpp
commit
|
commitdiff
|
tree
2017-11-02
David van der Spo
e
l
New mdp input for electric fiel
d
s
.
commit
|
commitdiff
|
tree
2017-10-30
Da
v
i
d
va
n
der Spoel
Fixe
d
mdp outp
u
t
fro
m
e
l
ectric field code
.
commit
|
commitdiff
|
tree
2017-10-30
Davi
d
van der Spoel
Added option -wa
t
er
tips3p to
p
db
2
g
m
x
.
commit
|
commitdiff
|
tree
2017-10-23
D
a
vi
d
van der S
p
oel
Split off the NMR related a
n
alyses from gmx energy
.
commit
|
commitdiff
|
tree
2017-10-17
Dav
i
d van d
e
r Spoel
Fixed missing entries
in n
r
nb arr
a
y
s
.
commit
|
commitdiff
|
tree
2017-08-15
Dav
i
d va
n
der Sp
o
el
Worked a
r
ound mis
s
i
n
g
O
penMP impl
e
m
e
ntation in orires
.
commit
|
commitdiff
|
tree
2017-08-03
David van de
r
Sp
o
e
l
Fixed bug in
gm
x
disres ind
e
xing
a
r
rays
.
commit
|
commitdiff
|
tree
2017-08-02
D
av
i
d van
der Spoel
Work
e
d ar
o
und missin
g
Ope
n
MP implementatio
n
i
n
o
r
ire
s
.
commit
|
commitdiff
|
tree
2017-07-28
D
av
i
d
v
an der Sp
o
el
Added
unit-te
s
t
for orientation
r
estraint
s
output
.
commit
|
commitdiff
|
tree
2017-07-19
D
a
vid van
der Sp
o
el
Removed unne
c
essary static dec
l
arations
for command
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van der
S
poel
Fixed test-order dependency i
n
gmx
p
r
eprocess
t
ests
.
commit
|
commitdiff
|
tree
2017-07-19
David van de
r
Spoel
F
i
x
non-repr
o
d
u
c
abili
t
y of c
l
ustsize test
s
.
commit
|
commitdiff
|
tree
2017-05-01
Da
v
id van der Spoel
Xpm test for gm
x
c
lustsize
commit
|
commitdiff
|
tree
2017-03-12
Da
v
id van
d
er
Spoel
Added tests for
g
mx c
l
u
sts
i
ze
.
commit
|
commitdiff
|
tree
2017-03-04
Dav
i
d van de
r
Spoe
l
Re
m
oves rogue printing to xv
g
f
ile in gmx mindist
commit
|
commitdiff
|
tree
2017-02-27
David van der Spoel
F
i
xes b
u
g in gmx solv
a
te with -shel
l
t
hat yielded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
D
avid van der
S
poel
Fixes SEG
V
in gmx or
d
er
.
commit
|
commitdiff
|
tree
2017-02-02
David
v
an der
Spoel
Onl
y
prin
t
all dangling at
o
ms with grompp
-v
commit
|
commitdiff
|
tree
2017-01-23
David
v
an de
r
Spoel
Added
r
e
ference
f
or dihedral functio
n
in OPLS
.
commit
|
commitdiff
|
tree
2016-12-07
David van der Spoel
Couple
o
f n
e
w quotes
commit
|
commitdiff
|
tree
2016-11-18
Dav
i
d
v
an der Spoe
l
A
d
ded first
t
es
t
s
of bonded
f
orce functions
.
commit
|
commitdiff
|
tree
2016-10-14
David v
a
n
der
Spoel
F
ixes some memo
r
y l
e
aks associated with
testing ap
p
lie
d
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
Dav
i
d
van der Spoel
Mod
u
lari
z
e
e
l
e
c
t
r
ic
f
i
eld handling
commit
|
commitdiff
|
tree
2016-09-27
David
v
an d
e
r Spoel
Fixed scri
p
t x
p
lo
r
2gmx
.
p
l to
wo
r
k with GM
X
D
A
TA
commit
|
commitdiff
|
tree
2016-09-26
David van
d
er Spoel
Fixes issue with Release b
u
ild in correlation functions
.
commit
|
commitdiff
|
tree
2016-09-20
David van der Spoel
Ma
d
e
co
r
relation fu
n
ction routine
u
se std
:
:vecto
r
commit
|
commitdiff
|
tree
2016-09-05
Dav
i
d
va
n
der Spoel
Merge "
M
er
g
e
branch release-2016"
commit
|
commitdiff
|
tree
2016-08-24
Davi
d
van der Spoel
Added document
a
tion
f
or shell potentials
.
commit
|
commitdiff
|
tree
2016-08-03
David van der Spoel
Thr
e
e new quotes
.
commit
|
commitdiff
|
tree
2016-07-31
David
v
an
der S
p
oel
Merge
"
M
erge
b
ranch releas
e
-5-1 into
release-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
David v
a
n
der Spo
e
l
Fixes inc
o
r
r
ect c
h
a
rges in OPLS/A
A
-L fo
r
HISD a
n
d HISE
commit
|
commitdiff
|
tree
2016-07-08
D
a
vid van
der Sp
o
el
M
erge "Merg
e
branch r
e
leas
e
-5-
1
i
n
to r
e
l
ease-2016
"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
David van d
e
r S
p
o
e
l
Introduce
f
atal error f
o
r
too
f
ew frames i
n
gmx do
s
.
commit
|
commitdiff
|
tree
2016-06-27
David van
d
e
r Spoel
Made gmx dos
w
o
rk again
.
commit
|
commitdiff
|
tree
2016-06-22
D
a
vid van der Spoel
R
emo
v
ed spurious r_ij in fo
r
c
e fo
r
Mo
r
se potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
Dav
i
d
van der
Spoel
Mod
i
f
y lmfit library to avoid clashes with other vers
i
ons
.
commit
|
commitdiff
|
tree
2016-03-23
David van der Spoel
Remo
v
ed srenew
t
hat was
making array s
m
a
ller incorrectly
.
commit
|
commitdiff
|
tree
2016-03-18
Dav
i
d van der Spoel
F
i
xed division by zero
in polarize
.
commit
|
commitdiff
|
tree
2016-01-20
David
van der Spoel
Couple of new quotes
commit
|
commitdiff
|
tree
2016-01-07
David van d
e
r Spoe
l
Made normal modes wo
r
k with shells an
d
vsi
t
e
s
commit
|
commitdiff
|
tree
2015-11-24
David van der
S
poel
Fix
e
s
n
ewly
i
nt
r
oduced bug
in make
_
ndx
.
commit
|
commitdiff
|
tree
2015-11-23
David van de
r
Spoel
Moved domdec st
r
uctures
out
of commrec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
Da
v
i
d
van der Spoel
Cleanup
s
in
lega
c
y
h
e
a
der/types
/
comm
r
ec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der Spoel
Merge
d
legacyhe
a
ders
/
typ
e
s/qmmmrec
.
h
into mdl
i
b/
q
mmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der Spoel
Merged
genborn
.
h from legacyheaders/t
y
pes int
o
mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Moved
legacyheaders/types/g
r
o
up
.
h to mdty
p
es
.
commit
|
commitdiff
|
tree
2015-11-20
D
avid
v
an der
Spoel
Merged leg
a
cyheaders
/
ty
p
es/ns
.
h and nb
l
ist
.
h to mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
Da
v
id van der Spoel
Com
b
i
n
e
enu
m
s
.
h and names*
.
commit
|
commitdiff
|
tree
2015-11-20
D
avid
v
an der Spoe
l
Merged legacyheader
s
/nrnb
.
h and types/nrnb
.
h to gmxlib
.
commit
|
commitdiff
|
tree
2015-11-20
David
van der Spoel
Moved mdatom
.
h
f
rom lega
c
yh
e
ader/
t
ypes to m
d
types
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Move
d
leg
a
cyhe
a
ders/ty
p
es/en
e
rgy
.
h to mdtyp
e
s
.
commit
|
commitdiff
|
tree
2015-11-15
David v
a
n der
S
poel
Merged lega
c
yhead
e
r
s/types/in
p
utrec
.
h int
o
mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
David van der Spoel
Merged legacy
h
eaders
/
types/sta
t
e
.
h
i
nto mdty
p
es/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
Da
v
id v
a
n der Spoe
l
Replaced at
o
m_id by int
.
commit
|
commitdiff
|
tree
2015-11-13
David van der
S
p
oel
Move
d
g
e
n
bo
r
n
.
h
t
o mdlib
commit
|
commitdiff
|
tree
2015-11-12
D
a
vid van der Spoe
l
Moved txtd
u
mp
.
*
to f
i
leio
.
commit
|
commitdiff
|
tree
2015-11-12
David v
a
n d
e
r Spoel
Moved co
p
yrite
.
* to fileio fro
m
gmxlib an
d
lega
c
yheaders
.
commit
|
commitdiff
|
tree
2015-11-11
David van der
S
po
e
l
M
o
v
ed inp
u
trec
.
*
from g
m
xlib and l
e
gac
y
h
eaders
to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-10
Da
v
id v
a
n
der
S
poel
Remov
e
d legac
y
headers/typ
e
defs
.
h
commit
|
commitdiff
|
tree
2015-11-03
Davi
d
va
n
d
e
r
S
poel
Mov
e
d df_
h
istory utility routines
f
rom ty
p
edefs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
David
v
an der Spoel
Replaced NOTSET from ty
p
e
d
efs
.
h
by local
solution
s
.
commit
|
commitdiff
|
tree
2015-10-23
Da
v
id van der Spoel
Remove
d
e
n
ergy
h
is
t
ory code from
t
ypedefs to a
s
e
parate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van d
e
r Spoel
Move
d
pbc/cut-
o
ff related
u
tiliti
e
s from ty
p
edefs to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
David van der Spoel
Freed
m
emory i
n
legacy
statistics
r
o
utines
.
commit
|
commitdiff
|
tree
2015-10-03
David
v
an d
e
r Spoel
Removed
simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van de
r
Spoel
R
emoved
s
impl
e
.
h from nb_kernel
_
sse4
_
1_X
X
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Rem
o
ved
si
m
p
l
e
.
h from nb
_
kernel_
s
se
2
_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Removed sim
p
le
.
h from
n
b_k
e
rnel_c and nb_kernel_s
p
a
rc64
_
hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
Removed include s
i
mple
.
h from nb
_
kern
e
l_a
v
x_128_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
David van der S
p
oel
Removed
simple
.
h
fr
o
m nb_k
e
rn
e
l_avx_
2
56_XX
commit
|
commitdiff
|
tree
2015-10-02
D
avid van
d
er S
p
oel
Removed
o
utp
u
t_
e
nv_t
,
now using gmx_output
_
e
n
v_t
*
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
D
avid v
a
n
d
er Spoel
Removed
t
ypes/nrnb
.
h from typ
e
defs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David van der Spoel
R
emoved types/nblist
.
h and types/
n
sgrid
.
h
f
rom
t
y
pedefs
.
h
commit
|
commitdiff
|
tree
2015-09-30
D
a
vid van der
S
p
o
el
Removed types/mdatom
.
h
from t
y
ped
e
fs
.
h
commit
|
commitdiff
|
tree
2015-09-29
Dav
i
d van de
r
Spoel
Rem
o
ved types/inputrec
.
h from
typedefs
.
h and releted
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David van der Spoel
Fixes bug in
t
he
c
o
m
put
a
tion of Coefficient
of Thermal
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
Da
v
id van
d
e
r Spoel
Remov
e
d
t
ype
s
/forcere
c
.
h
from typ
e
defs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David van de
r
Spoel
Re
m
o
v
e
d
inc
l
u
de of types/ifunc
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
D
a
vid van der
S
poe
l
R
e
moved fo
u
r includ
e
s from legacy
h
eaders/typedef
s
.
h
commit
|
commitdiff
|
tree
2015-09-22
Da
v
id van d
e
r
Spoel
Removed leg
a
cy
h
ead
e
r
s/type
s
/commrec
_
f
w
d
.
h f
r
om typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David van
der Spoel
Mo
v
ed content from
m
drun
.
h to se
p
arate
h
e
a
ders
.
commit
|
commitdiff
|
tree
2015-09-10
Dav
i
d
van de
r
Spoel
Removed <sys/type
s
.
h>
a
nd "types/cons
t
r
.
h" from
typ
e
defs
commit
|
commitdiff
|
tree
2015-09-09
D
avid v
a
n der Spoel
R
emoved fileio
/
trx
.
h from
t
y
p
edef
s
.
h
commit
|
commitdiff
|
tree
2015-09-08
David
van der S
p
oel
Moved functions
o
p
e
r
a
ting
on forc
e
rec
to separa
t
e header
.
commit
|
commitdiff
|
tree
2015-08-28
David v
a
n der Spoel
Added energy
(
edr)
file
type to O
p
tions head
e
rs
.
commit
|
commitdiff
|
tree
2015-08-28
David va
n
der Spoel
Added additional construc
t
o
r
to S
t
ringStream
clas
s
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David van d
e
r Spoel
Made output from dum
p
ing neightborlists ea
s
ier to read
.
commit
|
commitdiff
|
tree
2015-07-31
D
avid van der S
p
oel
Change initial p
a
rameters for test
i
ng expfit
.
commit
|
commitdiff
|
tree
2015-07-29
Dav
i
d van der S
p
oel
C
o
de for chec
k
ing xvg files in testu
t
ils
.
commit
|
commitdiff
|
tree
2015-04-17
David van der Spoe
l
Updated exponential fitting to make it robu
s
t
.
commit
|
commitdiff
|
tree
2015-04-09
D
avid van der Spoel
Clarif
i
e
d
comments for time-de
p
ende
n
t
ele
c
tric fi
e
lds
.
commit
|
commitdiff
|
tree
2015-04-08
Dav
i
d
van
der Spoel
Fixed inco
r
rect o
u
tput of
gb_algor
i
t
h
as
s
a_alg
o
rith
m
.
commit
|
commitdiff
|
tree
2015-03-02
Davi
d
va
n
der Spoel
Upd
a
t
e
d documentation for ele
c
tric fields
.
commit
|
commitdiff
|
tree
2014-12-13
David van
der Spoel
F
o
ur new quotes fro
m
around the world
.
commit
|
commitdiff
|
tree
2014-11-28
D
a
vid van der Spoel
Fixes recen
t
ly intro
d
uced bug in gmx ana
l
yze
.
commit
|
commitdiff
|
tree
2014-11-24
David va
n
der Spoel
Added
war
n
ings for ewald-geometry
and surface-epsilon
commit
|
commitdiff
|
tree
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