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Fix cmake Sphinx detection for versions >1.6.4
2018-03-21
Da
v
id van der Spoel
Re
n
a
med entropy
.
* to thermochemistr
y
.
*
commit
|
commitdiff
|
tree
2018-03-16
David van de
r
Spoe
l
Split of
f
entropy calculation t
o
se
p
ara
t
e file
.
commit
|
commitdiff
|
tree
2017-12-28
David van der S
p
oel
Fix
e
s and up
d
ate
s
for xplor2gm
l
.
pl and atom_nom
.
tbl
commit
|
commitdiff
|
tree
2017-11-06
David
v
a
n
d
e
r Spoel
Fixed check fo
r
water in gen_vsite
.
c
p
p
commit
|
commitdiff
|
tree
2017-11-02
D
a
vid
van der S
p
o
el
N
e
w mdp input for ele
c
tric fields
.
commit
|
commitdiff
|
tree
2017-10-30
David
v
an der Spoe
l
Fix
e
d mdp ou
t
pu
t
from ele
c
tr
i
c
f
ield c
o
de
.
commit
|
commitdiff
|
tree
2017-10-30
David van d
e
r Spo
e
l
A
d
ded
opti
o
n -water ti
p
s3p
to pdb2
g
mx
.
commit
|
commitdiff
|
tree
2017-10-23
D
a
vid
van der Spoel
Spli
t
off the NMR related
anal
y
ses
f
rom gmx
energy
.
commit
|
commitdiff
|
tree
2017-10-17
David van der
Spoel
Fixed m
i
ssing entrie
s
i
n
nrnb
a
r
rays
.
commit
|
commitdiff
|
tree
2017-08-15
Dav
i
d van der Spo
e
l
Worked
a
round missing
O
penMP impleme
n
tation in orires
.
commit
|
commitdiff
|
tree
2017-08-03
David
van der
S
p
oel
F
i
x
e
d bu
g
i
n g
m
x disre
s
indexin
g
arr
a
y
s
.
commit
|
commitdiff
|
tree
2017-08-02
David
v
an de
r
Spoel
Worked arou
n
d
missing OpenMP implementati
o
n in
o
rires
.
commit
|
commitdiff
|
tree
2017-07-28
Davi
d
van der Spoel
Added u
n
it-test for or
i
entation re
s
traints output
.
commit
|
commitdiff
|
tree
2017-07-19
David van der
S
poel
Rem
o
ved
u
nnec
e
s
s
ary sta
t
ic declarations for command
.
.
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoel
Fixed test-order
d
ep
e
n
d
ency
i
n gmxp
r
eprocess
tests
.
commit
|
commitdiff
|
tree
2017-07-19
David van der Spoel
Fix
n
on-r
e
produc
a
bility of clu
s
tsize tests
.
commit
|
commitdiff
|
tree
2017-05-01
David van der Spoel
Xpm test
for gmx clustsize
commit
|
commitdiff
|
tree
2017-03-12
David van
der Spo
e
l
A
dded t
e
s
ts for gmx c
l
ust
s
i
ze
.
commit
|
commitdiff
|
tree
2017-03-04
David van der Spoel
Removes rogue print
i
ng to xvg file in
g
m
x
m
indist
commit
|
commitdiff
|
tree
2017-02-27
David van der Spoel
Fixes
bug i
n
gmx
solvat
e
with
-s
h
e
ll th
a
t yielded 0
.
.
.
commit
|
commitdiff
|
tree
2017-02-03
D
avid
van der Spoel
Fix
e
s SEGV in
gmx order
.
commit
|
commitdiff
|
tree
2017-02-02
David van de
r
Spoel
Only
p
rint all d
a
ngling at
o
ms with
g
r
omp
p
-v
commit
|
commitdiff
|
tree
2017-01-23
D
a
vid van der S
p
oel
Added
reference for dihedral functi
o
n in OPL
S
.
commit
|
commitdiff
|
tree
2016-12-07
David
v
a
n
der Spoel
C
o
uple of
n
e
w quote
s
commit
|
commitdiff
|
tree
2016-11-18
D
avid van der
S
poel
Adde
d
first test
s
of bond
e
d f
o
rce functions
.
commit
|
commitdiff
|
tree
2016-10-14
David van der
Spo
e
l
F
i
xes som
e
m
emory leaks associated with testin
g
applie
d
.
.
.
commit
|
commitdiff
|
tree
2016-10-07
David van der Spoel
Modularize electric field handling
commit
|
commitdiff
|
tree
2016-09-27
David
van
d
er Spoel
Fi
x
ed script xplor2gmx
.
p
l
to w
o
rk
w
ith GMXD
A
TA
commit
|
commitdiff
|
tree
2016-09-26
David
van d
e
r Spoel
Fixes issue wi
t
h
R
e
lease bu
i
ld in co
r
relation function
s
.
commit
|
commitdiff
|
tree
2016-09-20
David van der Spoel
Made corre
l
atio
n
funct
i
on routine use std::vec
t
or
commit
|
commitdiff
|
tree
2016-09-05
David van der
S
poel
Me
r
ge "Merge
b
ra
n
ch
r
elease-2016"
commit
|
commitdiff
|
tree
2016-08-24
David van der Spoel
Ad
d
e
d
documentation fo
r
shell potential
s
.
commit
|
commitdiff
|
tree
2016-08-03
D
avid van d
e
r Spoel
Thr
e
e new
q
uotes
.
commit
|
commitdiff
|
tree
2016-07-31
D
avi
d
van der Spoel
Merge
"
M
erge
bra
n
ch re
l
ease-5-1 in
t
o rel
e
a
s
e-2016"
.
.
.
commit
|
commitdiff
|
tree
2016-07-29
David van de
r
Spoel
Fix
e
s incor
r
ect
charges in OPLS/AA-L for H
I
SD and HIS
E
commit
|
commitdiff
|
tree
2016-07-08
Davi
d
van de
r
Spoel
Merge
"Me
r
ge bran
c
h
r
e
l
e
ase
-
5-1
i
nto release
-
20
1
6"
.
.
.
commit
|
commitdiff
|
tree
2016-07-08
D
a
vid va
n
der Spo
e
l
I
n
troduce f
a
tal e
r
r
or for too few frames in g
m
x dos
.
commit
|
commitdiff
|
tree
2016-06-27
David van der Spoel
Made gmx
d
os w
o
rk again
.
commit
|
commitdiff
|
tree
2016-06-22
Da
v
id van de
r
Spoel
Removed sp
u
rio
u
s r_ij in force for Morse potential
.
.
.
commit
|
commitdiff
|
tree
2016-05-08
Da
v
id van der
Spoel
Modify l
m
fit libr
a
ry
t
o
a
v
oid clas
h
es with other versions
.
commit
|
commitdiff
|
tree
2016-03-23
David van der Spoel
Remov
e
d srenew that was making array
smaller incorrectly
.
commit
|
commitdiff
|
tree
2016-03-18
David va
n
der Spoel
Fixed
d
iv
i
sion
by ze
r
o
in polari
z
e
.
commit
|
commitdiff
|
tree
2016-01-20
David van der Spoe
l
Couple of new quotes
commit
|
commitdiff
|
tree
2016-01-07
David van der Spoel
Made norma
l
modes wo
r
k with shells and
v
sit
e
s
commit
|
commitdiff
|
tree
2015-11-24
David
van de
r
Spoel
Fixes
newly
intr
o
d
u
ced bug in make_ndx
.
commit
|
commitdiff
|
tree
2015-11-23
D
avid van der Spoel
Moved domdec stru
c
tures out of com
m
rec
.
h
.
commit
|
commitdiff
|
tree
2015-11-22
D
a
vid van der Spoel
Cleanups
i
n l
e
gacyheader/types/c
o
mmrec
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van der Spoel
Merged legacyhe
a
d
e
rs/types
/
qmmmrec
.
h into mdlib/qmmm
.
h
commit
|
commitdiff
|
tree
2015-11-21
David van d
e
r Spo
e
l
Merged genborn
.
h fro
m
legacyheaders/
t
y
p
es into mdlib
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David
v
an der
Spoe
l
Moved legacyhead
e
r
s
/types/group
.
h
t
o
m
d
types
.
commit
|
commitdiff
|
tree
2015-11-20
David van der Spoel
Merged legacyheaders/ty
p
e
s/ns
.
h
and nb
l
ist
.
h to m
d
t
y
pes
.
.
.
commit
|
commitdiff
|
tree
2015-11-20
David van der
S
p
oel
C
o
mb
i
n
e
enum
s
.
h and na
m
e
s
*
.
commit
|
commitdiff
|
tree
2015-11-20
Da
v
id
v
an der Spoe
l
Me
r
ged legacyheaders/nr
n
b
.
h a
n
d
ty
p
es/
n
rnb
.
h to g
m
xlib
.
commit
|
commitdiff
|
tree
2015-11-20
Davi
d
van der Spoel
Moved mdat
o
m
.
h from
legacy
h
eader
/
types to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-20
Dav
i
d van der
S
poel
Moved legacyheaders/
t
ypes/
e
n
ergy
.
h to m
d
types
.
commit
|
commitdiff
|
tree
2015-11-15
David van der Spoel
Merged
legacyheader
s
/t
y
pes/inputrec
.
h into mdtypes
.
.
.
commit
|
commitdiff
|
tree
2015-11-15
Davi
d
va
n
der Spoel
Merg
e
d le
g
acy
h
eaders/types/
s
tate
.
h
i
n
t
o
md
t
y
pes/state
.
h
commit
|
commitdiff
|
tree
2015-11-13
David
van
d
er Spoel
Repl
a
ced atom_i
d
b
y
i
n
t
.
commit
|
commitdiff
|
tree
2015-11-13
Dav
i
d van de
r
Spoel
Moved ge
n
born
.
h to md
l
ib
commit
|
commitdiff
|
tree
2015-11-12
David va
n
der S
p
oel
Moved txtdump
.
* to fil
e
io
.
commit
|
commitdiff
|
tree
2015-11-12
D
a
vid v
a
n de
r
S
p
oe
l
Move
d
copy
r
ite
.
*
to fileio from gmxlib and
legacy
h
eader
s
.
commit
|
commitdiff
|
tree
2015-11-11
David va
n
der Spoe
l
Moved input
r
ec
.
* from gm
x
l
i
b
and
l
e
g
acyheaders to mdtypes
.
commit
|
commitdiff
|
tree
2015-11-10
D
a
v
i
d
v
a
n der Spoel
Re
m
ov
e
d legacyh
e
ad
e
r
s
/ty
p
edefs
.
h
commit
|
commitdiff
|
tree
2015-11-03
David van der S
p
o
el
Moved d
f
_
h
istor
y
utility routines from ty
p
edefs to
.
.
.
commit
|
commitdiff
|
tree
2015-11-01
David van der Spoel
Replaced NOTSET fr
o
m typedefs
.
h by local sol
u
t
ions
.
commit
|
commitdiff
|
tree
2015-10-23
D
a
v
id van der Spo
e
l
Removed energyhistory code from ty
p
e
d
efs to a separate
.
.
.
commit
|
commitdiff
|
tree
2015-10-18
David van der Spoel
Moved pbc/cut-off related
u
tilities
from
typede
f
s to
.
.
.
commit
|
commitdiff
|
tree
2015-10-15
Da
v
id
van
der
S
po
e
l
Freed m
e
mory in le
g
acy stat
i
stics routine
s
.
commit
|
commitdiff
|
tree
2015-10-03
David van der Spoel
Removed simple
.
h
commit
|
commitdiff
|
tree
2015-10-02
David van der Spoel
R
e
moved s
i
m
p
le
.
h fro
m
nb_ke
r
nel
_
sse4_1_XX
commit
|
commitdiff
|
tree
2015-10-02
D
avid van
der Spoel
R
em
o
v
ed simple
.
h from nb_kernel
_
sse2_XX
commit
|
commitdiff
|
tree
2015-10-02
D
avid van der Spoel
Re
m
o
v
e
d
s
imple
.
h from nb
_
kernel_c and nb_ker
n
el
_
s
p
arc64_hpc
.
.
.
commit
|
commitdiff
|
tree
2015-10-02
D
a
vi
d
van der Spoel
Removed incl
u
de simple
.
h from
nb_ker
n
el_avx_128_fma_XX
commit
|
commitdiff
|
tree
2015-10-02
D
a
v
id van der Spoel
Remov
e
d
simple
.
h from nb
_
kernel_avx_256
_
XX
commit
|
commitdiff
|
tree
2015-10-02
David va
n
der Spoel
Removed output
_
env_t, now using
gmx_o
u
tp
u
t_env_t *
.
.
.
commit
|
commitdiff
|
tree
2015-10-01
D
a
v
i
d van d
e
r Spoe
l
Removed types/
n
rnb
.
h fro
m
t
y
pedefs
.
h
.
commit
|
commitdiff
|
tree
2015-09-30
David va
n
der Spo
e
l
Removed
t
ypes/nblis
t
.
h and types
/
nsgrid
.
h from t
y
pede
f
s
.
h
commit
|
commitdiff
|
tree
2015-09-30
D
av
i
d van der
Spo
e
l
Remov
e
d types
/
mdatom
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-29
David van der
S
p
oel
R
e
moved
types/
i
n
p
utrec
.
h from typedefs
.
h and relet
e
d
.
.
.
commit
|
commitdiff
|
tree
2015-09-29
David va
n
der Spoel
Fixes b
u
g in the computation
of Coe
f
fic
i
ent of Therma
l
.
.
.
commit
|
commitdiff
|
tree
2015-09-27
David v
a
n der
Spoel
R
e
moved
t
ypes/forcerec
.
h
from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-25
David
van d
e
r Spoel
R
e
moved
include of
types/ifunc
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
Da
v
id
van der Spoel
Removed fou
r
incl
u
des fr
o
m legac
y
heade
r
s/typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-22
David van der Spoel
Rem
o
v
e
d legacyhead
e
r
s
/ty
p
es/c
o
mmrec_fwd
.
h from typedef
.
h
commit
|
commitdiff
|
tree
2015-09-10
David
v
an der
Spoel
Move
d
content from mdrun
.
h to se
p
arate
h
e
aders
.
commit
|
commitdiff
|
tree
2015-09-10
David van der Spoel
R
emoved <sys/type
s
.
h> and
"ty
p
es/constr
.
h" from type
d
efs
commit
|
commitdiff
|
tree
2015-09-09
David van
der Spoe
l
R
emoved fil
e
io/trx
.
h from typedefs
.
h
commit
|
commitdiff
|
tree
2015-09-08
David van
d
er Spoel
Move
d
functions operati
n
g on forc
e
rec to se
p
arate
h
e
ad
e
r
.
commit
|
commitdiff
|
tree
2015-08-28
Da
v
id van der Spoel
Added energy (ed
r
) file type to Optio
n
s headers
.
commit
|
commitdiff
|
tree
2015-08-28
D
avid van d
e
r Spoel
A
dde
d
a
d
d
i
tional c
o
nstructor t
o
Stri
n
gSt
r
eam
c
lass
.
.
.
commit
|
commitdiff
|
tree
2015-08-03
David va
n
der Spoel
Made
output from dump
i
ng neightborlists
easier to read
.
commit
|
commitdiff
|
tree
2015-07-31
Dav
i
d van der S
p
o
e
l
Change initial parameters for testing expfit
.
commit
|
commitdiff
|
tree
2015-07-29
Davi
d
van der Spoel
Code for check
i
n
g xvg
f
ile
s
in t
e
s
tutils
.
commit
|
commitdiff
|
tree
2015-04-17
David van der Spo
e
l
U
p
d
ated e
x
ponenti
a
l fitti
n
g
to make it
robust
.
commit
|
commitdiff
|
tree
2015-04-09
David van de
r
S
poel
Clarified
comments fo
r
time-dependent electric
f
ields
.
commit
|
commitdiff
|
tree
2015-04-08
David van der Spoel
F
i
xed incorre
c
t
o
u
tput of gb_algorith
a
s sa_algorithm
.
commit
|
commitdiff
|
tree
2015-03-02
David van der Spoel
Updated documentation for elec
t
ric f
i
elds
.
commit
|
commitdiff
|
tree
2014-12-13
David van der Spoel
Four ne
w
q
u
otes from around t
h
e w
o
rld
.
commit
|
commitdiff
|
tree
2014-11-28
David van der Spoel
Fixe
s
rec
e
ntly i
n
troduced bu
g
in gmx
analyze
.
commit
|
commitdiff
|
tree
2014-11-24
Dav
i
d van der
Spoel
Add
e
d warnings for
e
w
ald-ge
o
metry
and surface-ep
s
ilon
commit
|
commitdiff
|
tree
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