1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
|
#!/bin/sh
# run from directory where this script is
cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname
EXAMPLE_DIR=`pwd`
# check whether echo has the -e option
if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi
$ECHO
$ECHO "$EXAMPLE_DIR : starting"
$ECHO
$ECHO "This example shows how to use cp.x to perform molecular dynamics"
$ECHO "simulation of NH3."
# set the needed environment variables
. ../../../environment_variables
# required executables and pseudopotentials
BIN_LIST="cp.x"
PSEUDO_LIST="N.blyp-mt.UPF H.blyp-vbc.UPF"
$ECHO
$ECHO " executables directory: $BIN_DIR"
$ECHO " pseudo directory: $PSEUDO_DIR"
$ECHO " temporary directory: $TMP_DIR"
$ECHO " checking that needed directories and files exist...\c"
# check for directories
for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do
if test ! -d $DIR ; then
$ECHO
$ECHO "ERROR: $DIR not existent or not a directory"
$ECHO "Aborting"
exit 1
fi
done
for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do
if test ! -d $DIR ; then
mkdir $DIR
fi
done
cd $EXAMPLE_DIR/results
# check for executables
for FILE in $BIN_LIST ; do
if test ! -x $BIN_DIR/$FILE ; then
$ECHO
$ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable"
$ECHO "Aborting"
exit 1
fi
done
# check for pseudopotentials
for FILE in $PSEUDO_LIST ; do
if test ! -r $PSEUDO_DIR/$FILE ; then
$ECHO
$ECHO "Downloading $FILE to $PSEUDO_DIR...\c"
$WGET $PSEUDO_DIR/$FILE $NETWORK_PSEUDO/$FILE 2> /dev/null
fi
if test $? != 0; then
$ECHO
$ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"
$ECHO "Aborting"
exit 1
fi
done
$ECHO " done"
# how to run executables
FPMD_COMMAND="$PARA_PREFIX $BIN_DIR/cp.x $PARA_POSTFIX"
$ECHO
$ECHO " running cp.x as: $FPMD_COMMAND"
$ECHO
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/cp*
$ECHO " done"
# molecular dynamics calculation
cat > nh3.in << EOF
&control
title = ' Ammonia Molecule ',
calculation = 'cp',
restart_mode = 'from_scratch', ! 'restart',
ndr = 51,
ndw = 51,
nstep = 100,
iprint = 10,
isave = 100,
tstress = .TRUE.,
tprnfor = .TRUE.,
dt = 5.0d0,
etot_conv_thr = 1.d-9,
ekin_conv_thr = 1.d-4,
prefix = 'nh3_mol'
pseudo_dir='$PSEUDO_DIR/',
outdir='$TMP_DIR/',
/
&system
ibrav = 14,
celldm(1) = 12.0,
celldm(2) = 1.0,
celldm(3) = 1.0,
celldm(4) = 0.0,
celldm(5) = 0.0,
celldm(6) = 0.0,
nat = 4,
ntyp = 2,
nbnd = 4,
ecutwfc = 80.0,
! ecfixed = 68.0,
! qcutz = 68.0,
! q2sigma = 8.0,
input_dft = 'BLYP'
/
&electrons
emass = 400.d0,
emass_cutoff = 2.5d0,
orthogonalization = 'ortho',
ortho_eps = 5.d-8,
ortho_max = 15,
electron_dynamics = 'sd',
! electron_damping = 0.3,
electron_velocities = 'zero',
electron_temperature = 'not_controlled',
/
&ions
ion_dynamics = 'damp',
ion_damping = 0.2,
ion_radius(1) = 0.8d0,
ion_radius(2) = 0.8d0,
ion_velocities = 'zero',
ion_temperature = 'not_controlled',
ion_nstepe = 10
/
&cell
cell_dynamics = 'none',
cell_velocities = 'zero',
press = 0.0d0,
/
ATOMIC_SPECIES
N 16.0d0 N.blyp-mt.UPF
H 1.0d0 H.blyp-vbc.UPF
ATOMIC_POSITIONS (bohr)
N 0.0099 0.0099 0.0000
H 1.9186 -0.2443 -0.2208
H -0.2305 1.9214 -0.2144
H -0.1795 -0.1807 1.9236
EOF
$ECHO " running the damped dynamics calculation...\c"
$FPMD_COMMAND < nh3.in > nh3.out
check_failure $?
$ECHO " done"
$ECHO
$ECHO "$EXAMPLE_DIR : done"
|
