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
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
|
#!/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 is a second example of how to use cp.x to calculate Wannier functions,"
$ECHO "using Jacobi Rotation as localization algorithm (courtesy of IRRMA Lausanne)."
# set the needed environment variables
. ../../../environment_variables
# required executables and pseudopotentials
BIN_LIST="cp.x"
PSEUDO_LIST="H.blyp-vbc.UPF O.blyp-mt.UPF"
$ECHO
$ECHO " executables directory: $BIN_DIR"
$ECHO " pseudo directory: $PSEUDO_DIR"
$ECHO " temporary directory: $TMP_DIR"
$ECHO
$ECHO " checking that needed directories and files exist...\c"
# check for directories
for DIR in "$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
$ECHO " done"
# how to run executables
CP_COMMAND="$PARA_PREFIX $BIN_DIR/cp.x $PARA_POSTFIX"
$ECHO
$ECHO " running cp.x as: $CP_COMMAND"
$ECHO
# clean TMP_DIR
$ECHO " cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/cp*
$ECHO " done"
cat > h2o.scf.in << EOF
&control
calculation = 'scf'
restart_mode='from_scratch',
prefix='h2o_mol',
tstress = .false.
tprnfor = .true.
saverho = .true.
pseudo_dir = "$PSEUDO_DIR/",
outdir = "$TMP_DIR/",
ndw=50
nstep=1000
iprint=1
dt = 1.0d0
ekin_conv_thr = 1.0d-8
etot_conv_thr = 1.0d-6
forc_conv_thr = 1.0d-2
verbosity="debug"
/
&system
ibrav= 1, celldm(1)=16.0, nat= 3, ntyp= 2,
ecutwfc = 70.0, ecutrho=280.0, nbnd=4,
/
&electrons
emass = 400.d0,
emass_cutoff = 3.d0,
orthogonalization = 'Gram-Schmidt',
tcg=.true.,
passop=0.3,
maxiter = 250,
conv_thr=1.d-8
/
ATOMIC_SPECIES
O 8 O.blyp-mt.UPF
H 1 H.blyp-vbc.UPF
ATOMIC_POSITIONS {bohr}
O 5.093750000000 5.093750000000 5.093750000000
H 3.648508572765 5.093750000000 3.967985471743
H 6.538991443058 5.093750000000 3.967985459417
EOF
$ECHO " running electronic minimization...\c"
$CP_COMMAND < h2o.scf.in > h2o.scf.out
check_failure $?
$ECHO " done"
cat > h2o.wannier.in << EOF
&control
calculation = 'cp-wf'
restart_mode='restart',
prefix='h2o_mol',
tstress = .false.
tprnfor = .true.
saverho = .true.
pseudo_dir = "$PSEUDO_DIR/",
outdir = "$TMP_DIR/",
ndr=50
ndw=51
nstep=1000
iprint=1
dt = 1.0d0
ekin_conv_thr = 1.0d-8
etot_conv_thr = 1.0d-6
forc_conv_thr = 1.0d-2
/
&system
ibrav= 1, celldm(1)=16.0, nat= 3, ntyp= 2,
ecutwfc = 70.0, ecutrho=280.0, nbnd=4,
/
&electrons
emass = 400.d0,
emass_cutoff = 3.d0,
orthogonalization = 'Gram-Schmidt',
tcg=.true.,
passop=0.3,
maxiter = 250,
conv_thr=1.d-8
/
&ions
ion_dynamics = 'none'
/
&wannier
wfsd = 3
calwf = 4
nit = 100
nsd = 100
nsteps = 200
tolw = 1.0D-14
/
ATOMIC_SPECIES
O 8 O.blyp-mt.UPF
H 1 H.blyp-vbc.UPF
ATOMIC_POSITIONS {bohr}
O 5.093750000000 5.093750000000 5.093750000000
H 3.648508572765 5.093750000000 3.967985471743
H 6.538991443058 5.093750000000 3.967985459417
EOF
$ECHO " running Wannier function calculation...\c"
$CP_COMMAND < h2o.wannier.in > h2o.wannier.out
check_failure $?
$ECHO " done"
$ECHO "">> h2o.wannier.out
$ECHO " Wannier functions centers:">> h2o.wannier.out
tail -4 $TMP_DIR/h2o_mol.wfc >> h2o.wannier.out
tail -4 fort.24 >> h2o.wannier.out
$ECHO
$ECHO "$EXAMPLE_DIR: done"
|
