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--></style></head><body lang=EN-US link=blue vlink="#954F72"><div class=WordSection1><p class=MsoNormal><span class=DefaultFontHxMailStyle><span style='font-size:12.0pt'>The Ca pseudo that you are using has 2 electrons in valence 4s plus semicore electrons in 3s and 3p, with your occupation you have to allocate 10 electrons, your input occupation should be something like <o:p></o:p></span></span></p><p class=MsoNormal><span class=DefaultFontHxMailStyle><span style='font-size:12.0pt'>2.0 2.0 2.0 2.0 2.0 <o:p></o:p></span></span></p><p class=MsoNormal><span class=DefaultFontHxMailStyle><span style='font-size:12.0pt'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=DefaultFontHxMailStyle><span style='font-size:12.0pt'><o:p> </o:p></span></span></p><p class=MsoNormal><span class=DefaultFontHxMailStyle><span style='font-size:12.0pt'><o:p> </o:p></span></span></p><p class=MsoNormal>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">Mail</a> for Windows 10</p><p class=MsoNormal><span class=DefaultFontHxMailStyle><span style='font-size:12.0pt'><o:p> </o:p></span></span></p><div style='mso-element:para-border-div;border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0in 0in 0in'><p class=MsoNormal style='border:none;padding:0in'><b>From: </b><a href="mailto:poojavyas595@gmail.com">Pooja Vyas</a><br><b>Sent: </b>Friday, June 26, 2020 8:40 AM<br><b>To: </b><a href="mailto:users@lists.quantum-espresso.org">Quantum ESPRESSO users Forum</a><br><b>Subject: </b>Re: [QE-users] Energy of isolated atom of CaO</p></div><p class=MsoNormal><span class=DefaultFontHxMailStyle><span style='font-size:12.0pt'><o:p> </o:p></span></span></p><div><div><p class=MsoNormal>I also tried to compute separate isolated energies for Ca and O (example05/PW). For Ca, I used the following script, But I face an error "strange occupations: number of electrons from occupations is wrong."</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>#!/bin/sh<br><br># run from directory where this script is<br>cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname<br>EXAMPLE_DIR=`pwd`<br><br># check whether echo has the -e option<br>if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi<br><br>$ECHO<br>$ECHO "$EXAMPLE_DIR : starting"<br>$ECHO<br>$ECHO "This example shows how to calculate the total energy of an isolated"<br>$ECHO "atom in a supercell with fixed occupations."<br>$ECHO "Energy of Ca"<br><br># set the needed environment variables<br>. ../../../environment_variables<br><br># required executables and pseudopotentials<br>BIN_LIST="pw.x"<br>PSEUDO_LIST=" Ca.pbe-nsp-van.UPF"<br><br>$ECHO<br>$ECHO " executables directory: $BIN_DIR"<br>$ECHO " pseudo directory: $PSEUDO_DIR"<br>$ECHO " temporary directory: $TMP_DIR"<br>$ECHO " checking that needed directories and files exist...\c"<br><br># check for directories<br>for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do<br> if test ! -d $DIR ; then<br> $ECHO<br> $ECHO "ERROR: $DIR not existent or not a directory"<br> $ECHO "Aborting"<br> exit 1<br> fi<br>done<br>for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do<br> if test ! -d $DIR ; then<br> mkdir $DIR<br> fi<br>done<br>cd $EXAMPLE_DIR/results<br><br># check for executables<br>for FILE in $BIN_LIST ; do<br> if test ! -x $BIN_DIR/$FILE ; then<br> $ECHO<br> $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable"<br> $ECHO "Aborting"<br> exit 1<br> fi<br>done<br><br># check for pseudopotentials<br>for FILE in $PSEUDO_LIST ; do<br> if test ! -r $PSEUDO_DIR/$FILE ; then<br> $ECHO<br> $ECHO "Downloading $FILE to $PSEUDO_DIR...\c"<br> $WGET $PSEUDO_DIR/$FILE $NETWORK_PSEUDO/$FILE 2> /dev/null<br> fi<br> if test $? != 0; then<br> $ECHO<br> $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"<br> $ECHO "Aborting"<br> exit 1<br> fi<br>done<br>$ECHO " done"<br><br># how to run executables<br>PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX"<br>$ECHO<br>$ECHO " running pw.x as: $PW_COMMAND"<br>$ECHO<br><br># self-consistent calculation for isolated Ca atom<br>cat > Ca.in << EOF<br> &control<br> calculation='scf',<br> restart_mode='from_scratch',<br> pseudo_dir='$PSEUDO_DIR/'<br> outdir='$TMP_DIR/'<br> /<br> &system<br> ibrav=1,<br> celldm(1)=24.0,<br> nat=1,<br> ntyp=1,<br> nbnd=12,<br> nosym=.true.,<br> ecutwfc=100.0,<br> occupations='from_input',<br> /<br> &electrons<br> mixing_beta=0.7,<br> conv_thr=1.0E-8,<br> /<br>ATOMIC_SPECIES<br>Ca 40.078 Ca.pbe-nsp-van.UPF<br>ATOMIC_POSITIONS<br>Ca 0.0 0.0 0.0<br>K_POINTS Gamma<br><br>OCCUPATIONS<br>2.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0<br>EOF<br>$ECHO " running self-consistent calculation for Al atom...\c"<br>$PW_COMMAND < Ca.in > Ca.out<br>check_failure $?<br>$ECHO " done"<br><br><br><br># clean TMP_DIR<br>$ECHO " cleaning $TMP_DIR...\c"<br>rm -rf $TMP_DIR/pwscf*<br>$ECHO " done"<br><br><br>$ECHO<br>$ECHO "$EXAMPLE_DIR: done"</p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Can anyone suggest how should the occupation number be written in above case?</p></div><div><p class=MsoNormal>Thanks and regards.</p></div></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Fri, Jun 26, 2020 at 11:58 AM Pietro Delugas <<a href="mailto:pdelugas@sissa.it">pdelugas@sissa.it</a>> wrote:</p></div><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-m-8681102370381522911defaultfonthxmailstyle><span style='font-size:12.0pt'>Hello </span></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-m-8681102370381522911defaultfonthxmailstyle><span style='font-size:12.0pt'> </span></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-m-8681102370381522911defaultfonthxmailstyle><span style='font-size:12.0pt'>In ATOMIC_POSITIONS you need to specify the units that you are using for the coordinates, if you don’t put anything he program assumes alat units and puts the 2 atoms very far apart. </span></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-m-8681102370381522911defaultfonthxmailstyle><span style='font-size:12.0pt'> </span></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-m-8681102370381522911defaultfonthxmailstyle><span style='font-size:12.0pt'>If you actually wanted compute the two separated atoms specifying startingwfc=’random’ in the &electrons name list may help. In this case I would also chose calculation=’scf’ in &control. </span></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-m-8681102370381522911defaultfonthxmailstyle><span style='font-size:12.0pt'> </span></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-m-8681102370381522911defaultfonthxmailstyle><span style='font-size:12.0pt'>Regards - Pietro </span></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-m-8681102370381522911defaultfonthxmailstyle><span style='font-size:12.0pt'> </span></span></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986" target="_blank">Mail</a> for Windows 10</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-m-8681102370381522911defaultfonthxmailstyle><span style='font-size:12.0pt'> </span></span></p><div style='border:none;border-top:solid windowtext 1.0pt;padding:3.0pt 0in 0in 0in;border-color:currentcolor currentcolor'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b>From: </b><a href="mailto:poojavyas595@gmail.com" target="_blank">Pooja Vyas</a><br><b>Sent: </b>Friday, June 26, 2020 8:12 AM<br><b>To: </b><a href="mailto:users@lists.quantum-espresso.org" target="_blank">Quantum ESPRESSO users Forum</a><br><b>Subject: </b>[QE-users] Energy of isolated atom of CaO</p></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-m-8681102370381522911defaultfonthxmailstyle><span style='font-size:12.0pt'> </span></span></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dear users,</p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I want to calculate cohesive energy of CaO. I'm using cluster_example/PW which uses assume_isolated = 'martyna_tuckerman' . Following is my input script:</p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>#!/bin/sh<br>for a in 30<br>do<br>cat > ${a}.in << EOF<br>&CONTROL<br> calculation = 'relax'<br> prefix = "${a}",<br> pseudo_dir = "/home/user/pv/cohesive/pseudo/",<br> outdir = "/home/user/pv/cohesive/",<br>/<br>&SYSTEM<br> ibrav = 1,<br> celldm(1) = $a,<br> nat = 2,<br> ntyp = 2,<br> ecutwfc = 100.D0,<br> assume_isolated = 'martyna-tuckerman'<br>/<br>&ELECTRONS<br> conv_thr = 1.D-8,<br> mixing_beta = 0.7D0,<br>/<br>&IONS<br>/<br>ATOMIC_SPECIES<br>Ca 40.078 Ca.pbe-nsp-van.UPF<br>O 15.999 O.pbe-van_ak.UPF<br>ATOMIC_POSITIONS <br>Ca 0.0 0.0 0.0<br>O 0.5 0.5 0.5<br>K_POINTS Gamma<br><br>EOF<br><br>mpirun -np 40 -machinefile x1 /apps/codes/qe/6.4/bin/pw.x < ${a}.in > ${a}.out<br>done<br>done</p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> </p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>My lattice constant is around 8 a.u , so I assumed the box size to be 3 times of it. But when I run the script, the convergence was not achieved even after 100 iterations. Then I tried to take small box size of about 16 bohr. That too didn't work. Then I even tried reducing ecutwfc and mixing_beta..but same error was obtained. Can anyone suggest what can I do to resolve the issue?</p></div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Any kind of help is appreciated.</p></div></div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Thanks and regards.</p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><span class=gmail-m-8681102370381522911defaultfonthxmailstyle><span style='font-size:12.0pt'> </span></span></p></div></div></blockquote></div><p class=MsoNormal style='margin-left:4.8pt'>_______________________________________________<br>Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br><a href="https://lists.quantum-espresso.org/mailman/listinfo/users" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></p><p class=MsoNormal><span class=DefaultFontHxMailStyle><span style='font-size:12.0pt'><o:p> </o:p></span></span></p></div></body></html>