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# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
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# SMTBQ parameter for Al-Al interaction.
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# Edited by N. Salles Univ. Bourgogne and E. Maras from Aalto Univ.
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# year: 2014
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# =========================================================================
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' Nombre.de.type.d.atome..........:' 1
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' ====== atomic parameters ======= '
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' Cation.de.l.oxyde..Stoechio.....:' 'Al' 1
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' Qform.....masse.................:' 3.0 26.98
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' Param.QEq.(ne,.Chi,.J,.R_eff)...:' 3 1.19258 11.05345 0.57701
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' Nbre.d.etats.partage.par.cation.:' 3
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' ===== potential Parameter ======'
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' Atom1..atom2..potential..mode....' 'Al' 'Al' 'second_moment' 'metal'
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' Potentiel.Cat-Ox.(A,.p,.Ksi,.q).:' 0.1221 8.612 1.316 2.516
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' Pot..Cat-Ox.(rc1,.rc2,.r0).Iota.:' 5.6 7.0 2.863 2.0
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' ======== Parametre tab ========= '
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' Rcoul...........................:' 11.1714
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' rmin...dr.......................:' 1.18845 0.001
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' ======== IFQM Parameter ======== '
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' Frenquency.Q.resolution..........' 0
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' loopmax.-.precision..............' 5000 0.0002
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' ==== Coordination parameters ===='
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' .r1n................r2n..........' 2.5 3.2
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' ========== QInitMode ========= '
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' QInitMode....QInit(if.needed)....' 'false' 0.0
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' ======== Mode for QEq ======== '
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' mode(see.end.of.this.file.)......' 'QEqAllParallel'
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' parameters.for.mode..............'
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' ========== Verbose ============ '
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' Verbose(true.or.false)...........' 'false'
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' Print.Energy.components..........' 'false' 300.0
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' Print.electroneg...components....' 'false' 300.0
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# =========================== END's parameters =========================
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@ -0,0 +1,56 @@
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# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
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# SMTBQ parameter for AlO interaction with a limit length 'rc2sm=dc2**2'.
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# Edited by N. Salles from Univ Bourgogne and E. Maras from Aalto Univ.
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#
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# Presentation atom : nature
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# q, qmin, qmax, masse
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# parameter QEq : Chi, J, R_eff
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# Parameter SM : A, p, Ksi, q
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# CutOff SM : dc1, dc2, r0
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# =========================================================================
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# -------------------------- Begin's parameters ---------------------------
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' Number.of.atoms.type............:' 2
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' ====== atomic parameters ======= '
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' 1st.element.(Oxygen).Stoechio...:' 'O' 3
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' Qform.....mass..................:' -2.0 16.00
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' Param.QEq.(ne,.Chi0,.JiO).......:' 2 6.57 10.22
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' coordBB.coordB.coordS.rBB.rB.rS.:' 6. 4. 3.00 0.529 0.529 0.529
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' Number.of.shared.state.by.ions..:' 3
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' -------------------------------- '
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' 2nd.element.(metal).Stoechio....:' 'Al' 2
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' Qform.....mass..................:' 3.0 26.98
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' Param.QEq.(ne,.Chi0,.Ji0,.R_eff):' 3 1.19009 11.1903 0.56619
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' Number.of.shared.state.by.ions..:' 4
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' ===== potential Parameter ======'
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' Atom1..atom2..potential..mode....' 'Al' 'O' 'second_moment' 'oxide'
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' Pot.CatOx.(A,.p,.Ksi(ref=O),.q).:' 0.18176 8.80041 0.26044 1.58851
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' Pot..Cat-Ox.(rc1,.rc2,.r0)......:' 4. 5.6 1.91
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' -------------------------------- '
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' atom1..atom2..potential..........' 'O' 'O' 'buck'
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' Potentiel.O-O...(C,.Rho)........:' 580.440 0.3540
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' ======== Parametre tab ========= '
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' Rcoul=a*rc(SMASH)...............:' 11.1714
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' rmin...dr.......................:' 1.18845 0.001
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' ======== IFQM Parameter ======== '
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' Nevery.charge.calculation........' 1
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' loopmax....precision.............' 7000 0.000001
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' ==== Coordination parameters ===='
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' .r1n................r2n..........' 2.5 3.2
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' ========== QInitMode ========= '
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' QInitMode....QInit(if.needed)....' 'false' -1.8
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' ======== Mode for QEq ======== '
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' mode(see.end.of.this.file.)......' 'QEqAll'
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' parameters.for.mode..............'
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' ========== Verbose ============ '
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' Verbose(true.or.false)...........' 'false'
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' Print.Energy.components..........' 'false' 300.0
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' Print.electroneg...components....' 'false' 300.0
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# =========================== FIN des parametres =========================
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#Possible QInit modes
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# true (then initialize all the oxygen charges to QOxInit and set the cation charge in order to keep the charge balance (neutrality of the box)
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#any other name would lead to either 0 charges or charge read from the lammps atomic position file
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#Possible QEq modes | parameters
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# QEqAll | no parameters
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# QEqAllParallel | no parameters
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# Surface | zlim (QEq only for z>zlim)
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@ -0,0 +1,53 @@
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# DATE: 2015-10-22 CONTRIBUTOR: Nicolas Salles, nsalles@laas.fr CITATION: N. Salles, O. Politano, E. Amzallag and R. Tetot, Comput. Mater. Sci. 111 (2016) 181-189
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# ========================================================================
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# SMTBQ parameter for Ti-O interaction with a limit length 'rc2sm=dc2**2'.
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# Edited by N. Salles from Univ Bourgogne and E. Maras from Aalto Univ
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# september 2014
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# ========================================================================
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' Number.of.atoms.type............:' 2
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' ====== atomic parameters ======= '
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' 1st.element.(Oxygen).Stoechio...:' 'O' 2
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' Qform.....mass..................:' -2.0 16.00
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' Param.QEq.(ne,.Chi0,.JiO).......:' 2 6.57 10.22
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' coordBB.coordB.coordS.rBB.rB.rS.:' 6. 3. 2.00 0.52 0.54348 0.58
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' Number.of.shared.state.by.ions..:' 3
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' -------------------------------- '
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' 2nd.element.(metal).Stoechio....:' 'Ti' 1
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' Qform.....mass..................:' 4.0 26.98
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' Param.QEq.(nq,.Chi0,.Ji0,.R_eff):' 3 0.00 10.572 0.734
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' Number.of.shared.state.by.ions..:' 5
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' ===== potential Parameter ======'
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' Atom1..atom2..potential..mode....' 'Ti' 'O' 'second_moment' 'oxide'
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' Pot.CatOx.(A,.p,.Ksi(ref=O),.q).:' 0.134 12.609 0.5434 2.0965
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' Pot..Cat-Ox.(rc1,.rc2,.r0)......:' 3.6 6.0 1.95
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' -------------------------------- '
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' atom1..atom2..potential..........' 'O' 'O' 'buckPlusAttr'
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' Potential.O-O...(C,.Rho)........:' 580.440 0.3540
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' Potential.O-O...(D.B.r1OO.r2OO).:' -20.86 -0.916 1.4 1.8
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' ======== Tab Parameter ========= '
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' Rcoul=a*rc(SMASH)...............:' 12.1744
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' rmin...dr.......................:' 1.0675 0.001
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' ======== IFQM Parameter ======== '
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' Nevery.charge.calculation........' 1
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' loopmax....precision.............' 7000 0.000001
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' ==== Coordination parameters ===='
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' .r1n................r2n..........' 2.0 3.5
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' ========== QInitMode ========= '
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' QInitMode....QInit(if.needed)....' 'false' -1.0
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' ======== Mode for QEq ======== '
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' mode(see.end.of.this.file.)......' 'QEqAll'
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' parameters.for.mode..............'
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' ========== Verbose ============ '
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' Verbose(true.or.false)...........' 'false'
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' Print.Energy.components..........' 'false' 300.0
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' Print.electroneg...components....' 'false' 300.0
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# =========================== END's parameters =========================
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#Possible QInit modes
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# true (then initialize all the oxygen charges to QOxInit and set the cation charge in order to keep the charge balance (neutrality of the box)
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#any other name would lead to either 0 charges or charge read from the lammps atomic position file
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#Possible QEq modes | parameters
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# QEqAll | no parameters
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# QEqAllParallel | no parameters
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# Surface | zlim (QEq only for z>zlim)
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# BulkFromSlab | zlim1 zlim2 (QEq only for zlim1<z<zlim2)
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# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
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variable T_depart equal 300
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variable dt equal 0.0002
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#Constante
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variable rac3 equal sqrt(3.0)
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variable rac1_2 equal sqrt(0.5)
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variable rac3_2 equal sqrt(1.5)
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#Structure
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variable a equal 4.05
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variable nx equal 10
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variable ny equal 7
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variable nz equal 4
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variable bx equal ${a}*${nx}*${rac1_2}
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variable by equal ${a}*${ny}*${rac3_2}
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variable bz equal ${a}*${nz}*${rac3}
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# =======================================================================
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units metal
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atom_style charge
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dimension 3
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boundary p p p
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lattice sc 1.0
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region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
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create_box 1 box_vide
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# Aluminium atoms z = [111]
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lattice custom ${a} a1 ${rac1_2} 0.0 0.0 &
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a2 0.0 ${rac3_2} 0.0 &
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a3 0.0 0.0 ${rac3} &
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basis 0.0 0.0 0.0 &
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basis 0.5 0.5 0.0 &
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basis 0.5 0.166666667 0.33333 &
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basis 0.0 0.666666667 0.33333 &
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basis 0.0 0.333333333 0.66667 &
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basis 0.5 0.833333333 0.66667
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create_atoms 1 region box_vide
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mass 1 26.98
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velocity all create ${T_depart} 277387
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pair_style smtbq
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pair_coeff * * ffield.smtbq.Al Al
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neighbor 0.5 bin
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neigh_modify every 20 delay 0 check yes
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timestep ${dt}
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thermo_style custom step temp press pe ke etotal lx ly lz vol
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thermo_modify flush yes
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thermo 1
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#dump 5 all custom 1 box_Al.lammpstrj id type q x y z
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fix 3 all nve
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run 10
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unfix 3
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#thermo 15
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fix 1 all box/relax tri 0.0 vmax 0.001
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minimize 1.0e-8 1.0e-10 1000 10000
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unfix 1
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thermo 1
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fix 3 all nve
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run 10
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# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
|
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|
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variable T_depart equal 300
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variable dt equal 0.0002
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# =======================================================================
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units metal
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atom_style charge
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dimension 3
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boundary p p p
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read_data data.Alpha
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# ^ Orthorombic box of corundum strcture
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mass 1 16.00
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group Oxy type 1
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compute chargeOxy Oxy property/atom q
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compute q_Oxy Oxy reduce ave c_chargeOxy
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mass 2 26.98
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group Al type 2
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compute chargeAl Al property/atom q
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compute q_Al Al reduce ave c_chargeAl
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velocity all create ${T_depart} 277387
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pair_style smtbq
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pair_coeff * * ffield.smtbq.Al2O3 O Al
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neighbor 0.5 bin
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neigh_modify every 20 delay 0 check yes
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timestep ${dt}
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thermo_style custom step temp press pe ke etotal c_q_Al c_q_Oxy lx ly lz vol
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thermo_modify flush yes
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thermo 1
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#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
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fix 3 all nve
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run 10
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unfix 3
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thermo 1
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fix 1 all box/relax tri 0.0 vmax 0.001
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minimize 1.0e-3 1.0e-5 1000 10000
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unfix 1
|
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thermo 1
|
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fix 3 all nve
|
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run 10
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@ -0,0 +1,97 @@
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# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
|
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|
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variable T_depart equal 300
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|
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variable dt equal 0.0002
|
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variable a equal 4.5937
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variable c equal 2.9587
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variable ca equal ${c}/${a}
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variable nx equal 6
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variable ny equal 6
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variable nz equal 11
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variable bx equal ${a}*${nx}
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variable by equal ${a}*${ny}
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variable bz equal ${c}*${nz}
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# =======================================================================
|
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|
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units metal
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atom_style charge
|
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dimension 3
|
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boundary p p p
|
||||
|
||||
|
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lattice sc 1.0
|
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region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
|
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create_box 2 box_vide
|
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|
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#lattice sc 1.0
|
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#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz}
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|
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# titanium atoms
|
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lattice custom ${a} origin 0.0 0.0 0.0 &
|
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orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 &
|
||||
a1 1.0 0.0 0.0 &
|
||||
a2 0.0 1.0 0.0 &
|
||||
a3 0.0 0.0 ${ca} &
|
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basis 0.0 0.0 0.0 &
|
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basis 0.5 0.5 0.5
|
||||
|
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create_atoms 2 region box_vide
|
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|
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# Oxygen atoms
|
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lattice custom ${a} origin 0.0 0.0 0.0 &
|
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orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 &
|
||||
a1 1.0 0.0 0.0 &
|
||||
a2 0.0 1.0 0.0 &
|
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a3 0.0 0.0 ${ca} &
|
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basis 0.30478 0.30478 0.0 &
|
||||
basis 0.69522 0.69522 0.0 &
|
||||
basis 0.19522 0.80478 0.5 &
|
||||
basis 0.80478 0.19522 0.5
|
||||
|
||||
create_atoms 1 region box_vide
|
||||
|
||||
|
||||
mass 1 16.00
|
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group Oxy type 1
|
||||
compute chargeOxy Oxy property/atom q
|
||||
compute q_Oxy Oxy reduce ave c_chargeOxy
|
||||
|
||||
mass 2 47.867
|
||||
group Ti type 2
|
||||
compute chargeTi Ti property/atom q
|
||||
compute q_Ti Ti reduce ave c_chargeTi
|
||||
|
||||
velocity all create ${T_depart} 277387
|
||||
|
||||
pair_style smtbq
|
||||
pair_coeff * * ffield.smtbq.TiO2 O Ti
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 20 delay 0 check yes
|
||||
|
||||
timestep ${dt}
|
||||
|
||||
thermo_style custom step temp press pe ke etotal c_q_Ti c_q_Oxy lx ly lz vol
|
||||
thermo_modify flush yes
|
||||
thermo 1
|
||||
|
||||
|
||||
#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
|
||||
|
||||
fix 3 all nve
|
||||
run 10
|
||||
|
||||
unfix 3
|
||||
#thermo 15
|
||||
fix 1 all box/relax tri 0.0 vmax 0.001
|
||||
minimize 1.0e-3 1.0e-5 1000 10000
|
||||
|
||||
unfix 1
|
||||
thermo 1
|
||||
fix 3 all nve
|
||||
run 10
|
||||
|
||||
|
|
@ -0,0 +1,279 @@
|
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LAMMPS (23 Oct 2015)
|
||||
# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
|
||||
|
||||
variable T_depart equal 300
|
||||
variable dt equal 0.0002
|
||||
|
||||
#Constante
|
||||
variable rac3 equal sqrt(3.0)
|
||||
variable rac1_2 equal sqrt(0.5)
|
||||
variable rac3_2 equal sqrt(1.5)
|
||||
|
||||
#Structure
|
||||
variable a equal 4.05
|
||||
|
||||
variable nx equal 10
|
||||
variable ny equal 7
|
||||
variable nz equal 4
|
||||
|
||||
variable bx equal ${a}*${nx}*${rac1_2}
|
||||
variable bx equal 4.05*${nx}*${rac1_2}
|
||||
variable bx equal 4.05*10*${rac1_2}
|
||||
variable bx equal 4.05*10*0.707106781186548
|
||||
variable by equal ${a}*${ny}*${rac3_2}
|
||||
variable by equal 4.05*${ny}*${rac3_2}
|
||||
variable by equal 4.05*7*${rac3_2}
|
||||
variable by equal 4.05*7*1.22474487139159
|
||||
variable bz equal ${a}*${nz}*${rac3}
|
||||
variable bz equal 4.05*${nz}*${rac3}
|
||||
variable bz equal 4.05*4*${rac3}
|
||||
variable bz equal 4.05*4*1.73205080756888
|
||||
# =======================================================================
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
|
||||
lattice sc 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
|
||||
region box_vide prism 0 28.6378246380552 0 ${by} 0 ${bz} 0.0 0.0 0.0
|
||||
region box_vide prism 0 28.6378246380552 0 34.7215171039516 0 ${bz} 0.0 0.0 0.0
|
||||
region box_vide prism 0 28.6378246380552 0 34.7215171039516 0 28.0592230826159 0.0 0.0 0.0
|
||||
create_box 1 box_vide
|
||||
Created triclinic box = (0 0 0) to (28.6378 34.7215 28.0592) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
# Aluminium atoms z = [111]
|
||||
lattice custom ${a} a1 ${rac1_2} 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
|
||||
lattice custom 4.05 a1 ${rac1_2} 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
|
||||
lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 ${rac3_2} 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
|
||||
lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 1.22474487139159 0.0 a3 0.0 0.0 ${rac3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
|
||||
lattice custom 4.05 a1 0.707106781186548 0.0 0.0 a2 0.0 1.22474487139159 0.0 a3 0.0 0.0 1.73205080756888 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0 basis 0.5 0.166666667 0.33333 basis 0.0 0.666666667 0.33333 basis 0.0 0.333333333 0.66667 basis 0.5 0.833333333 0.66667
|
||||
Lattice spacing in x,y,z = 2.86378 4.96022 7.01481
|
||||
|
||||
create_atoms 1 region box_vide
|
||||
Created 1680 atoms
|
||||
|
||||
mass 1 26.98
|
||||
|
||||
velocity all create ${T_depart} 277387
|
||||
velocity all create 300 277387
|
||||
|
||||
pair_style smtbq
|
||||
pair_coeff * * ffield.smtbq.Al Al
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 20 delay 0 check yes
|
||||
|
||||
timestep ${dt}
|
||||
timestep 0.0002
|
||||
|
||||
thermo_style custom step temp press pe ke etotal lx ly lz vol
|
||||
thermo_modify flush yes
|
||||
thermo 1
|
||||
|
||||
|
||||
#dump 5 all custom 1 box_Al.lammpstrj id type q x y z
|
||||
|
||||
fix 3 all nve
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 20 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.6714
|
||||
ghost atom cutoff = 11.6714
|
||||
binsize = 5.8357 -> bins = 5 6 5
|
||||
Memory usage per processor = 4.52298 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
|
||||
0 300 729.26605 -5600.8541 65.108335 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
1 299.98323 729.90439 -5600.8505 65.104695 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
2 299.93288 731.82072 -5600.8395 65.093767 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
3 299.84896 735.01448 -5600.8213 65.075556 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
4 299.7315 739.48472 -5600.7958 65.050064 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
5 299.58053 745.23012 -5600.7631 65.017299 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
6 299.39609 752.24896 -5600.723 64.977269 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
7 299.17822 760.5391 -5600.6757 64.929985 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
8 298.92698 770.098 -5600.6212 64.875459 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
9 298.64244 780.92261 -5600.5595 64.813707 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
10 298.32468 793.00943 -5600.4905 64.744743 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
Loop time of 5.10336 on 1 procs for 10 steps with 1680 atoms
|
||||
|
||||
Performance: 0.034 ns/day, 708.800 hours/ns, 1.959 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.1023 | 5.1023 | 5.1023 | 0.0 | 99.98
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00045538 | 0.00045538 | 0.00045538 | 0.0 | 0.01
|
||||
Output | 0.00024509 | 0.00024509 | 0.00024509 | 0.0 | 0.00
|
||||
Modify | 0.00026131 | 0.00026131 | 0.00026131 | 0.0 | 0.01
|
||||
Other | | 0.0001056 | | | 0.00
|
||||
|
||||
Nlocal: 1680 ave 1680 max 1680 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7518 ave 7518 max 7518 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 638400 ave 638400 max 638400 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 638400
|
||||
Ave neighs/atom = 380
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
#thermo 15
|
||||
fix 1 all box/relax tri 0.0 vmax 0.001
|
||||
minimize 1.0e-8 1.0e-10 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.6714
|
||||
ghost atom cutoff = 11.6714
|
||||
binsize = 5.8357 -> bins = 5 6 5
|
||||
Memory usage per processor = 5.64798 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
|
||||
10 298.32468 793.00943 -5600.4905 64.744743 -5535.7458 28.637825 34.721517 28.059223 27900.653
|
||||
11 298.32468 2483.3228 -5600.5212 64.744743 -5535.7764 28.617938 34.697425 28.039771 27842.617
|
||||
12 298.32468 3102.6624 -5600.6242 64.744743 -5535.8795 28.594201 34.68783 28.048729 27820.715
|
||||
13 298.32468 1681.0688 -5600.6477 64.744743 -5535.903 28.619779 34.708131 28.055945 27869.065
|
||||
14 298.32468 949.90841 -5600.6635 64.744743 -5535.9187 28.648416 34.718691 28.044409 27893.966
|
||||
15 298.32468 2009.1662 -5600.7072 64.744743 -5535.9625 28.652241 34.703261 28.01635 27857.391
|
||||
16 298.32468 2867.1434 -5600.7192 64.744743 -5535.9744 28.626861 34.69005 28.022309 27828.038
|
||||
17 298.32468 2480.3207 -5600.7238 64.744743 -5535.9791 28.618046 34.695106 28.040113 27841.2
|
||||
18 298.32468 2482.4906 -5600.7249 64.744743 -5535.9802 28.614169 34.704237 28.036452 27841.119
|
||||
19 298.32468 2495.6209 -5600.7261 64.744743 -5535.9813 28.616207 34.697481 28.039453 27840.662
|
||||
20 298.32468 2210.2897 -5600.7271 64.744743 -5535.9823 28.620852 34.699678 28.042926 27850.393
|
||||
21 298.32468 2464.137 -5600.734 64.744743 -5535.9893 28.625239 34.687085 28.040022 27841.67
|
||||
22 298.32468 3091.7034 -5600.7471 64.744743 -5536.0024 28.623565 34.674943 28.02983 27820.181
|
||||
23 298.32468 2334.9443 -5600.7598 64.744743 -5536.0151 28.634413 34.684598 28.037298 27845.891
|
||||
24 298.32468 2462.2836 -5600.7767 64.744743 -5536.032 28.615834 34.692433 28.044664 27841.422
|
||||
25 298.32468 2652.08 -5600.7914 64.744743 -5536.0466 28.61528 34.695645 28.035991 27834.85
|
||||
26 298.32468 2365.4126 -5600.7923 64.744743 -5536.0476 28.618526 34.699347 28.039662 27844.623
|
||||
27 298.32468 2334.9429 -5600.7934 64.744743 -5536.0486 28.61826 34.698136 28.041941 27845.656
|
||||
28 298.32468 2501.1598 -5600.7937 64.744743 -5536.0489 28.616356 34.695993 28.039825 27839.982
|
||||
29 298.32468 2506.0962 -5600.794 64.744743 -5536.0493 28.617255 34.699031 28.036317 27839.811
|
||||
30 298.32468 2400.7588 -5600.7942 64.744743 -5536.0495 28.618372 34.698464 28.039299 27843.404
|
||||
31 298.32468 2499.8528 -5600.7945 64.744743 -5536.0497 28.61702 34.69385 28.040945 27840.021
|
||||
32 298.32468 2629.5393 -5600.7967 64.744743 -5536.0519 28.619399 34.691546 28.036003 27835.58
|
||||
33 298.32468 2397.5939 -5600.7973 64.744743 -5536.0526 28.621863 34.69535 28.03848 27843.488
|
||||
34 298.32468 2222.7714 -5600.8007 64.744743 -5536.056 28.609815 34.705091 28.048395 27849.426
|
||||
35 298.32468 2748.5871 -5600.8042 64.744743 -5536.0594 28.600322 34.6998 28.043876 27831.457
|
||||
36 298.32468 2661.1018 -5600.8166 64.744743 -5536.0719 28.615123 34.696499 28.034947 27834.344
|
||||
37 298.32468 2255.4994 -5600.8185 64.744743 -5536.0737 28.618919 34.702261 28.040497 27848.173
|
||||
38 298.32468 2260.815 -5600.8239 64.744743 -5536.0791 28.614993 34.70246 28.043972 27847.962
|
||||
39 298.32468 2549.2876 -5600.8248 64.744743 -5536.0801 28.612892 34.697988 28.039725 27838.113
|
||||
40 298.32468 2488.3825 -5600.8266 64.744743 -5536.0819 28.623347 34.695524 28.033557 27840.182
|
||||
41 298.32468 2400.9714 -5600.8283 64.744743 -5536.0835 28.619176 34.695733 28.040468 27843.155
|
||||
42 298.32468 2496.6566 -5600.8284 64.744743 -5536.0837 28.617629 34.694692 28.039536 27839.89
|
||||
43 298.32468 2486.2773 -5600.8285 64.744743 -5536.0838 28.617585 34.697413 28.037736 27840.243
|
||||
44 298.32468 2446.3916 -5600.8287 64.744743 -5536.0839 28.617115 34.696389 28.040393 27841.603
|
||||
45 298.32468 2547.2311 -5600.8288 64.744743 -5536.0841 28.615267 34.694882 28.039956 27838.161
|
||||
46 298.32468 2479.9982 -5600.8321 64.744743 -5536.0874 28.603008 34.71581 28.037344 27840.427
|
||||
47 298.32468 2449.645 -5600.8444 64.744743 -5536.0997 28.612743 34.683541 28.054837 27841.375
|
||||
48 298.32468 2682.7109 -5600.8695 64.744743 -5536.1248 28.617414 34.683477 28.042139 27833.265
|
||||
49 298.32468 2350.1707 -5600.8711 64.744743 -5536.1263 28.619236 34.694213 28.043092 27844.6
|
||||
50 298.32468 2486.1481 -5600.8719 64.744743 -5536.1271 28.615167 34.699435 28.038181 27839.955
|
||||
51 298.32468 2498.3384 -5600.8721 64.744743 -5536.1274 28.616069 34.696071 28.039596 27839.537
|
||||
52 298.32468 2443.1247 -5600.8722 64.744743 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
Loop time of 36.9389 on 1 procs for 42 steps with 1680 atoms
|
||||
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-5600.49050006 -5600.87213771 -5600.87218615
|
||||
Force two-norm initial, final = 50.879 1.39888
|
||||
Force max component initial, final = 29.3783 0.749036
|
||||
Final line search alpha, max atom move = 0.0013373 0.00100168
|
||||
Iterations, force evaluations = 42 71
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 36.918 | 36.918 | 36.918 | 0.0 | 99.94
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0033035 | 0.0033035 | 0.0033035 | 0.0 | 0.01
|
||||
Output | 0.0011785 | 0.0011785 | 0.0011785 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.01603 | | | 0.04
|
||||
|
||||
Nlocal: 1680 ave 1680 max 1680 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7518 ave 7518 max 7518 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 638400 ave 638400 max 638400 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 638400
|
||||
Ave neighs/atom = 380
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
thermo 1
|
||||
fix 3 all nve
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 20 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.6714
|
||||
ghost atom cutoff = 11.6714
|
||||
binsize = 5.8357 -> bins = 5 6 5
|
||||
Memory usage per processor = 4.52298 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng Lx Ly Lz Volume
|
||||
52 298.32468 2443.1247 -5600.8722 64.744743 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
53 298.28341 2444.4342 -5600.8632 64.735788 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
54 298.20852 2447.019 -5600.847 64.719534 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
55 298.1 2450.8786 -5600.8234 64.695982 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
56 297.95788 2456.0119 -5600.7926 64.665139 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
57 297.7822 2462.4173 -5600.7545 64.62701 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
58 297.57298 2470.0928 -5600.709 64.581604 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
59 297.33028 2479.0363 -5600.6564 64.528932 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
60 297.05416 2489.245 -5600.5964 64.469006 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
61 296.74469 2500.7159 -5600.5293 64.401842 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
62 296.40194 2513.4457 -5600.4549 64.327455 -5536.1274 28.617616 34.696737 28.039439 27841.421
|
||||
Loop time of 5.13028 on 1 procs for 10 steps with 1680 atoms
|
||||
|
||||
Performance: 0.034 ns/day, 712.539 hours/ns, 1.949 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 5.1292 | 5.1292 | 5.1292 | 0.0 | 99.98
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00045729 | 0.00045729 | 0.00045729 | 0.0 | 0.01
|
||||
Output | 0.00024509 | 0.00024509 | 0.00024509 | 0.0 | 0.00
|
||||
Modify | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.01
|
||||
Other | | 0.0001016 | | | 0.00
|
||||
|
||||
Nlocal: 1680 ave 1680 max 1680 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 7518 ave 7518 max 7518 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 638400 ave 638400 max 638400 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 638400
|
||||
Ave neighs/atom = 380
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:49
|
||||
|
|
@ -0,0 +1,210 @@
|
|||
LAMMPS (23 Oct 2015)
|
||||
# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
|
||||
|
||||
variable T_depart equal 300
|
||||
|
||||
variable dt equal 0.0002
|
||||
|
||||
# =======================================================================
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
read_data data.Alpha
|
||||
triclinic box = (0 0 0) to (23.769 24.7015 25.9564) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1800 atoms
|
||||
# ^ Orthorombic box of corundum strcture
|
||||
|
||||
mass 1 16.00
|
||||
group Oxy type 1
|
||||
1080 atoms in group Oxy
|
||||
compute chargeOxy Oxy property/atom q
|
||||
compute q_Oxy Oxy reduce ave c_chargeOxy
|
||||
|
||||
mass 2 26.98
|
||||
group Al type 2
|
||||
720 atoms in group Al
|
||||
compute chargeAl Al property/atom q
|
||||
compute q_Al Al reduce ave c_chargeAl
|
||||
|
||||
velocity all create ${T_depart} 277387
|
||||
velocity all create 300 277387
|
||||
|
||||
pair_style smtbq
|
||||
pair_coeff * * ffield.smtbq.Al2O3 O Al
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 20 delay 0 check yes
|
||||
|
||||
timestep ${dt}
|
||||
timestep 0.0002
|
||||
|
||||
thermo_style custom step temp press pe ke etotal c_q_Al c_q_Oxy lx ly lz vol
|
||||
thermo_modify flush yes
|
||||
thermo 1
|
||||
|
||||
|
||||
#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
|
||||
|
||||
fix 3 all nve
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 20 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.6714
|
||||
ghost atom cutoff = 11.6714
|
||||
binsize = 5.8357 -> bins = 5 5 5
|
||||
Memory usage per processor = 4.12573 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
|
||||
0 300 91921.482 -11494.543 69.7617 -11424.781 2.6095997 -1.7397331 23.769 24.7015 25.9564 15239.78
|
||||
1 299.96467 91922.303 -11494.535 69.753485 -11424.781 2.6095996 -1.739733 23.769 24.7015 25.9564 15239.78
|
||||
2 299.75126 91933.246 -11494.485 69.703859 -11424.781 2.6095978 -1.7397318 23.769 24.7015 25.9564 15239.78
|
||||
3 299.36045 91954.835 -11494.394 69.61298 -11424.781 2.6095941 -1.7397294 23.769 24.7015 25.9564 15239.78
|
||||
4 298.79335 91986.343 -11494.262 69.481107 -11424.781 2.6095886 -1.7397257 23.769 24.7015 25.9564 15239.78
|
||||
5 298.05151 92027.62 -11494.09 69.3086 -11424.781 2.6095812 -1.7397208 23.769 24.7015 25.9564 15239.78
|
||||
6 297.13689 92078.615 -11493.877 69.095915 -11424.781 2.6095721 -1.7397147 23.769 24.7015 25.9564 15239.78
|
||||
7 296.05187 92139.141 -11493.625 68.843606 -11424.781 2.6095613 -1.7397075 23.769 24.7015 25.9564 15239.78
|
||||
8 294.79923 92209.15 -11493.334 68.552319 -11424.781 2.6095488 -1.7396992 23.769 24.7015 25.9564 15239.78
|
||||
9 293.38215 92288.12 -11493.004 68.222793 -11424.781 2.6095347 -1.7396898 23.769 24.7015 25.9564 15239.78
|
||||
10 291.80421 92376.81 -11492.637 67.855859 -11424.781 2.6095191 -1.7396794 23.769 24.7015 25.9564 15239.78
|
||||
Loop time of 169.694 on 1 procs for 10 steps with 1800 atoms
|
||||
|
||||
Performance: 0.001 ns/day, 23568.600 hours/ns, 0.059 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 169.69 | 169.69 | 169.69 | 0.0 |100.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00075507 | 0.00075507 | 0.00075507 | 0.0 | 0.00
|
||||
Output | 0.00078607 | 0.00078607 | 0.00078607 | 0.0 | 0.00
|
||||
Modify | 0.00034666 | 0.00034666 | 0.00034666 | 0.0 | 0.00
|
||||
Other | | 0.0001752 | | | 0.00
|
||||
|
||||
Nlocal: 1800 ave 1800 max 1800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11490 ave 11490 max 11490 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.4472e+06 ave 1.4472e+06 max 1.4472e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1447200
|
||||
Ave neighs/atom = 804
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
thermo 1
|
||||
fix 1 all box/relax tri 0.0 vmax 0.001
|
||||
minimize 1.0e-3 1.0e-5 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.6714
|
||||
ghost atom cutoff = 11.6714
|
||||
binsize = 5.8357 -> bins = 5 5 5
|
||||
Memory usage per processor = 5.50073 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
|
||||
10 291.80421 92376.81 -11492.637 67.855859 -11424.781 2.6095191 -1.7396794 23.769 24.7015 25.9564 15239.78
|
||||
11 291.80421 84416.246 -11494.722 67.855859 -11426.866 2.6087748 -1.7391832 23.787835 24.721015 25.982356 15279.17
|
||||
Loop time of 25.4145 on 1 procs for 1 steps with 1800 atoms
|
||||
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-11492.6369832 -11492.6369832 -11494.7221261
|
||||
Force two-norm initial, final = 1453.27 1325.26
|
||||
Force max component initial, final = 968.201 892.249
|
||||
Final line search alpha, max atom move = 1.03284e-06 0.000921553
|
||||
Iterations, force evaluations = 1 1
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 25.414 | 25.414 | 25.414 | -nan |100.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00013995 | 0.00013995 | 0.00013995 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0005064 | | | 0.00
|
||||
|
||||
Nlocal: 1800 ave 1800 max 1800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11408 ave 11408 max 11408 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.44456e+06 ave 1.44456e+06 max 1.44456e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1444562
|
||||
Ave neighs/atom = 802.534
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
thermo 1
|
||||
fix 3 all nve
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 20 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 11.6714
|
||||
ghost atom cutoff = 11.6714
|
||||
binsize = 5.8357 -> bins = 5 5 5
|
||||
Memory usage per processor = 4.37573 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng q_Al q_Oxy Lx Ly Lz Volume
|
||||
11 291.80421 84416.246 -11494.722 67.855859 -11426.866 2.6087748 -1.7391832 23.787835 24.721015 25.982356 15279.17
|
||||
12 290.08293 84514.767 -11494.322 67.455594 -11426.866 2.6087578 -1.7391718 23.787835 24.721015 25.982356 15279.17
|
||||
13 288.21041 84622.406 -11493.886 67.020161 -11426.866 2.6087394 -1.7391596 23.787835 24.721015 25.982356 15279.17
|
||||
14 286.19128 84738.689 -11493.417 66.550634 -11426.866 2.6087199 -1.7391466 23.787835 24.721015 25.982356 15279.17
|
||||
15 284.03049 84864.242 -11492.914 66.048166 -11426.866 2.6086993 -1.7391329 23.787835 24.721015 25.982356 15279.17
|
||||
16 281.73331 84998.125 -11492.38 65.513983 -11426.866 2.6086776 -1.7391184 23.787835 24.721015 25.982356 15279.17
|
||||
17 279.30534 85140.233 -11491.815 64.949384 -11426.866 2.6086551 -1.7391034 23.787835 24.721015 25.982356 15279.17
|
||||
18 276.75244 85290.405 -11491.221 64.355737 -11426.866 2.6086319 -1.7390879 23.787835 24.721015 25.982356 15279.17
|
||||
19 274.08079 85448.449 -11490.6 63.734472 -11426.866 2.608608 -1.739072 23.787835 24.721015 25.982356 15279.17
|
||||
20 271.29678 85614.064 -11489.953 63.087082 -11426.866 2.6085837 -1.7390558 23.787835 24.721015 25.982356 15279.17
|
||||
21 268.40708 85786.72 -11489.281 62.415114 -11426.865 2.608559 -1.7390393 23.787835 24.721015 25.982356 15279.17
|
||||
Loop time of 170.699 on 1 procs for 10 steps with 1800 atoms
|
||||
|
||||
Performance: 0.001 ns/day, 23708.143 hours/ns, 0.059 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 170.7 | 170.7 | 170.7 | 0.0 |100.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00068879 | 0.00068879 | 0.00068879 | 0.0 | 0.00
|
||||
Output | 0.0008359 | 0.0008359 | 0.0008359 | 0.0 | 0.00
|
||||
Modify | 0.00031424 | 0.00031424 | 0.00031424 | 0.0 | 0.00
|
||||
Other | | 0.0001593 | | | 0.00
|
||||
|
||||
Nlocal: 1800 ave 1800 max 1800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11222 ave 11222 max 11222 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.44126e+06 ave 1.44126e+06 max 1.44126e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1441262
|
||||
Ave neighs/atom = 800.701
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:06:42
|
||||
|
|
@ -0,0 +1,255 @@
|
|||
LAMMPS (23 Oct 2015)
|
||||
# Al2O3 crystal, qeq on, minimizes, then calculates elastic constants
|
||||
|
||||
variable T_depart equal 300
|
||||
|
||||
variable dt equal 0.0002
|
||||
|
||||
variable a equal 4.5937
|
||||
variable c equal 2.9587
|
||||
variable ca equal ${c}/${a}
|
||||
variable ca equal 2.9587/${a}
|
||||
variable ca equal 2.9587/4.5937
|
||||
|
||||
variable nx equal 6
|
||||
variable ny equal 6
|
||||
variable nz equal 11
|
||||
|
||||
variable bx equal ${a}*${nx}
|
||||
variable bx equal 4.5937*${nx}
|
||||
variable bx equal 4.5937*6
|
||||
variable by equal ${a}*${ny}
|
||||
variable by equal 4.5937*${ny}
|
||||
variable by equal 4.5937*6
|
||||
variable bz equal ${c}*${nz}
|
||||
variable bz equal 2.9587*${nz}
|
||||
variable bz equal 2.9587*11
|
||||
# =======================================================================
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
|
||||
lattice sc 1.0
|
||||
Lattice spacing in x,y,z = 1 1 1
|
||||
region box_vide prism 0 ${bx} 0 ${by} 0 ${bz} 0.0 0.0 0.0
|
||||
region box_vide prism 0 27.5622 0 ${by} 0 ${bz} 0.0 0.0 0.0
|
||||
region box_vide prism 0 27.5622 0 27.5622 0 ${bz} 0.0 0.0 0.0
|
||||
region box_vide prism 0 27.5622 0 27.5622 0 32.5457 0.0 0.0 0.0
|
||||
create_box 2 box_vide
|
||||
Created triclinic box = (0 0 0) to (27.5622 27.5622 32.5457) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
#lattice sc 1.0
|
||||
#region box_TiO2 block 0 ${bx} 0 ${by} 0 ${bz}
|
||||
|
||||
# titanium atoms
|
||||
lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
|
||||
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
|
||||
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.0 0.0 0.0 basis 0.5 0.5 0.5
|
||||
Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
|
||||
|
||||
create_atoms 2 region box_vide
|
||||
Created 792 atoms
|
||||
|
||||
# Oxygen atoms
|
||||
lattice custom ${a} origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
|
||||
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 ${ca} basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
|
||||
lattice custom 4.5937 origin 0.0 0.0 0.0 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 0.644077758669482 basis 0.30478 0.30478 0.0 basis 0.69522 0.69522 0.0 basis 0.19522 0.80478 0.5 basis 0.80478 0.19522 0.5
|
||||
Lattice spacing in x,y,z = 4.5937 4.5937 2.9587
|
||||
|
||||
create_atoms 1 region box_vide
|
||||
Created 1584 atoms
|
||||
|
||||
|
||||
mass 1 16.00
|
||||
group Oxy type 1
|
||||
1584 atoms in group Oxy
|
||||
compute chargeOxy Oxy property/atom q
|
||||
compute q_Oxy Oxy reduce ave c_chargeOxy
|
||||
|
||||
mass 2 47.867
|
||||
group Ti type 2
|
||||
792 atoms in group Ti
|
||||
compute chargeTi Ti property/atom q
|
||||
compute q_Ti Ti reduce ave c_chargeTi
|
||||
|
||||
velocity all create ${T_depart} 277387
|
||||
velocity all create 300 277387
|
||||
|
||||
pair_style smtbq
|
||||
pair_coeff * * ffield.smtbq.TiO2 O Ti
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 20 delay 0 check yes
|
||||
|
||||
timestep ${dt}
|
||||
timestep 0.0002
|
||||
|
||||
thermo_style custom step temp press pe ke etotal c_q_Ti c_q_Oxy lx ly lz vol
|
||||
thermo_modify flush yes
|
||||
thermo 1
|
||||
|
||||
|
||||
#dump 5 all custom 500 boxAlpha_alumina.lammpstrj id type q x y z
|
||||
|
||||
fix 3 all nve
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 20 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.6744
|
||||
ghost atom cutoff = 12.6744
|
||||
binsize = 6.3372 -> bins = 5 5 6
|
||||
Memory usage per processor = 4.77264 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
|
||||
0 300 44365.066 -15815.239 92.097853 -15723.142 2.5521775 -1.2760888 27.5622 27.5622 32.5457 24724.15
|
||||
1 299.90455 44375.373 -15815.21 92.06855 -15723.142 2.552178 -1.276089 27.5622 27.5622 32.5457 24724.15
|
||||
2 299.63739 44392.241 -15815.128 91.986534 -15723.142 2.5521725 -1.2760863 27.5622 27.5622 32.5457 24724.15
|
||||
3 299.19899 44415.606 -15814.994 91.85195 -15723.142 2.5521616 -1.2760808 27.5622 27.5622 32.5457 24724.15
|
||||
4 298.59012 44445.345 -15814.808 91.665031 -15723.143 2.5521454 -1.2760727 27.5622 27.5622 32.5457 24724.15
|
||||
5 297.81185 44481.382 -15814.57 91.426105 -15723.144 2.5521238 -1.2760619 27.5622 27.5622 32.5457 24724.15
|
||||
6 296.86552 44523.683 -15814.28 91.135592 -15723.144 2.5520969 -1.2760484 27.5622 27.5622 32.5457 24724.15
|
||||
7 295.75281 44572.175 -15813.939 90.793996 -15723.145 2.5520648 -1.2760324 27.5622 27.5622 32.5457 24724.15
|
||||
8 294.47564 44626.778 -15813.548 90.401913 -15723.147 2.5520274 -1.2760137 27.5622 27.5622 32.5457 24724.15
|
||||
9 293.03623 44687.401 -15813.108 89.960027 -15723.148 2.5519849 -1.2759925 27.5622 27.5622 32.5457 24724.15
|
||||
10 291.43711 44753.932 -15812.618 89.469107 -15723.149 2.5519374 -1.2759687 27.5622 27.5622 32.5457 24724.15
|
||||
Loop time of 570.52 on 1 procs for 10 steps with 2376 atoms
|
||||
|
||||
Performance: 0.000 ns/day, 79238.948 hours/ns, 0.018 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 570.52 | 570.52 | 570.52 | 0.0 |100.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00087428 | 0.00087428 | 0.00087428 | 0.0 | 0.00
|
||||
Output | 0.00091386 | 0.00091386 | 0.00091386 | 0.0 | 0.00
|
||||
Modify | 0.00045085 | 0.00045085 | 0.00045085 | 0.0 | 0.00
|
||||
Other | | 0.0001979 | | | 0.00
|
||||
|
||||
Nlocal: 2376 ave 2376 max 2376 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 13138 ave 13138 max 13138 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.9705e+06 ave 1.9705e+06 max 1.9705e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1970496
|
||||
Ave neighs/atom = 829.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
#thermo 15
|
||||
fix 1 all box/relax tri 0.0 vmax 0.001
|
||||
minimize 1.0e-3 1.0e-5 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168)
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.6744
|
||||
ghost atom cutoff = 12.6744
|
||||
binsize = 6.3372 -> bins = 5 5 6
|
||||
Memory usage per processor = 6.14764 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
|
||||
10 291.43711 44753.932 -15812.618 89.469107 -15723.149 2.5519374 -1.2759687 27.5622 27.5622 32.5457 24724.15
|
||||
11 291.43711 39000.467 -15814.109 89.469107 -15724.639 2.5514249 -1.2757124 27.582771 27.582775 32.578246 24785.834
|
||||
Loop time of 80.5411 on 1 procs for 1 steps with 2376 atoms
|
||||
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-15812.6183471 -15812.6183471 -15814.1085593
|
||||
Force two-norm initial, final = 1104.2 951.386
|
||||
Force max component initial, final = 759.352 657.815
|
||||
Final line search alpha, max atom move = 1.31691e-06 0.000866285
|
||||
Iterations, force evaluations = 1 1
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 80.54 | 80.54 | 80.54 | 0.0 |100.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00016761 | 0.00016761 | 0.00016761 | 0.0 | 0.00
|
||||
Output | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0006053 | | | 0.00
|
||||
|
||||
Nlocal: 2376 ave 2376 max 2376 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 13138 ave 13138 max 13138 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.96864e+06 ave 1.96864e+06 max 1.96864e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1968636
|
||||
Ave neighs/atom = 828.551
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
thermo 1
|
||||
fix 3 all nve
|
||||
run 10
|
||||
Neighbor list info ...
|
||||
1 neighbor list requests
|
||||
update every 20 steps, delay 0 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12.6744
|
||||
ghost atom cutoff = 12.6744
|
||||
binsize = 6.3372 -> bins = 5 5 6
|
||||
Memory usage per processor = 5.02264 Mbytes
|
||||
Step Temp Press PotEng KinEng TotEng q_Ti q_Oxy Lx Ly Lz Volume
|
||||
11 291.43711 39000.467 -15814.109 89.469107 -15724.639 2.5514249 -1.2757124 27.582771 27.582775 32.578246 24785.834
|
||||
12 289.69465 39072.309 -15813.575 88.934185 -15724.641 2.551372 -1.275686 27.582771 27.582775 32.578246 24785.834
|
||||
13 287.79928 39149.855 -15812.994 88.352321 -15724.642 2.5513146 -1.2756573 27.582771 27.582775 32.578246 24785.834
|
||||
14 285.75427 39232.968 -15812.368 87.724515 -15724.644 2.5512525 -1.2756262 27.582771 27.582775 32.578246 24785.834
|
||||
15 283.56312 39321.472 -15811.697 87.05185 -15724.645 2.5511856 -1.2755928 27.582771 27.582775 32.578246 24785.834
|
||||
16 281.22962 39415.185 -15810.983 86.335481 -15724.647 2.5511143 -1.2755571 27.582771 27.582775 32.578246 24785.834
|
||||
17 278.75777 39513.921 -15810.226 85.57664 -15724.649 2.5510384 -1.2755192 27.582771 27.582775 32.578246 24785.834
|
||||
18 276.15182 39617.471 -15809.428 84.776632 -15724.651 2.5509583 -1.2754791 27.582771 27.582775 32.578246 24785.834
|
||||
19 273.41625 39725.622 -15808.591 83.936831 -15724.654 2.5508739 -1.275437 27.582771 27.582775 32.578246 24785.834
|
||||
20 270.55575 39838.144 -15807.715 83.058679 -15724.656 2.5507855 -1.2753928 27.582771 27.582775 32.578246 24785.834
|
||||
21 267.57523 39954.804 -15806.802 82.14368 -15724.659 2.5506932 -1.2753466 27.582771 27.582775 32.578246 24785.834
|
||||
Loop time of 606.774 on 1 procs for 10 steps with 2376 atoms
|
||||
|
||||
Performance: 0.000 ns/day, 84274.222 hours/ns, 0.016 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 606.77 | 606.77 | 606.77 | 0.0 |100.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00085855 | 0.00085855 | 0.00085855 | 0.0 | 0.00
|
||||
Output | 0.00087833 | 0.00087833 | 0.00087833 | 0.0 | 0.00
|
||||
Modify | 0.00041723 | 0.00041723 | 0.00041723 | 0.0 | 0.00
|
||||
Other | | 0.0001888 | | | 0.00
|
||||
|
||||
Nlocal: 2376 ave 2376 max 2376 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 13138 ave 13138 max 13138 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.96049e+06 ave 1.96049e+06 max 1.96049e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1960492
|
||||
Ave neighs/atom = 825.123
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:23:48
|
||||
Loading…
Reference in New Issue