diff --git a/examples/latte/data.ch4 b/examples/latte/data.ch4 new file mode 100644 index 0000000000..fc8d48d244 --- /dev/null +++ b/examples/latte/data.ch4 @@ -0,0 +1,23 @@ + LAMMPS Description + + 5 atoms + + 2 atom types + + 0.0000000000000000 19.523000000000000 xlo xhi + 0.0000000000000000 12.757999999999999 ylo yhi + 0.0000000000000000 11.692000000000000 zlo zhi + 0.0000000000000000 0.0000000000000000 0.0000000000000000 xy xz yz + + Masses + + 1 12.010000000000000 + 2 1.0078250169754028 + + Atoms + + 1 1 1 0.0 -9.16600 2.05200 0.00000 + 2 1 2 0.0 -8.09600 2.05200 0.00000 + 3 1 2 0.0 -9.52300 2.75800 -0.72000 + 4 1 2 0.0 -9.52300 2.32200 0.97200 + 5 1 2 0.0 -9.52300 1.07500 -0.25200 diff --git a/examples/latte/data.graphene.boxrel b/examples/latte/data.graphene similarity index 100% rename from examples/latte/data.graphene.boxrel rename to examples/latte/data.graphene diff --git a/examples/latte/in.graphene.boxrel b/examples/latte/in.graphene.boxrel index 876dedd2b1..721b7f014f 100644 --- a/examples/latte/in.graphene.boxrel +++ b/examples/latte/in.graphene.boxrel @@ -4,7 +4,7 @@ units metal atom_style full atom_modify sort 0 0.0 # turn off sorting of the coordinates -read_data data.graphene.boxrel +read_data data.graphene # replicate system if requested diff --git a/examples/latte/in.latte.sucrose.md b/examples/latte/in.latte.sucrose.md new file mode 100644 index 0000000000..a10dae5c5e --- /dev/null +++ b/examples/latte/in.latte.sucrose.md @@ -0,0 +1,40 @@ +# simple sucrose model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.sucrose + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 diff --git a/examples/latte/in.latte.water.ch4.consecutive.md b/examples/latte/in.latte.water.ch4.consecutive.md new file mode 100644 index 0000000000..4888d14ebc --- /dev/null +++ b/examples/latte/in.latte.water.ch4.consecutive.md @@ -0,0 +1,65 @@ +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 + +# Clear up previus calculation + +clear + +# simple CH4 molecule with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.ch4 + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 10 + diff --git a/examples/latte/in.latte.water.md b/examples/latte/in.latte.water.md new file mode 100644 index 0000000000..e1185602b4 --- /dev/null +++ b/examples/latte/in.latte.water.md @@ -0,0 +1,40 @@ +# simple water model with LATTE + +units metal +atom_style full +atom_modify sort 0 0.0 # turn off sorting of the coordinates + +read_data data.water + +# replicate system if requested + +variable x index 1 +variable y index 1 +variable z index 1 + +variable nrep equal v_x*v_y*v_z +if "${nrep} > 1" then "replicate $x $y $z" + +# initialize system + +velocity all create 0.0 87287 loop geom + +pair_style zero 1.0 +pair_coeff * * + +neighbor 1.0 bin +neigh_modify every 1 delay 0 check yes + +timestep 0.00025 + +fix 1 all nve + +fix 2 all latte NULL +fix_modify 2 energy yes + +thermo_style custom step temp pe etotal press + +# dynamics + +thermo 10 +run 100 diff --git a/examples/latte/latte.in b/examples/latte/latte.in index c5a1cb4714..a00fcf4bba 100644 --- a/examples/latte/latte.in +++ b/examples/latte/latte.in @@ -21,9 +21,8 @@ CONTROL{ BREAKTOL= 1.0E-6 MINSP2ITER= 22 SP2CONV= REL FULLQCONV= 1 QITER= 3 QMIX= 0.25 SPINMIX= 0.25 MDMIX= 0.25 - SPARSEON= 1 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4 + SPARSEON= 0 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4 MSPARSE= 1500 - RELAX= 0 RELAXTYPE= SD MAXITER= 100000 RLXFTOL= 0.0000001 SKIN= 1.0 CHARGE= 0 XBO= 1 diff --git a/examples/latte/log.19Sep17.latte.sucrose.md.g++.1 b/examples/latte/log.19Sep17.latte.sucrose.md.g++.1 new file mode 100644 index 0000000000..bc8843ef7f --- /dev/null +++ b/examples/latte/log.19Sep17.latte.sucrose.md.g++.1 @@ -0,0 +1,406 @@ + The log file for latte_lib + + CONTROL{ } + + WARNING: variable JobName= is missing. I will use a default value instead ... + WARNING: variable PARAMPATH= is missing. I will use a default value instead ... + WARNING: variable DEBUGON= is missing. I will use a default value instead ... + WARNING: variable FERMIM= is missing. I will use a default value instead ... + WARNING: variable CGORLIB= is missing. I will use a default value instead ... + WARNING: variable NORECS= is missing. I will use a default value instead ... + WARNING: variable VDWON= is missing. I will use a default value instead ... + WARNING: variable ORDERNMOL= is missing. I will use a default value instead ... + WARNING: variable LCNON= is missing. I will use a default value instead ... + WARNING: variable LCNITER= is missing. I will use a default value instead ... + WARNING: variable MDON= is missing. I will use a default value instead ... + WARNING: variable PBCON= is missing. I will use a default value instead ... + WARNING: variable RESTART= is missing. I will use a default value instead ... + WARNING: variable NGPU= is missing. I will use a default value instead ... + WARNING: variable COMPFORCE= is missing. I will use a default value instead ... + WARNING: variable DOSFIT= is missing. I will use a default value instead ... + WARNING: variable INTS2FIT= is missing. I will use a default value instead ... + WARNING: variable NFITSTEP= is missing. I will use a default value instead ... + WARNING: variable QFIT= is missing. I will use a default value instead ... + WARNING: variable PPFITON= is missing. I will use a default value instead ... + WARNING: variable ALLFITON= is missing. I will use a default value instead ... + WARNING: variable PPSTEP= is missing. I will use a default value instead ... + WARNING: variable BISTEP= is missing. I will use a default value instead ... + WARNING: variable PP2FIT= is missing. I will use a default value instead ... + WARNING: variable BINT2FIT= is missing. I will use a default value instead ... + WARNING: variable PPNMOL= is missing. I will use a default value instead ... + WARNING: variable PPNGEOM= is missing. I will use a default value instead ... + WARNING: variable PARREP= is missing. I will use a default value instead ... + WARNING: variable VERBOSE= is missing. I will use a default value instead ... + WARNING: variable MIXER= is missing. I will use a default value instead ... + WARNING: variable RESTARTLIB= is missing. I will use a default value instead ... + WARNING: variable CGTOL= is missing. I will use a default value instead ... + WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ... + WARNING: variable COULACC= is missing. I will use a default value instead ... + WARNING: variable COULCUT= is missing. I will use a default value instead ... + WARNING: variable COULR1= is missing. I will use a default value instead ... + WARNING: variable CHTOL= is missing. I will use a default value instead ... + WARNING: variable BETA= is missing. I will use a default value instead ... + WARNING: variable MCSIGMA= is missing. I will use a default value instead ... + WARNING: variable PPBETA= is missing. I will use a default value instead ... + WARNING: variable PPSIGMA= is missing. I will use a default value instead ... + WARNING: variable ER= is missing. I will use a default value instead ... + WARNING: variable INITIALIZED= is missing. I will use a default value instead ... + + + ############### Parameters used for this run ################ + CONTROL{ + xControl= 1 + DEBUGON= 0 + FERMIM= 6 + CGORLIB= 1 + NORECS= 1 + ENTROPYKIND= 1 + PPOTON= 1 + VDWON= 0 + SPINON= 0 + ELECTRO= 1 + ELECMETH= 0 + MAXSCF= 450 + MINSP2ITER= 22 + FULLQCONV= 1 + QITER= 3 + ORDERNMOL= 0 + SPARSEON= 1 + THRESHOLDON= 1 + FILLINSTOP= 100 + BLKSZ= 4 + MSPARSE= 1500 + LCNON= 0 + LCNITER= 4 + RELAX= 0 + MAXITER= 100000 + MDON= 1 + PBCON= 1 + RESTART= 0 + CHARGE= 0 + XBO= 1 + XBODISON= 1 + XBODISORDER= 5 + NGPU= 2 + KON= 0 + COMPFORCE= 1 + DOSFIT= 0 + INTS2FIT= 1 + NFITSTEP= 5000 + QFIT= 0 + PPFITON= 0 + ALLFITON= 0 + PPSTEP= 500 + BISTEP= 500 + PP2FIT= 2 + BINT2FIT= 6 + PPNMOL= 10 + PPNGEOM= 200 + PARREP= 0 + VERBOSE= 0 + MIXER= 0 + RESTARTLIB= 0 + CGTOL= 9.9999999747524271E-007 + KBT= 0.0000000000000000 + SPINTOL= 1.0000000000000000E-004 + ELEC_ETOL= 1.0000000474974513E-003 + ELEC_QTOL= 1.0000000000000000E-008 + COULACC= 9.9999999747524271E-007 + COULCUT= -500.00000000000000 + COULR1= 500.00000000000000 + BREAKTOL= 9.9999999999999995E-007 + QMIX= 0.25000000000000000 + SPINMIX= 0.25000000000000000 + MDMIX= 0.25000000000000000 + NUMTHRESH= 9.9999999999999995E-007 + CHTOL= 9.9999997764825821E-003 + SKIN= 1.0000000000000000 + RLXFTOL= 9.9999999999999995E-008 + BETA= 1000.0000000000000 + MCSIGMA= 0.20000000298023224 + PPBETA= 1000.0000000000000 + PPSIGMA= 9.9999997764825821E-003 + ER= 1.0000000000000000 + JobName=MyJob + BASISTYPE=NONORTHO + SP2CONV=REL + RELAXTYPE=SD + PARAMPATH=./TBparam + COORDSFILE=./coords.dat + INITIALIZED= F + } + + ./TBparam/electrons.dat + MDCONTROL{ } + + WARNING: variable RNDIST= is missing. I will use a default value instead ... + WARNING: variable SEEDINIT= is missing. I will use a default value instead ... + WARNING: variable NPTTYPE= is missing. I will use a default value instead ... + WARNING: variable UDNEIGH= is missing. I will use a default value instead ... + WARNING: variable DUMPFREQ= is missing. I will use a default value instead ... + WARNING: variable RSFREQ= is missing. I will use a default value instead ... + WARNING: variable WRTFREQ= is missing. I will use a default value instead ... + WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ... + WARNING: variable THERMPER= is missing. I will use a default value instead ... + WARNING: variable THERMRUN= is missing. I will use a default value instead ... + WARNING: variable NVTON= is missing. I will use a default value instead ... + WARNING: variable NPTON= is missing. I will use a default value instead ... + WARNING: variable AVEPER= is missing. I will use a default value instead ... + WARNING: variable SEED= is missing. I will use a default value instead ... + WARNING: variable SHOCKON= is missing. I will use a default value instead ... + WARNING: variable SHOCKSTART= is missing. I will use a default value instead ... + WARNING: variable SHOCKDIR= is missing. I will use a default value instead ... + WARNING: variable MDADAPT= is missing. I will use a default value instead ... + WARNING: variable GETHUG= is missing. I will use a default value instead ... + WARNING: variable RSLEVEL= is missing. I will use a default value instead ... + WARNING: variable DT= is missing. I will use a default value instead ... + WARNING: variable TEMPERATURE= is missing. I will use a default value instead ... + WARNING: variable FRICTION= is missing. I will use a default value instead ... + WARNING: variable PTARGET= is missing. I will use a default value instead ... + WARNING: variable UPARTICLE= is missing. 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0000000000..f4603f5963 --- /dev/null +++ b/examples/latte/log.19Sep17.latte.water.md.g++.1 @@ -0,0 +1,406 @@ + The log file for latte_lib + + CONTROL{ } + + WARNING: variable JobName= is missing. I will use a default value instead ... + WARNING: variable PARAMPATH= is missing. I will use a default value instead ... + WARNING: variable DEBUGON= is missing. I will use a default value instead ... + WARNING: variable FERMIM= is missing. I will use a default value instead ... + WARNING: variable CGORLIB= is missing. I will use a default value instead ... + WARNING: variable NORECS= is missing. I will use a default value instead ... + WARNING: variable VDWON= is missing. I will use a default value instead ... + WARNING: variable ORDERNMOL= is missing. I will use a default value instead ... + WARNING: variable LCNON= is missing. I will use a default value instead ... + WARNING: variable LCNITER= is missing. I will use a default value instead ... + WARNING: variable MDON= is missing. I will use a default value instead ... + WARNING: variable PBCON= is missing. I will use a default value instead ... + WARNING: variable RESTART= is missing. I will use a default value instead ... + WARNING: variable NGPU= is missing. I will use a default value instead ... + WARNING: variable COMPFORCE= is missing. I will use a default value instead ... + WARNING: variable DOSFIT= is missing. I will use a default value instead ... + WARNING: variable INTS2FIT= is missing. I will use a default value instead ... + WARNING: variable NFITSTEP= is missing. I will use a default value instead ... + WARNING: variable QFIT= is missing. I will use a default value instead ... + WARNING: variable PPFITON= is missing. I will use a default value instead ... + WARNING: variable ALLFITON= is missing. I will use a default value instead ... + WARNING: variable PPSTEP= is missing. I will use a default value instead ... + WARNING: variable BISTEP= is missing. I will use a default value instead ... + WARNING: variable PP2FIT= is missing. I will use a default value instead ... + WARNING: variable BINT2FIT= is missing. I will use a default value instead ... + WARNING: variable PPNMOL= is missing. I will use a default value instead ... + WARNING: variable PPNGEOM= is missing. I will use a default value instead ... + WARNING: variable PARREP= is missing. I will use a default value instead ... + WARNING: variable VERBOSE= is missing. I will use a default value instead ... + WARNING: variable MIXER= is missing. I will use a default value instead ... + WARNING: variable RESTARTLIB= is missing. I will use a default value instead ... + WARNING: variable CGTOL= is missing. I will use a default value instead ... + WARNING: variable ELEC_ETOL= is missing. I will use a default value instead ... + WARNING: variable COULACC= is missing. I will use a default value instead ... + WARNING: variable COULCUT= is missing. I will use a default value instead ... + WARNING: variable COULR1= is missing. I will use a default value instead ... + WARNING: variable CHTOL= is missing. I will use a default value instead ... + WARNING: variable BETA= is missing. I will use a default value instead ... + WARNING: variable MCSIGMA= is missing. I will use a default value instead ... + WARNING: variable PPBETA= is missing. I will use a default value instead ... + WARNING: variable PPSIGMA= is missing. I will use a default value instead ... + WARNING: variable ER= is missing. I will use a default value instead ... + WARNING: variable INITIALIZED= is missing. I will use a default value instead ... + + + ############### Parameters used for this run ################ + CONTROL{ + xControl= 1 + DEBUGON= 0 + FERMIM= 6 + CGORLIB= 1 + NORECS= 1 + ENTROPYKIND= 1 + PPOTON= 1 + VDWON= 0 + SPINON= 0 + ELECTRO= 1 + ELECMETH= 0 + MAXSCF= 450 + MINSP2ITER= 22 + FULLQCONV= 1 + QITER= 3 + ORDERNMOL= 0 + SPARSEON= 1 + THRESHOLDON= 1 + FILLINSTOP= 100 + BLKSZ= 4 + MSPARSE= 1500 + LCNON= 0 + LCNITER= 4 + RELAX= 0 + MAXITER= 100000 + MDON= 1 + PBCON= 1 + RESTART= 0 + CHARGE= 0 + XBO= 1 + XBODISON= 1 + XBODISORDER= 5 + NGPU= 2 + KON= 0 + COMPFORCE= 1 + DOSFIT= 0 + INTS2FIT= 1 + NFITSTEP= 5000 + QFIT= 0 + PPFITON= 0 + ALLFITON= 0 + PPSTEP= 500 + BISTEP= 500 + PP2FIT= 2 + BINT2FIT= 6 + PPNMOL= 10 + PPNGEOM= 200 + PARREP= 0 + VERBOSE= 0 + MIXER= 0 + RESTARTLIB= 0 + CGTOL= 9.9999999747524271E-007 + KBT= 0.0000000000000000 + SPINTOL= 1.0000000000000000E-004 + ELEC_ETOL= 1.0000000474974513E-003 + ELEC_QTOL= 1.0000000000000000E-008 + COULACC= 9.9999999747524271E-007 + COULCUT= -500.00000000000000 + COULR1= 500.00000000000000 + BREAKTOL= 9.9999999999999995E-007 + QMIX= 0.25000000000000000 + SPINMIX= 0.25000000000000000 + MDMIX= 0.25000000000000000 + NUMTHRESH= 9.9999999999999995E-007 + CHTOL= 9.9999997764825821E-003 + SKIN= 1.0000000000000000 + RLXFTOL= 9.9999999999999995E-008 + BETA= 1000.0000000000000 + MCSIGMA= 0.20000000298023224 + PPBETA= 1000.0000000000000 + PPSIGMA= 9.9999997764825821E-003 + ER= 1.0000000000000000 + JobName=MyJob + BASISTYPE=NONORTHO + SP2CONV=REL + RELAXTYPE=SD + PARAMPATH=./TBparam + COORDSFILE=./coords.dat + INITIALIZED= F + } + + ./TBparam/electrons.dat + MDCONTROL{ } + + WARNING: variable RNDIST= is missing. I will use a default value instead ... + WARNING: variable SEEDINIT= is missing. I will use a default value instead ... + WARNING: variable NPTTYPE= is missing. I will use a default value instead ... + WARNING: variable UDNEIGH= is missing. I will use a default value instead ... + WARNING: variable DUMPFREQ= is missing. I will use a default value instead ... + WARNING: variable RSFREQ= is missing. I will use a default value instead ... + WARNING: variable WRTFREQ= is missing. I will use a default value instead ... + WARNING: variable TOINITTEMP5= is missing. I will use a default value instead ... + WARNING: variable THERMPER= is missing. I will use a default value instead ... + WARNING: variable THERMRUN= is missing. I will use a default value instead ... + WARNING: variable NVTON= is missing. I will use a default value instead ... + WARNING: variable NPTON= is missing. I will use a default value instead ... + WARNING: variable AVEPER= is missing. I will use a default value instead ... + WARNING: variable SEED= is missing. I will use a default value instead ... + WARNING: variable SHOCKON= is missing. I will use a default value instead ... + WARNING: variable SHOCKSTART= is missing. I will use a default value instead ... + WARNING: variable SHOCKDIR= is missing. I will use a default value instead ... + WARNING: variable MDADAPT= is missing. I will use a default value instead ... + WARNING: variable GETHUG= is missing. I will use a default value instead ... + WARNING: variable RSLEVEL= is missing. I will use a default value instead ... + WARNING: variable DT= is missing. I will use a default value instead ... + WARNING: variable TEMPERATURE= is missing. I will use a default value instead ... + WARNING: variable FRICTION= is missing. I will use a default value instead ... + WARNING: variable PTARGET= is missing. I will use a default value instead ... + WARNING: variable UPARTICLE= is missing. 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I will use a default value instead ... + + + ############### Parameters used for this run ################ + MDCONTROL{ + MAXITER= -1 + UDNEIGH= 1 + DUMPFREQ= 250 + RSFREQ= 500 + WRTFREQ= 25 + TOINITTEMP5= 1 + THERMPER= 500 + THERMRUN= 50000 + NVTON= 0 + NPTON= 0 + AVEPER= 1000 + SEED= 54 + SHOCKON= 0 + SHOCKSTART= 100000 + SHOCKDIR= 1 + MDADAPT= 0 + GETHUG= 0 + RSLEVEL= 0 + DT= 0.25000000000000000 + TEMPERATURE= 300.00000000000000 + FRICTION= 1000.0000000000000 + PTARGET= 0.0000000000000000 + UPARTICLE= 500.00000000000000 + USHOCK= -4590.0000000000000 + C0= 1300.0000000000000 + E0= -795.72497558593750 + V0= 896.98486328125000 + P0= 8.3149001002311707E-002 + RNDIST=GAUSSIAN + SEEDINIT=UNIFORM + NPTTYPE=ISO + DUMMY= F + } + + LIBCALLS 0 + Energy Components (TRRHOH, EREP, ENTE, ECOUL) -110.94281402417451 9.3197859655447317 0.0000000000000000 3.3331152608769714 + LIBCALLS 1 + Energy Components (TRRHOH, EREP, ENTE, ECOUL) -111.00875524736128 9.3653691493930946 0.0000000000000000 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b/src/LATTE/fix_latte.cpp @@ -37,8 +37,8 @@ using namespace FixConst; extern "C" { void latte(int *, int *, double *, int *, int *, double *, double *, double *, double *, - double *, double *, double *, int*, - double *, double *, double *, double *, bool *); + double *, double *, double *, int *, + double *, double *, double *, double *, int * , bool *); int latte_abiversion(); } @@ -191,14 +191,18 @@ void FixLatte::init_list(int id, NeighList *ptr) void FixLatte::setup(int vflag) { + newsystem = 1; post_force(vflag); + newsystem = 0; } /* ---------------------------------------------------------------------- */ void FixLatte::min_setup(int vflag) { + newsystem = 1; post_force(vflag); + newsystem = 0; } /* ---------------------------------------------------------------------- */ @@ -288,10 +292,10 @@ void FixLatte::post_force(int vflag) if (coulomb) forces = &flatte[0][0]; else forces = &atom->f[0][0]; int maxiter = -1; - + latte(flags,&natoms,coords,type,&ntypes,mass,boxlo,boxhi,&domain->xy, &domain->xz,&domain->yz,forces,&maxiter,&latte_energy, - &atom->v[0][0],&update->dt,virial,&latteerror); + &atom->v[0][0],&update->dt,virial,&newsystem,&latteerror); if (latteerror) error->all(FLERR,"Internal LATTE problem"); diff --git a/src/LATTE/fix_latte.h b/src/LATTE/fix_latte.h index 46c65b2016..6d30ced0a0 100644 --- a/src/LATTE/fix_latte.h +++ b/src/LATTE/fix_latte.h @@ -48,7 +48,7 @@ class FixLatte : public Fix { int coulomb,pbcflag,pe_peratom,virial_global,virial_peratom,neighflag; int eflag_caller; - int nmax; + int nmax,newsystem; double *qpotential; double **flatte; double latte_energy;