From 27f07206f691c3e6f56ec6ddb283363fb5510029 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Wed, 22 Feb 2023 17:15:13 +0200 Subject: [PATCH 001/109] Include method declaration in angle_harmonic.h --- src/MOLECULE/angle_harmonic.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/MOLECULE/angle_harmonic.h b/src/MOLECULE/angle_harmonic.h index c50df2ab4e..284a5316ef 100644 --- a/src/MOLECULE/angle_harmonic.h +++ b/src/MOLECULE/angle_harmonic.h @@ -35,6 +35,7 @@ class AngleHarmonic : public Angle { void read_restart(FILE *) override; void write_data(FILE *) override; double single(int, int, int, int) override; + void born_matrix(int type, int i1, int i2, int i3, double &du, double &du2) override; void *extract(const char *, int &) override; protected: From c1a37ac00fc0a5b67a8187c112161ab9430c434e Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Wed, 22 Feb 2023 17:16:56 +0200 Subject: [PATCH 002/109] Implement born_matrix in angle_harmonic.cpp --- src/MOLECULE/angle_harmonic.cpp | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index 4d0683b9bc..64f1c62f1e 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -35,6 +35,7 @@ static constexpr double SMALL = 0.001; AngleHarmonic::AngleHarmonic(LAMMPS *_lmp) : Angle(_lmp) { + born_matrix_enable = 1; k = nullptr; theta0 = nullptr; } @@ -266,6 +267,35 @@ double AngleHarmonic::single(int type, int i1, int i2, int i3) return tk * dtheta; } +/* ---------------------------------------------------------------------- */ + +void AngleHarmonic::born_matrix(int type, int i1, int i2, int i3, double &du, double &du2) +{ + double **x = atom->x; + + double delx1 = x[i1][0] - x[i2][0]; + double dely1 = x[i1][1] - x[i2][1]; + double delz1 = x[i1][2] - x[i2][2]; + domain->minimum_image(delx1,dely1,delz1); + double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1); + + double delx2 = x[i3][0] - x[i2][0]; + double dely2 = x[i3][1] - x[i2][1]; + double delz2 = x[i3][2] - x[i2][2]; + domain->minimum_image(delx2,dely2,delz2); + double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2); + + double c = delx1*delx2 + dely1*dely2 + delz1*delz2; + c /= r1*r2; + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + double theta = acos(c); + + double dtheta = theta - theta0[type]; + du = -2 * k[type] * dtheta / sin(theta); + du2 = 2 * k[type] * (sin(theta) - dtheta * cos(theta)) / pow(sin(theta), 3) +} + /* ---------------------------------------------------------------------- return ptr to internal members upon request ------------------------------------------------------------------------ */ From 4814578d85a5ca089b2ac1d9dfbd97e0a2f1a8a9 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Wed, 22 Feb 2023 17:22:17 +0200 Subject: [PATCH 003/109] Fixing missing semicolon --- src/MOLECULE/angle_harmonic.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MOLECULE/angle_harmonic.cpp b/src/MOLECULE/angle_harmonic.cpp index 64f1c62f1e..e9f1c528ef 100644 --- a/src/MOLECULE/angle_harmonic.cpp +++ b/src/MOLECULE/angle_harmonic.cpp @@ -293,7 +293,7 @@ void AngleHarmonic::born_matrix(int type, int i1, int i2, int i3, double &du, do double dtheta = theta - theta0[type]; du = -2 * k[type] * dtheta / sin(theta); - du2 = 2 * k[type] * (sin(theta) - dtheta * cos(theta)) / pow(sin(theta), 3) + du2 = 2 * k[type] * (sin(theta) - dtheta * cos(theta)) / pow(sin(theta), 3); } /* ---------------------------------------------------------------------- From 5fb11e3f06e07407b95feb22ff96802a439122e0 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 23 Feb 2023 18:14:23 +0200 Subject: [PATCH 004/109] Include method declaration in bond_fene.h --- src/MOLECULE/bond_fene.h | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/MOLECULE/bond_fene.h b/src/MOLECULE/bond_fene.h index eb9e981a32..1628e7a2a2 100644 --- a/src/MOLECULE/bond_fene.h +++ b/src/MOLECULE/bond_fene.h @@ -26,7 +26,7 @@ namespace LAMMPS_NS { class BondFENE : public Bond { public: - BondFENE(class LAMMPS *_lmp) : Bond(_lmp) {} + BondFENE(class LAMMPS *); ~BondFENE() override; void compute(int, int) override; void coeff(int, char **) override; @@ -36,6 +36,7 @@ class BondFENE : public Bond { void read_restart(FILE *) override; void write_data(FILE *) override; double single(int, double, int, int, double &) override; + void born_matrix(int, double, int, int, double &, double &) override; void *extract(const char *, int &) override; protected: From bb75ed50718c1080854713e9dcdb7bdc45c63cb4 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 23 Feb 2023 18:15:43 +0200 Subject: [PATCH 005/109] Implement born_matrix in bond_fene.cpp --- src/MOLECULE/bond_fene.cpp | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/src/MOLECULE/bond_fene.cpp b/src/MOLECULE/bond_fene.cpp index 0f279fccb6..7f55c89296 100644 --- a/src/MOLECULE/bond_fene.cpp +++ b/src/MOLECULE/bond_fene.cpp @@ -30,6 +30,13 @@ using MathConst::MY_CUBEROOT2; /* ---------------------------------------------------------------------- */ +BondFENE::BondFENE(LAMMPS *_lmp) : Bond(_lmp) +{ + born_matrix_enable = 1; +} + +/* ---------------------------------------------------------------------- */ + BondFENE::~BondFENE() { if (allocated && !copymode) { @@ -262,6 +269,28 @@ double BondFENE::single(int type, double rsq, int /*i*/, int /*j*/, double &ffor /* ---------------------------------------------------------------------- */ +void BondFENE::born_matrix(int type, double rsq, int /*i*/, int /*j*/, double &du, double &du2) +{ + double r = sqrt(rsq); + double r0sq = r0[type] * r0[type]; + double rlogarg = 1.0 - rsq / r0sq; + + // Contribution from the attractive term + du = k[type] * r / rlogarg; + du2 = k[type] * (1.0 + rsq / r0sq) / (rlogarg * rlogarg); + + // Contribution from the repulsive Lennard-Jones term + if (rsq < MY_CUBEROOT2 * sigma[type] * sigma[type]) { + double sr2 = sigma[type] * sigma[type] / rsq; + double sr6 = sr2 * sr2 * sr2; + + du += 48.0 * epsilon[type] * sr6 * (0.5 - sr6) / r; + du2 += 48.0 * epsilon[type] * sr6 * (13.0 * sr6 - 3.5) / rsq; + } +} + +/* ---------------------------------------------------------------------- */ + void *BondFENE::extract(const char *str, int &dim) { dim = 1; From e61092464143452d5149e0fb005910c78533c301 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 24 Feb 2023 08:48:40 +0200 Subject: [PATCH 006/109] Include method declaration in dihedral_opls.h --- src/MOLECULE/dihedral_opls.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/MOLECULE/dihedral_opls.h b/src/MOLECULE/dihedral_opls.h index c6286b3b6f..82180cf323 100644 --- a/src/MOLECULE/dihedral_opls.h +++ b/src/MOLECULE/dihedral_opls.h @@ -33,6 +33,7 @@ class DihedralOPLS : public Dihedral { void write_restart(FILE *) override; void read_restart(FILE *) override; void write_data(FILE *) override; + void born_matrix(int, int, int, int, int, double &, double &) override; protected: double *k1, *k2, *k3, *k4; From c35b32961b28b1509643b7c905c7c049aca13391 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 24 Feb 2023 08:51:25 +0200 Subject: [PATCH 007/109] Implement born_matrix in dihedral_opls.cpp --- src/MOLECULE/dihedral_opls.cpp | 99 ++++++++++++++++++++++++++++++++++ 1 file changed, 99 insertions(+) diff --git a/src/MOLECULE/dihedral_opls.cpp b/src/MOLECULE/dihedral_opls.cpp index af34cd24db..eced454d68 100644 --- a/src/MOLECULE/dihedral_opls.cpp +++ b/src/MOLECULE/dihedral_opls.cpp @@ -37,6 +37,7 @@ static constexpr double SMALLER = 0.00001; DihedralOPLS::DihedralOPLS(LAMMPS *_lmp) : Dihedral(_lmp) { writedata = 1; + born_matrix_enable = 1; } /* ---------------------------------------------------------------------- */ @@ -332,3 +333,101 @@ void DihedralOPLS::write_data(FILE *fp) for (int i = 1; i <= atom->ndihedraltypes; i++) fprintf(fp, "%d %g %g %g %g\n", i, 2.0 * k1[i], 2.0 * k2[i], 2.0 * k3[i], 2.0 * k4[i]); } + +/* ----------------------------------------------------------------------*/ + +void DihedralOPLS::born_matrix(int nd, int i1, int i2, int i3, int i4, + double &du, double &du2) +{ + double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm; + double sb1, sb3, rb1, rb3, c0, b1mag2, b1mag, b2mag2; + double b2mag, b3mag2, b3mag, ctmp, r12c1, c1mag, r12c2; + double c2mag, sc1, sc2, s12, c; + double cx, cy, cz, cmag, dx, phi, si, sin2; + + double **x = atom->x; + int **dihedrallist = neighbor->dihedrallist; + + int type = dihedrallist[nd][4]; + + // 1st bond + vb1x = x[i1][0] - x[i2][0]; + vb1y = x[i1][1] - x[i2][1]; + vb1z = x[i1][2] - x[i2][2]; + + // 2nd bond + vb2x = x[i3][0] - x[i2][0]; + vb2y = x[i3][1] - x[i2][1]; + vb2z = x[i3][2] - x[i2][2]; + + vb2xm = -vb2x; + vb2ym = -vb2y; + vb2zm = -vb2z; + + // 3rd bond + vb3x = x[i4][0] - x[i3][0]; + vb3y = x[i4][1] - x[i3][1]; + vb3z = x[i4][2] - x[i3][2]; + + // c0 calculation + sb1 = 1.0 / (vb1x * vb1x + vb1y * vb1y + vb1z * vb1z); + sb3 = 1.0 / (vb3x * vb3x + vb3y * vb3y + vb3z * vb3z); + + rb1 = sqrt(sb1); + rb3 = sqrt(sb3); + + c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * rb1 * rb3; + + // 1st and 2nd angle + b1mag2 = vb1x * vb1x + vb1y * vb1y + vb1z * vb1z; + b1mag = sqrt(b1mag2); + b2mag2 = vb2x * vb2x + vb2y * vb2y + vb2z * vb2z; + b2mag = sqrt(b2mag2); + b3mag2 = vb3x * vb3x + vb3y * vb3y + vb3z * vb3z; + b3mag = sqrt(b3mag2); + + ctmp = vb1x * vb2x + vb1y * vb2y + vb1z * vb2z; + r12c1 = 1.0 / (b1mag * b2mag); + c1mag = ctmp * r12c1; + + ctmp = vb2xm * vb3x + vb2ym * vb3y + vb2zm * vb3z; + r12c2 = 1.0 / (b2mag * b3mag); + c2mag = ctmp * r12c2; + + // cos and sin of 2 angles and final c + sin2 = MAX(1.0 - c1mag * c1mag, 0.0); + sc1 = sqrt(sin2); + if (sc1 < SMALL) sc1 = SMALL; + sc1 = 1.0 / sc1; + + sin2 = MAX(1.0 - c2mag * c2mag, 0.0); + sc2 = sqrt(sin2); + if (sc2 < SMALL) sc2 = SMALL; + sc2 = 1.0 / sc2; + + s12 = sc1 * sc2; + c = (c0 + c1mag * c2mag) * s12; + + cx = vb1y * vb2z - vb1z * vb2y; + cy = vb1z * vb2x - vb1x * vb2z; + cz = vb1x * vb2y - vb1y * vb2x; + cmag = sqrt(cx * cx + cy * cy + cz * cz); + dx = (cx * vb3x + cy * vb3y + cz * vb3z) / cmag / b3mag; + + // error check + if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4); + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + phi = acos(c); + if (dx < 0.0) phi *= -1.0; + si = sin(phi); + if (fabs(si) < SMALLER) si = SMALLER; + + du = k1[type] - 2.0 * k2[type] * sin(2.0 * phi) / si + 3.0 * k3[type] * sin(3.0 * phi) / si + - 4.0 * k4[type] * sin(4.0 * phi) / si; + du2 = (4.0 * k2[type] * si * cos(2.0 * phi) - 2.0 * k2[type] * sin(2.0 * phi) + - 9.0 * k3[type] * si * cos(3.0 * phi) + 3.0 * k3[type] * sin(3.0 * phi) + + 16.0 * k4[type] * si * cos(4.0 * phi) - 4.0 * k4[type] * sin(4.0 * phi)) / (si * si * si); +} From c4bf0f0ab52eec3ee8734a0455e8c3c4b14250e8 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 24 Feb 2023 09:39:38 +0200 Subject: [PATCH 008/109] Include method declaration in dihedral_multi_harmonic.h --- src/MOLECULE/dihedral_multi_harmonic.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/MOLECULE/dihedral_multi_harmonic.h b/src/MOLECULE/dihedral_multi_harmonic.h index 4780028181..45f1112b4f 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.h +++ b/src/MOLECULE/dihedral_multi_harmonic.h @@ -33,6 +33,7 @@ class DihedralMultiHarmonic : public Dihedral { void write_restart(FILE *) override; void read_restart(FILE *) override; void write_data(FILE *) override; + void born_matrix(int, int, int, int, int, double &, double &) override; protected: double *a1, *a2, *a3, *a4, *a5; From 3ea04477157e66514031af4831e3014398fd467f Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 24 Feb 2023 09:41:52 +0200 Subject: [PATCH 009/109] Implement born_matrix in dihedral_multi_harmonic.cpp --- src/MOLECULE/dihedral_multi_harmonic.cpp | 85 ++++++++++++++++++++++++ 1 file changed, 85 insertions(+) diff --git a/src/MOLECULE/dihedral_multi_harmonic.cpp b/src/MOLECULE/dihedral_multi_harmonic.cpp index 11213b59cd..8e6685cac9 100644 --- a/src/MOLECULE/dihedral_multi_harmonic.cpp +++ b/src/MOLECULE/dihedral_multi_harmonic.cpp @@ -36,6 +36,7 @@ static constexpr double SMALL = 0.001; DihedralMultiHarmonic::DihedralMultiHarmonic(LAMMPS *_lmp) : Dihedral(_lmp) { writedata = 1; + born_matrix_enable = 1; } /* ---------------------------------------------------------------------- */ @@ -322,3 +323,87 @@ void DihedralMultiHarmonic::write_data(FILE *fp) for (int i = 1; i <= atom->ndihedraltypes; i++) fprintf(fp, "%d %g %g %g %g %g\n", i, a1[i], a2[i], a3[i], a4[i], a5[i]); } + +/* ---------------------------------------------------------------------- */ + +void DihedralMultiHarmonic::born_matrix(int nd, int i1, int i2, int i3, int i4, + double &du, double &du2) +{ + double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm; + double sb1, sb3, rb1, rb3, c0, b1mag2, b1mag, b2mag2; + double b2mag, b3mag2, b3mag, ctmp, r12c1, c1mag, r12c2; + double c2mag, sc1, sc2, s12, c; + double sin2; + + double **x = atom->x; + int **dihedrallist = neighbor->dihedrallist; + + int type = dihedrallist[nd][4]; + + // 1st bond + vb1x = x[i1][0] - x[i2][0]; + vb1y = x[i1][1] - x[i2][1]; + vb1z = x[i1][2] - x[i2][2]; + + // 2nd bond + vb2x = x[i3][0] - x[i2][0]; + vb2y = x[i3][1] - x[i2][1]; + vb2z = x[i3][2] - x[i2][2]; + + vb2xm = -vb2x; + vb2ym = -vb2y; + vb2zm = -vb2z; + + // 3rd bond + vb3x = x[i4][0] - x[i3][0]; + vb3y = x[i4][1] - x[i3][1]; + vb3z = x[i4][2] - x[i3][2]; + + // c0 calculation + sb1 = 1.0 / (vb1x * vb1x + vb1y * vb1y + vb1z * vb1z); + sb3 = 1.0 / (vb3x * vb3x + vb3y * vb3y + vb3z * vb3z); + + rb1 = sqrt(sb1); + rb3 = sqrt(sb3); + + c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * rb1 * rb3; + + // 1st and 2nd angle + b1mag2 = vb1x * vb1x + vb1y * vb1y + vb1z * vb1z; + b1mag = sqrt(b1mag2); + b2mag2 = vb2x * vb2x + vb2y * vb2y + vb2z * vb2z; + b2mag = sqrt(b2mag2); + b3mag2 = vb3x * vb3x + vb3y * vb3y + vb3z * vb3z; + b3mag = sqrt(b3mag2); + + ctmp = vb1x * vb2x + vb1y * vb2y + vb1z * vb2z; + r12c1 = 1.0 / (b1mag * b2mag); + c1mag = ctmp * r12c1; + + ctmp = vb2xm * vb3x + vb2ym * vb3y + vb2zm * vb3z; + r12c2 = 1.0 / (b2mag * b3mag); + c2mag = ctmp * r12c2; + + // cos and sin of 2 angles and final c + sin2 = MAX(1.0 - c1mag * c1mag, 0.0); + sc1 = sqrt(sin2); + if (sc1 < SMALL) sc1 = SMALL; + sc1 = 1.0 / sc1; + + sin2 = MAX(1.0 - c2mag * c2mag, 0.0); + sc2 = sqrt(sin2); + if (sc2 < SMALL) sc2 = SMALL; + sc2 = 1.0 / sc2; + + s12 = sc1 * sc2; + c = (c0 + c1mag * c2mag) * s12; + + // error check + if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4); + + if (c > 1.0) c = 1.0; + if (c < -1.0) c = -1.0; + + du = a2[type] + c * (2.0 * a3[type] + c * (3.0 * a4[type] + c * 4.0 * a5[type])); + du2 = 2.0 * a3[type] + 6.0 * c * (a4[type] + 2.0 * a5[type] * c); +} From 885c4d76093435b0bcf8caa1515ec9f85cf439c6 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 24 Feb 2023 11:56:22 +0200 Subject: [PATCH 010/109] Include method declaration in bond_fene_nm.h --- src/EXTRA-MOLECULE/bond_fene_nm.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/EXTRA-MOLECULE/bond_fene_nm.h b/src/EXTRA-MOLECULE/bond_fene_nm.h index 07da20e425..4e9899648b 100644 --- a/src/EXTRA-MOLECULE/bond_fene_nm.h +++ b/src/EXTRA-MOLECULE/bond_fene_nm.h @@ -35,6 +35,7 @@ class BondFENENM : public BondFENE { void read_restart(FILE *) override; void write_data(FILE *) override; double single(int, double, int, int, double &) override; + void born_matrix(int, double, int, int, double &, double &) override; void *extract(const char *, int &) override; protected: From a32440cdef5f90ea1daa812394304c640d2e9193 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 24 Feb 2023 11:58:42 +0200 Subject: [PATCH 011/109] Implement born_matrix in bond_fene_nm.cpp --- src/EXTRA-MOLECULE/bond_fene_nm.cpp | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/src/EXTRA-MOLECULE/bond_fene_nm.cpp b/src/EXTRA-MOLECULE/bond_fene_nm.cpp index 5451479881..59f60379bd 100644 --- a/src/EXTRA-MOLECULE/bond_fene_nm.cpp +++ b/src/EXTRA-MOLECULE/bond_fene_nm.cpp @@ -28,7 +28,10 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -BondFENENM::BondFENENM(LAMMPS *lmp) : BondFENE(lmp), nn(nullptr), mm(nullptr) {} +BondFENENM::BondFENENM(LAMMPS *lmp) : BondFENE(lmp), nn(nullptr), mm(nullptr) +{ + born_matrix_enable = 1; +} /* ---------------------------------------------------------------------- */ @@ -270,6 +273,27 @@ double BondFENENM::single(int type, double rsq, int /*i*/, int /*j*/, double &ff /* ---------------------------------------------------------------------- */ +void BondFENENM::born_matrix(int type, double rsq, int /*i*/, int /*j*/, double &du, double &du2) +{ + double r = sqrt(rsq); + double r0sq = r0[type] * r0[type]; + double rlogarg = 1.0 - rsq / r0sq; + + // Contribution from the attractive term + du = k[type] * r / rlogarg; + du2 = k[type] * (1.0 + rsq / r0sq) / (rlogarg * rlogarg); + + // Contribution from the repulsive Lennard-Jones term + if (rsq < sigma[type] * sigma[type]) { + double prefactor = epsilon[type] * nn[type] * mm[type] / (nn[type] - mm[type]); + du += prefactor * (pow(sigma[type] / r, mm[type]) - pow(sigma[type] / r, nn[type])) / r; + du2 += prefactor * ((nn[type] + 1.0) * pow(sigma[type] / r, nn[type]) - + (mm[type] + 1.0) * pow(sigma[type] / r, mm[type])) / rsq; + } +} + +/* ---------------------------------------------------------------------- */ + void *BondFENENM::extract(const char *str, int &dim) { dim = 1; From f264631267fc8bd170b3c32f0a70fc8c870c4012 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 24 Feb 2023 12:24:45 +0200 Subject: [PATCH 012/109] Include method declaration in pair_nm_cut.h --- src/EXTRA-PAIR/pair_nm_cut.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/EXTRA-PAIR/pair_nm_cut.h b/src/EXTRA-PAIR/pair_nm_cut.h index ab91747252..a9a800af23 100644 --- a/src/EXTRA-PAIR/pair_nm_cut.h +++ b/src/EXTRA-PAIR/pair_nm_cut.h @@ -40,6 +40,7 @@ class PairNMCut : public Pair { void write_data(FILE *) override; void write_data_all(FILE *) override; double single(int, int, int, int, double, double, double, double &) override; + void born_matrix(int, int, int, int, double, double, double, double &, double &) override; void *extract(const char *, int &) override; protected: From 8ba61e11a24b94929fe68b22585245d078aa0d84 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 24 Feb 2023 12:25:55 +0200 Subject: [PATCH 013/109] Implement born_matrix in pair_nm_cut.cpp --- src/EXTRA-PAIR/pair_nm_cut.cpp | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/src/EXTRA-PAIR/pair_nm_cut.cpp b/src/EXTRA-PAIR/pair_nm_cut.cpp index 18b5810abc..3156ec224d 100644 --- a/src/EXTRA-PAIR/pair_nm_cut.cpp +++ b/src/EXTRA-PAIR/pair_nm_cut.cpp @@ -36,6 +36,7 @@ using namespace MathConst; PairNMCut::PairNMCut(LAMMPS *lmp) : Pair(lmp) { + born_matrix_enable = 1; writedata = 1; } @@ -416,6 +417,25 @@ double PairNMCut::single(int /*i*/, int /*j*/, int itype, int jtype, /* ---------------------------------------------------------------------- */ +void PairNMCut::born_matrix(int /*i*/, int /*j*/, int itype, int jtype, double rsq, + double /*factor_coul*/, double factor_lj, double &dupair, + double &du2pair) +{ + double r = sqrt(rsq); + double prefactor = e0nm[itype][jtype]*nm[itype][jtype]; + + double du = prefactor * + (r0m[itype][jtype]/pow(r,mm[itype][jtype]) - r0n[itype][jtype]/pow(r,nn[itype][jtype])) / r; + double du2 = prefactor * + (r0n[itype][jtype]*(nn[itype][jtype] + 1.0) / pow(r,nn[itype][jtype]) - + r0m[itype][jtype]*(mm[itype][jtype] + 1.0) / pow(r,mm[itype][jtype])) / rsq; + + dupair = factor_lj * du; + du2pair = factor_lj * du2; +} + +/* ---------------------------------------------------------------------- */ + void *PairNMCut::extract(const char *str, int &dim) { dim = 2; From d831562e1fb3f45dce34ecf79c5347b1e8fb8ca9 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Fri, 24 Feb 2023 12:27:53 +0200 Subject: [PATCH 014/109] Fixing typo in equation for fene/nm --- doc/src/bond_fene.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/bond_fene.rst b/doc/src/bond_fene.rst index be7775489a..24b3a4e1e2 100644 --- a/doc/src/bond_fene.rst +++ b/doc/src/bond_fene.rst @@ -51,7 +51,7 @@ in the same form as in pair style :doc:`nm/cut `. The bond energy is th .. math:: - E = -0.5 K r_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + \frac{E_0}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n - n \left(\frac{r_0}{r}\right)^m \right] + E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + \frac{E_0}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n - n \left(\frac{r_0}{r}\right)^m \right] Similar to the *fene* style, the generalized Lennard-Jones is cut off at the potential minimum, :math:`r_0`, to be repulsive only. The following From 81b0bb47be24eda4acb7e3a73fb943245c93fb28 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 25 Feb 2023 12:03:05 -0500 Subject: [PATCH 015/109] allow dynamic groups with fix oneway --- src/EXTRA-FIX/fix_oneway.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/EXTRA-FIX/fix_oneway.cpp b/src/EXTRA-FIX/fix_oneway.cpp index d514a081f1..f31781d936 100644 --- a/src/EXTRA-FIX/fix_oneway.cpp +++ b/src/EXTRA-FIX/fix_oneway.cpp @@ -35,6 +35,7 @@ FixOneWay::FixOneWay(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), region(nullptr), idregion(nullptr) { direction = NONE; + dynamic_group_allow = 1; if (narg < 6) error->all(FLERR, "Illegal fix oneway command"); From 828b70fbfa45b43ef88852beb51c4891fa2cfc8b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 25 Feb 2023 13:58:58 -0500 Subject: [PATCH 016/109] silence warning --- doc/src/fix_pimd.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_pimd.rst b/doc/src/fix_pimd.rst index 0a4f9a38fb..84c6e47c1f 100644 --- a/doc/src/fix_pimd.rst +++ b/doc/src/fix_pimd.rst @@ -1,7 +1,7 @@ .. index:: fix pimd/nvt fix pimd/nvt command -================ +==================== Syntax """""" From 666be5c3d90268fc80baa3e5427ce1432b11685e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 25 Feb 2023 23:46:58 -0500 Subject: [PATCH 017/109] add log files for example run --- .../pimd/para-h2/log.25Feb23.scp.g++.8 | 2 + .../pimd/para-h2/log.25Feb23.scp.g++.8.0 | 199 ++++++++++++++++++ .../pimd/para-h2/log.25Feb23.scp.g++.8.1 | 197 +++++++++++++++++ .../pimd/para-h2/log.25Feb23.scp.g++.8.2 | 197 +++++++++++++++++ .../pimd/para-h2/log.25Feb23.scp.g++.8.3 | 197 +++++++++++++++++ .../pimd/para-h2/log.25Feb23.scp.g++.8.4 | 197 +++++++++++++++++ .../pimd/para-h2/log.25Feb23.scp.g++.8.5 | 197 +++++++++++++++++ .../pimd/para-h2/log.25Feb23.scp.g++.8.6 | 197 +++++++++++++++++ .../pimd/para-h2/log.25Feb23.scp.g++.8.7 | 197 +++++++++++++++++ 9 files changed, 1580 insertions(+) create mode 100644 examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8 create mode 100644 examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.0 create mode 100644 examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.1 create mode 100644 examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.2 create mode 100644 examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.3 create mode 100644 examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.4 create mode 100644 examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.5 create mode 100644 examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.6 create mode 100644 examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.7 diff --git a/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8 b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8 new file mode 100644 index 0000000000..14b41c14f3 --- /dev/null +++ b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8 @@ -0,0 +1,2 @@ +LAMMPS (8 Feb 2023) +Running on 8 partitions of processors diff --git a/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.0 b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.0 new file mode 100644 index 0000000000..037ad3f2d3 --- /dev/null +++ b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.0 @@ -0,0 +1,199 @@ +LAMMPS (8 Feb 2023) +Processor partition = 0 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 32 pad +variable out_freq string 100 +variable job_name string H2 + +units real +atom_style full +pair_style table linear 10000 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no + +read_data H2.data +Reading data file ... + orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 180 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +pair_coeff 1 * pair.table PAIR_H2 +WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466) + +timestep 0.001 + +velocity all create 1.0 1985 rot yes dist gaussian + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4 + +thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +thermo ${out_freq} +thermo 100 + +#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd + +#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2 + +run 10000 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Fix pimd/nvt -P/(beta^2 * hbar^2) = -2.0510430e-01 (kcal/mol/A^2) + +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.55117 + ghost atom cutoff = 11.55117 + binsize = 5.775585, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes + Step Temp PotEng TotEng Pzz espring T_ring virial + 0 1 -50.292986 -49.759421 16.18218 0 2.4190752e-312 4.331435e-14 + 100 1.0017926 -50.292812 -49.758291 16.197861 4.265072e-05 0.99622709 -0.027624534 + 200 1.0071966 -50.292414 -49.755009 16.235286 0.00017002327 1.0016011 -0.055248299 + 300 1.0162913 -50.291757 -49.7495 16.297361 0.00038044032 1.0106453 -0.082873452 + 400 1.0292116 -50.290849 -49.741697 16.38451 0.00067129747 1.0234938 -0.11047807 + 500 1.046152 -50.289692 -49.731502 16.497053 0.0010393068 1.0403401 -0.13806207 + 600 1.0673727 -50.288298 -49.718785 16.634959 0.0014807685 1.0614428 -0.16561253 + 700 1.0932075 -50.286675 -49.703378 16.798983 0.0019918311 1.0871342 -0.19314289 + 800 1.1240754 -50.284828 -49.68506 16.990234 0.0025687136 1.1178306 -0.22065895 + 900 1.1604938 -50.28276 -49.663562 17.210179 0.0032078786 1.1540466 -0.24818038 + 1000 1.2030968 -50.280481 -49.638551 17.460167 0.0039061562 1.196413 -0.27572028 + 1100 1.2526583 -50.277991 -49.609616 17.742341 0.0046608267 1.2456991 -0.30331246 + 1200 1.3101204 -50.275294 -49.576259 18.059364 0.0054696709 1.3028419 -0.33099732 + 1300 1.3766308 -50.272386 -49.537864 18.415203 0.0063309999 1.3689828 -0.35880748 + 1400 1.4535894 -50.269262 -49.493677 18.814095 0.007243672 1.4455139 -0.38678366 + 1500 1.5427084 -50.265919 -49.442783 19.261431 0.0082071044 1.5341378 -0.41499269 + 1600 1.6460882 -50.262344 -49.384049 19.763852 0.0092212862 1.6369433 -0.44348166 + 1700 1.7663158 -50.25853 -49.316086 20.329991 0.010286796 1.756503 -0.47232409 + 1800 1.9065905 -50.254461 -49.237171 20.96974 0.01140483 1.8959983 -0.50158483 + 1900 2.0708856 -50.250115 -49.145163 21.696809 0.012577241 2.0593807 -0.53134846 + 2000 2.2641571 -50.245477 -49.037402 22.525956 0.013806592 2.2515785 -0.5617101 + 2100 2.4926123 -50.240516 -48.910546 23.477847 0.015096239 2.4787644 -0.59276642 + 2200 2.7640541 -50.2352 -48.760398 24.577541 0.01645042 2.7486983 -0.62463764 + 2300 3.088323 -50.229491 -48.58167 25.856282 0.017874391 3.0711656 -0.65745388 + 2400 3.4778567 -50.223344 -48.367681 27.353194 0.01937458 3.4585353 -0.69135912 + 2500 3.9483938 -50.216703 -48.109978 29.11873 0.020958791 3.9264583 -0.72652121 + 2600 4.5198403 -50.209503 -47.797875 31.215234 0.02263645 4.4947301 -0.76313188 + 2700 5.2173107 -50.201663 -47.417889 33.721815 0.024418904 5.1883257 -0.80140558 + 2800 6.0723283 -50.193089 -46.953107 36.73757 0.026319777 6.0385931 -0.84159436 + 2900 7.1241213 -50.183668 -46.382487 40.38551 0.028355393 7.0845429 -0.88396874 + 3000 8.4208727 -50.173266 -45.680183 44.816478 0.030545255 8.3740901 -0.9288431 + 3100 10.020649 -50.161717 -44.81505 50.212214 0.032912578 9.9649788 -0.97656436 + 3200 11.991558 -50.148837 -43.750561 56.786471 0.035484852 11.924938 -1.0275116 + 3300 14.410456 -50.134392 -42.445477 64.781319 0.038294377 14.330398 -1.0821007 + 3400 17.359303 -50.11813 -40.855813 74.455919 0.041378722 17.262863 -1.14076 + 3500 20.918126 -50.099744 -38.938564 86.068376 0.044780961 20.801915 -1.2039443 + 3600 25.153676 -50.078895 -36.657774 99.840861 0.048549564 25.013933 -1.2720773 + 3700 30.103431 -50.055212 -33.993075 115.91254 0.052737712 29.93619 -1.3455663 + 3800 35.755845 -50.028299 -30.950232 134.28175 0.057401834 35.557201 -1.4247605 + 3900 42.029581 -49.997746 -27.572232 154.74519 0.062599126 41.796084 -1.5098692 + 4000 48.756702 -49.963159 -23.948289 176.84543 0.06838392 48.485832 -1.6010084 + 4100 55.676392 -49.924188 -20.217214 199.84979 0.074802896 55.367079 -1.6980754 + 4200 62.445716 -49.880563 -16.561714 222.7783 0.081889414 62.098795 -1.8007866 + 4300 68.671023 -49.832118 -13.191664 244.49021 0.089657516 68.289518 -1.9086164 + 4400 73.957826 -49.778843 -10.317535 263.82539 0.098096488 73.546949 -2.0208305 + 4500 77.969954 -49.7209 -8.1188616 279.77238 0.10716704 77.536788 -2.1364913 + 4600 80.483598 -49.658617 -6.7153862 291.6285 0.11680011 80.036467 -2.254524 + 4700 81.421471 -49.592506 -6.1488596 299.10183 0.12689894 80.969129 -2.3737378 + 4800 80.857888 -49.523204 -6.3802649 302.3328 0.13734453 80.408677 -2.492954 + 4900 78.994781 -49.451459 -7.3026086 301.83334 0.14800388 78.555921 -2.6110228 + 5000 76.117367 -49.378045 -8.7644823 298.36557 0.15873983 75.694493 -2.7269278 + 5100 72.542745 -49.303735 -10.597466 292.79593 0.16942116 72.139729 -2.8398052 + 5200 68.573953 -49.22923 -12.640569 285.96472 0.17993138 68.192987 -2.949009 + 5300 64.467624 -49.155126 -14.757458 278.59037 0.19017535 64.10947 -3.0540851 + 5400 60.41785 -49.081671 -16.844821 271.22804 0.20008281 60.082195 -3.1546148 + 5500 56.554431 -49.009666 -18.834201 264.2355 0.20960898 56.24024 -3.250862 + 5600 52.95111 -48.938861 -20.686002 257.84121 0.21873248 52.656937 -3.3428291 + 5700 49.638794 -48.869827 -22.384304 252.12886 0.22745138 49.363023 -3.4305128 + 5800 46.619514 -48.801888 -23.927347 247.13356 0.23577844 46.360517 -3.5141755 + 5900 43.878389 -48.73593 -25.323958 242.80111 0.24373625 43.634621 -3.5942967 + 6000 41.392437 -48.671406 -26.585851 239.09246 0.25135296 41.162479 -3.6710953 + 6100 39.136252 -48.60798 -27.726246 235.9541 0.25865905 38.918828 -3.7449553 + 6200 37.085195 -48.545774 -28.758412 233.32233 0.26568495 36.879167 -3.8159439 + 6300 35.216896 -48.484909 -29.694407 231.1392 0.27245965 35.021246 -3.884503 + 6400 33.511732 -48.42458 -30.543893 229.37842 0.2790099 33.325556 -3.9507385 + 6500 31.952789 -48.365385 -31.316496 227.98228 0.2853599 31.775274 -4.0149897 + 6600 30.525576 -48.307233 -32.019853 226.91697 0.29153132 30.35599 -4.0774486 + 6700 29.217672 -48.24981 -32.660283 226.16022 0.29754342 29.055351 -4.1382338 + 6800 28.018378 -48.192803 -33.243177 225.69366 0.30341329 27.862721 -4.1974677 + 6900 26.918418 -48.136622 -33.773896 225.48194 0.30915615 26.768871 -4.2553485 + 7000 25.909681 -48.08096 -34.256461 225.51257 0.31478562 25.765738 -4.311968 + 7100 24.985015 -48.025534 -34.694405 225.77479 0.32031392 24.84621 -4.3675242 + 7200 24.138072 -47.970746 -35.091516 226.24048 0.32575216 24.003972 -4.4219335 + 7300 23.36317 -47.916089 -35.450319 226.90757 0.33111051 23.233375 -4.4754578 + 7400 22.655198 -47.861976 -35.773956 227.75054 0.33639834 22.529336 -4.5280134 + 7500 22.009532 -47.808135 -36.064618 228.76407 0.34162439 21.887257 -4.5797622 + 7600 21.421974 -47.754508 -36.324492 229.93785 0.34679689 21.302963 -4.6307739 + 7700 20.888691 -47.700827 -36.555352 231.26801 0.35192361 20.772643 -4.6812057 + 7800 20.406177 -47.64705 -36.759028 232.73618 0.35701201 20.292809 -4.7306795 + 7900 19.971205 -47.593833 -36.937897 234.33449 0.36206923 19.860254 -4.7798815 + 8000 19.580795 -47.540435 -37.092808 236.06384 0.36710221 19.472013 -4.8285632 + 8100 19.232176 -47.487281 -37.225665 237.90655 0.37211768 19.125331 -4.8768578 + 8200 18.922755 -47.4341 -37.33758 239.86116 0.37712221 18.817628 -4.9247735 + 8300 18.650078 -47.380856 -37.429827 241.92202 0.38212226 18.546466 -4.972363 + 8400 18.4118 -47.327508 -37.503616 244.08393 0.38712418 18.309512 -5.0196756 + 8500 18.205651 -47.273789 -37.559891 246.34742 0.3921342 18.104508 -5.06671 + 8600 18.029398 -47.219424 -37.599568 248.71065 0.39715848 17.929235 -5.1133124 + 8700 17.880815 -47.165549 -37.624972 251.14475 0.4022031 17.781477 -5.1600447 + 8800 17.757645 -47.110958 -37.636101 253.66312 0.40727406 17.658991 -5.2066259 + 8900 17.657573 -47.056554 -37.635091 256.25454 0.41237724 17.559475 -5.2531731 + 9000 17.578197 -47.001835 -37.622724 258.91696 0.41751847 17.48054 -5.2996769 + 9100 17.517006 -46.946535 -37.600073 261.64727 0.42270345 17.41969 -5.3462575 + 9200 17.471368 -46.890625 -37.568515 264.44427 0.42793776 17.374305 -5.3925966 + 9300 17.438519 -46.834765 -37.530181 267.28872 0.43322691 17.341639 -5.4391596 + 9400 17.415579 -46.778464 -37.486121 270.18178 0.43857628 17.318826 -5.485798 + 9500 17.399563 -46.721685 -37.437887 273.11812 0.44399119 17.302899 -5.5325337 + 9600 17.387425 -46.664405 -37.387083 276.08982 0.44947693 17.290829 -5.5793912 + 9700 17.376109 -46.606364 -37.335081 279.09236 0.45503878 17.279575 -5.6264788 + 9800 17.362615 -46.547755 -37.283671 282.11747 0.46068208 17.266156 -5.6736623 + 9900 17.344087 -46.488783 -37.234585 285.15699 0.46641232 17.247731 -5.7209993 + 10000 17.317913 -46.42918 -37.188947 288.20641 0.4722352 17.221703 -5.7685405 +Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms + +Performance: 0.059 ns/day, 408.083 hours/ns, 680.689 timesteps/s, 122.524 katom-step/s +96.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.0453 | 3.0453 | 3.0453 | 0.0 | 20.73 +Bond | 0.00108 | 0.00108 | 0.00108 | 0.0 | 0.01 +Neigh | 6.6815 | 6.6815 | 6.6815 | 0.0 | 45.48 +Comm | 0.55477 | 0.55477 | 0.55477 | 0.0 | 3.78 +Output | 0.0028885 | 0.0028885 | 0.0028885 | 0.0 | 0.02 +Modify | 4.3341 | 4.3341 | 4.3341 | 0.0 | 29.50 +Other | | 0.07136 | | | 0.49 + +Nlocal: 180 ave 180 max 180 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1510 ave 1510 max 1510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 13729 ave 13729 max 13729 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 13729 +Ave neighs/atom = 76.272222 +Ave special neighs/atom = 0 +Neighbor list builds = 10000 +Dangerous builds not checked +Total wall time: 0:00:14 diff --git a/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.1 b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.1 new file mode 100644 index 0000000000..cd5ea56a2e --- /dev/null +++ b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.1 @@ -0,0 +1,197 @@ +LAMMPS (8 Feb 2023) +Processor partition = 1 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 32 pad +variable out_freq string 100 +variable job_name string H2 + +units real +atom_style full +pair_style table linear 10000 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no + +read_data H2.data +Reading data file ... + orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 180 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +pair_coeff 1 * pair.table PAIR_H2 +WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466) + +timestep 0.001 + +velocity all create 1.0 1985 rot yes dist gaussian + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4 + +thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +thermo ${out_freq} +thermo 100 + +#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd + +#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2 + +run 10000 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.55117 + ghost atom cutoff = 11.55117 + binsize = 5.775585, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes + Step Temp PotEng TotEng Pzz espring T_ring virial + 0 1 -50.292986 -49.759421 16.18218 0 0 4.331435e-14 + 100 1.0008585 -50.292908 -49.758885 16.189586 7.3078196e-06 4.6642574 -0.013945396 + 200 1.0034473 -50.292787 -49.757382 16.20341 2.9015288e-05 4.6763219 -0.027851725 + 300 1.0078065 -50.292593 -49.754863 16.225711 6.4500006e-05 4.6966366 -0.041662754 + 400 1.0140035 -50.29233 -49.751293 16.257176 0.00011280318 4.7255165 -0.055352542 + 500 1.022135 -50.292004 -49.746629 16.297097 0.000172727 4.7634112 -0.068879202 + 600 1.0323282 -50.291621 -49.740807 16.346105 0.00024293886 4.810914 -0.082221014 + 700 1.044744 -50.291188 -49.733749 16.404167 0.00032206529 4.8687751 -0.095360512 + 800 1.0595808 -50.290712 -49.725357 16.471712 0.00040876559 4.9379182 -0.10826526 + 900 1.0770788 -50.290199 -49.715507 16.549069 0.00050178229 5.0194635 -0.1209272 + 1000 1.0975268 -50.289655 -49.704053 16.636751 0.00059997025 5.1147563 -0.13335203 + 1100 1.1212697 -50.289087 -49.690817 16.735749 0.00070230922 5.2254045 -0.14552504 + 1200 1.1487191 -50.288499 -49.675582 16.846901 0.00080790454 5.3533259 -0.15745048 + 1300 1.1803661 -50.287894 -49.658092 16.971484 0.00091598038 5.5008089 -0.16912662 + 1400 1.2167975 -50.287272 -49.638032 17.111786 0.001025869 5.6705884 -0.18056175 + 1500 1.2587169 -50.286644 -49.615037 17.26922 0.0011369979 5.8659438 -0.19176702 + 1600 1.3069713 -50.286008 -49.588654 17.446637 0.0012488773 6.0908216 -0.20274823 + 1700 1.3625842 -50.285365 -49.558338 17.646978 0.0013610874 6.349992 -0.21351296 + 1800 1.4267987 -50.284719 -49.523429 17.874056 0.0014732674 6.6492481 -0.2240754 + 1900 1.5011316 -50.284073 -49.483122 18.132347 0.0015851058 6.9956586 -0.23443788 + 2000 1.5874426 -50.283426 -49.436422 18.428012 0.0016963317 7.3978897 -0.24461477 + 2100 1.6880217 -50.282783 -49.382113 18.767914 0.0018067084 7.866614 -0.25461336 + 2200 1.805701 -50.282144 -49.318685 19.160875 0.0019160281 8.4150298 -0.26443254 + 2300 1.9439951 -50.281509 -49.244262 19.617751 0.0020241086 9.0595157 -0.27408815 + 2400 2.1072772 -50.280879 -49.15651 20.152728 0.0021307926 9.8204522 -0.28357876 + 2500 2.3009976 -50.28026 -49.052528 20.78256 0.0022359485 10.723239 -0.29290505 + 2600 2.5319494 -50.279651 -48.928691 21.528586 0.0023394759 11.799534 -0.30206821 + 2700 2.8085834 -50.279048 -48.780486 22.417919 0.0024413142 13.088719 -0.31106836 + 2800 3.1413661 -50.278457 -48.602334 23.483643 0.0025414581 14.639572 -0.31990395 + 2900 3.5431594 -50.277876 -48.38737 24.766603 0.0026399801 16.512032 -0.32855403 + 3000 4.029577 -50.277305 -48.127264 26.316279 0.0027370628 18.778862 -0.33702346 + 3100 4.6192292 -50.276739 -47.81208 28.192254 0.0028330445 21.526793 -0.3452905 + 3200 5.333716 -50.276174 -47.43029 30.464107 0.0029284791 24.856485 -0.35332773 + 3300 6.1971481 -50.275605 -46.969024 33.208128 0.0030242128 28.8803 -0.36114465 + 3400 7.2349012 -50.27502 -46.41473 36.506582 0.0031214781 33.716495 -0.36868512 + 3500 8.4712457 -50.274401 -45.754441 40.437918 0.0032219998 39.478178 -0.37595678 + 3600 9.9255066 -50.273728 -44.977825 45.065017 0.0033281047 46.255407 -0.38292345 + 3700 11.606561 -50.27297 -44.080116 50.41841 0.0034428151 54.089554 -0.38955061 + 3800 13.505865 -50.272095 -43.065838 56.472981 0.0035698989 62.940797 -0.39583139 + 3900 15.589837 -50.271059 -41.952868 63.125206 0.0037138374 72.652639 -0.40173444 + 4000 17.793286 -50.26982 -40.775945 70.171007 0.0038796665 82.921278 -0.40724146 + 4100 20.016352 -50.26833 -39.588305 77.297059 0.0040726574 93.281337 -0.350557 + 4200 22.127692 -50.266548 -38.459986 84.091411 0.0042978175 103.12072 -0.42427987 + 4300 23.975875 -50.264442 -37.471754 90.07826 0.0045592402 111.73373 -0.44332019 + 4400 25.408871 -50.262001 -36.704717 94.780152 0.0048593802 118.41186 -0.4712594 + 4500 26.298516 -50.259233 -36.227265 97.796601 0.0051983826 122.55783 -0.48751932 + 4600 26.564146 -50.256176 -36.082477 98.874143 0.0055736202 123.79574 -0.50751557 + 4700 26.188683 -50.252888 -36.279523 97.96053 0.0059795748 122.04598 -0.53463961 + 4800 25.22218 -50.249455 -36.791783 95.211762 0.0064081371 117.54183 -0.56057187 + 4900 23.771743 -50.245971 -37.562201 90.960801 0.0068493041 110.78242 -0.58649549 + 5000 21.981009 -50.242542 -38.514245 85.651619 0.0072921623 102.43714 -0.58569676 + 5100 20.005118 -50.239262 -39.565231 79.762203 0.0077259803 93.228984 -0.58814947 + 5200 17.987555 -50.236217 -40.638687 73.732022 0.0081412203 83.826622 -0.64456631 + 5300 16.043551 -50.23346 -41.673183 67.91308 0.0085303062 74.767062 -0.66253179 + 5400 14.252123 -50.231042 -42.626609 62.542995 0.0088880521 66.418547 -0.67647833 + 5500 12.656267 -50.228973 -43.476032 57.750687 0.0092117291 58.981452 -0.69035428 + 5600 11.269006 -50.227253 -44.214506 53.573237 0.0095008225 52.516458 -0.70182381 + 5700 10.082247 -50.225863 -44.846329 49.983875 0.0097565822 46.985857 -0.71107461 + 5800 9.075711 -50.224777 -45.382295 46.920816 0.0099814848 42.295142 -0.72796918 + 5900 8.2241323 -50.223954 -45.835845 44.308503 0.010178713 38.326566 -0.7341011 + 6000 7.5020778 -50.223364 -46.220518 42.071534 0.010351726 34.961607 -0.73860614 + 6100 6.8865776 -50.222972 -46.548535 40.142111 0.010503944 32.093218 -0.74169302 + 6200 6.3581625 -50.222743 -46.83025 38.464555 0.010638555 29.630669 -0.74355815 + 6300 5.9009471 -50.222651 -47.074112 36.993223 0.010758413 27.499927 -0.72351831 + 6400 5.5022478 -50.222668 -47.286861 35.692229 0.010866003 25.641886 -0.72491142 + 6500 5.1520445 -50.222775 -47.473825 34.533075 0.010963451 24.009849 -0.72550196 + 6600 4.842444 -50.222956 -47.639197 33.493966 0.011052555 22.567032 -0.72539576 + 6700 4.5672154 -50.223194 -47.786287 32.557859 0.011134828 21.284396 -0.72468094 + 6800 4.3214112 -50.22348 -47.917726 31.710288 0.011211542 20.138885 -0.69977477 + 6900 4.1010719 -50.223805 -48.035616 30.941022 0.011283771 19.112047 -0.6977173 + 7000 3.9029992 -50.224161 -48.141657 30.240625 0.011352422 18.188977 -0.69521625 + 7100 3.7245829 -50.22454 -48.237233 29.602229 0.011418274 17.357512 -0.69232721 + 7200 3.5636708 -50.224941 -48.323491 29.019374 0.011482 16.60762 -0.68909561 + 7300 3.4184697 -50.225359 -48.401383 28.487117 0.011544187 15.930946 -0.68553322 + 7400 3.2874703 -50.225791 -48.471712 28.00136 0.011605358 15.320455 -0.68167743 + 7500 3.1693898 -50.226236 -48.53516 27.5579 0.01166598 14.77017 -0.67389187 + 7600 3.0631284 -50.226689 -48.592311 27.15399 0.011726479 14.274964 -0.66987688 + 7700 2.9677349 -50.227151 -48.643671 26.786563 0.011787244 13.830406 -0.66561073 + 7800 2.8823804 -50.227616 -48.689679 26.453373 0.011848631 13.432632 -0.66110134 + 7900 2.8063371 -50.228091 -48.730728 26.151709 0.011910973 13.078251 -0.65637083 + 8000 2.7389612 -50.228567 -48.767153 25.879876 0.011974573 12.764262 -0.65142182 + 8100 2.6796793 -50.229048 -48.799265 25.636155 0.01203971 12.487993 -0.64626697 + 8200 2.6279769 -50.229528 -48.827332 25.418653 0.012106636 12.247046 -0.64092634 + 8300 2.583388 -50.230009 -48.851603 25.225967 0.012175578 12.039251 -0.63576886 + 8400 2.5454874 -50.230488 -48.872305 25.056681 0.012246734 11.862624 -0.63004687 + 8500 2.5138825 -50.230965 -48.889645 24.909342 0.012320275 11.715337 -0.62413585 + 8600 2.4882074 -50.231439 -48.903818 24.782526 0.012396346 11.595685 -0.65229004 + 8700 2.468117 -50.231904 -48.915003 24.674923 0.012475068 11.502059 -0.64624002 + 8800 2.4532823 -50.232364 -48.923378 24.585268 0.012556541 11.432925 -0.6399876 + 8900 2.4433865 -50.232811 -48.929106 24.512562 0.012640854 11.386808 -0.63354 + 9000 2.4381226 -50.233249 -48.932352 24.45498 0.012728083 11.362277 -0.62690844 + 9100 2.4371917 -50.233668 -48.933268 24.411953 0.012818306 11.357939 -0.62009589 + 9200 2.4403031 -50.234074 -48.932014 24.381442 0.012911605 11.372438 -0.61311776 + 9300 2.4471754 -50.234458 -48.928731 24.362769 0.013008072 11.404465 -0.60599097 + 9400 2.4575396 -50.234822 -48.923565 24.354135 0.013107819 11.452765 -0.60061336 + 9500 2.4711435 -50.235157 -48.916642 24.354998 0.013210974 11.516163 -0.59323525 + 9600 2.4877569 -50.235465 -48.908085 24.363855 0.013317688 11.593585 -0.58576008 + 9700 2.5071778 -50.235743 -48.898 24.380012 0.013428136 11.684092 -0.57821051 + 9800 2.5292388 -50.235983 -48.886469 24.402788 0.013542514 11.786902 -0.57061067 + 9900 2.5538131 -50.236185 -48.873559 24.431609 0.013661041 11.901424 -0.56299206 + 10000 2.5808184 -50.236346 -48.859312 24.466316 0.013783954 12.027276 -0.55538687 +Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms + +Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s +98.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.8924 | 2.8924 | 2.8924 | 0.0 | 19.69 +Bond | 0.00092288 | 0.00092288 | 0.00092288 | 0.0 | 0.01 +Neigh | 6.5718 | 6.5718 | 6.5718 | 0.0 | 44.73 +Comm | 0.55162 | 0.55162 | 0.55162 | 0.0 | 3.75 +Output | 0.0029431 | 0.0029431 | 0.0029431 | 0.0 | 0.02 +Modify | 4.6104 | 4.6104 | 4.6104 | 0.0 | 31.38 +Other | | 0.06102 | | | 0.42 + +Nlocal: 180 ave 180 max 180 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1510 ave 1510 max 1510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 13680 ave 13680 max 13680 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 13680 +Ave neighs/atom = 76 +Ave special neighs/atom = 0 +Neighbor list builds = 10000 +Dangerous builds not checked +Total wall time: 0:00:14 diff --git a/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.2 b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.2 new file mode 100644 index 0000000000..5ac1655e40 --- /dev/null +++ b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.2 @@ -0,0 +1,197 @@ +LAMMPS (8 Feb 2023) +Processor partition = 2 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 32 pad +variable out_freq string 100 +variable job_name string H2 + +units real +atom_style full +pair_style table linear 10000 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no + +read_data H2.data +Reading data file ... + orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 180 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +pair_coeff 1 * pair.table PAIR_H2 +WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466) + +timestep 0.001 + +velocity all create 1.0 1985 rot yes dist gaussian + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4 + +thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +thermo ${out_freq} +thermo 100 + +#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd + +#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2 + +run 10000 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.55117 + ghost atom cutoff = 11.55117 + binsize = 5.775585, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes + Step Temp PotEng TotEng Pzz espring T_ring virial + 0 1 -50.292986 -49.759421 16.18218 0 0 4.331435e-14 + 100 1.0008585 -50.292972 -49.758949 16.185544 6.2619058e-07 4.6642574 -0.0025876701 + 200 1.0034473 -50.292959 -49.757555 16.193637 2.4778684e-06 4.6763219 -0.0051513312 + 300 1.0078065 -50.292946 -49.755216 16.20654 5.4785827e-06 4.6966366 -0.0076677455 + 400 1.0140035 -50.292935 -49.751898 16.224472 9.5136721e-06 4.7255165 -0.010116117 + 500 1.022135 -50.292924 -49.747548 16.247769 1.4445387e-05 4.7634112 -0.012478816 + 600 1.0323281 -50.292913 -49.742099 16.276857 2.0128019e-05 4.810914 -0.014741354 + 700 1.044744 -50.292903 -49.735464 16.312269 2.6420278e-05 4.868775 -0.01689316 + 800 1.0595807 -50.292893 -49.727538 16.354636 3.3193675e-05 4.9379181 -0.018925599 + 900 1.0770788 -50.292883 -49.718191 16.404759 4.0337059e-05 5.0194633 -0.020834008 + 1000 1.0975267 -50.292873 -49.707271 16.463535 4.7758112e-05 5.114756 -0.022615739 + 1100 1.1212696 -50.292864 -49.694594 16.532005 5.5382858e-05 5.2254042 -0.024272115 + 1200 1.1487191 -50.292855 -49.679939 16.611504 6.3154057e-05 5.3533255 -0.025805429 + 1300 1.180366 -50.292847 -49.663045 16.703525 7.1029151e-05 5.5008084 -0.027221135 + 1400 1.2167974 -50.292839 -49.643599 16.809904 7.8978147e-05 5.6705878 -0.028525093 + 1500 1.2587168 -50.292831 -49.621224 16.932872 8.6981686e-05 5.8659431 -0.029723588 + 1600 1.3069711 -50.292824 -49.59547 17.075101 9.5029394e-05 6.0908207 -0.030823313 + 1700 1.362584 -50.292817 -49.56579 17.239763 0.00010311856 6.3499909 -0.031831844 + 1800 1.4267984 -50.29281 -49.53152 17.430752 0.00011125314 6.6492468 -0.032756757 + 1900 1.5011313 -50.292803 -49.491852 17.652797 0.00011944307 6.995657 -0.033606551 + 2000 1.5874422 -50.292796 -49.445792 17.911722 0.00012770381 7.3978879 -0.034390022 + 2100 1.6880212 -50.292789 -49.39212 18.214723 0.00013605623 7.866612 -0.035116463 + 2200 1.8057005 -50.292782 -49.329324 18.570726 0.00014452669 8.4150275 -0.035795677 + 2300 1.9439945 -50.292774 -49.255527 18.990774 0.00015314733 9.0595131 -0.036438481 + 2400 2.1072765 -50.292765 -49.168396 19.488686 0.00016195668 9.8204493 -0.037057048 + 2500 2.3009969 -50.292755 -49.065024 20.081627 0.00017100046 10.723236 -0.037663926 + 2600 2.5319487 -50.292742 -48.941783 20.791154 0.00018033268 11.799531 -0.038274916 + 2700 2.8085828 -50.292725 -48.794164 21.644055 0.00019001711 13.088716 -0.038907942 + 2800 3.1413656 -50.292704 -48.616581 22.673549 0.00020012896 14.63957 -0.039579122 + 2900 3.5431592 -50.292679 -48.402173 23.920341 0.00021075711 16.512031 -0.040310879 + 3000 4.0295773 -50.292645 -48.142604 25.434299 0.00022200654 18.778864 -0.041129941 + 3100 4.6192303 -50.292603 -47.827943 27.274622 0.00023400135 21.526798 -0.042063049 + 3200 5.3337183 -50.292548 -47.446663 29.510189 0.00024688797 24.856495 -0.043138944 + 3300 6.1971521 -50.292476 -46.985893 32.218076 0.00026083874 28.880319 -0.044388363 + 3400 7.2349077 -50.292383 -46.432089 35.479408 0.00027605543 33.716526 -0.04584988 + 3500 8.4712558 -50.292263 -45.772298 39.371841 0.00029277252 39.478225 -0.04755723 + 3600 9.9255215 -50.292106 -44.996195 43.95768 0.00031125948 46.255476 -0.04955234 + 3700 11.606583 -50.291907 -44.099041 49.265647 0.00033182131 54.089653 -0.051868152 + 3800 13.505895 -50.291653 -43.08538 55.269674 0.00035479603 62.940934 -0.060893692 + 3900 15.589876 -50.291332 -41.973119 61.864426 0.00038054772 72.652823 -0.064129637 + 4000 17.793337 -50.290932 -40.79703 68.843904 0.00040945342 82.921517 -0.070448746 + 4100 20.016417 -50.290444 -39.610385 75.893194 0.0004418827 93.281639 -0.087116518 + 4200 22.127771 -50.289857 -38.483253 82.59793 0.00047816979 103.12109 -0.097527157 + 4300 23.975968 -50.289169 -37.496432 88.481352 0.00051857989 111.73416 -0.10722194 + 4400 25.408977 -50.288385 -36.731045 93.065749 0.00056327427 118.41235 -0.11892611 + 4500 26.298632 -50.287506 -36.255477 95.950674 0.0006122807 122.55837 -0.1303584 + 4600 26.564268 -50.286547 -36.112784 96.88563 0.00066547749 123.79631 -0.14166752 + 4700 26.188807 -50.285529 -36.312099 95.820823 0.00072259756 122.04656 -0.15261419 + 4800 25.222299 -50.284475 -36.826739 92.916226 0.00078325554 117.54238 -0.16209083 + 4900 23.771855 -50.283413 -37.599583 88.509238 0.00084699472 110.78294 -0.17260047 + 5000 21.98111 -50.282357 -38.554006 83.049726 0.00091334478 102.43761 -0.18258656 + 5100 20.005206 -50.281326 -39.607248 77.020285 0.0009818775 93.229392 -0.17186696 + 5200 17.987631 -50.28033 -40.68276 70.86497 0.0010522474 83.826973 -0.18260146 + 5300 16.043616 -50.279377 -41.719065 64.938011 0.0011242079 74.767366 -0.18655435 + 5400 14.252181 -50.278457 -42.673992 59.48099 0.0011976018 66.41882 -0.20222138 + 5500 12.656323 -50.277568 -43.524597 54.622777 0.0012723319 58.981714 -0.21168712 + 5600 11.269064 -50.276696 -44.263917 50.401002 0.0013483229 52.516731 -0.20187998 + 5700 10.082312 -50.275828 -44.896259 46.788408 0.0014254889 46.986161 -0.22324171 + 5800 9.0757866 -50.274951 -45.432429 43.722025 0.0015037137 42.295494 -0.23860695 + 5900 8.2242212 -50.274058 -45.885902 41.123761 0.0015828465 38.326981 -0.25414759 + 6000 7.5021821 -50.273138 -46.270236 38.916656 0.0016627103 34.962093 -0.26976048 + 6100 6.8866987 -50.272182 -46.597681 37.031655 0.0017431162 32.093783 -0.28539248 + 6200 6.3583012 -50.27119 -46.878623 35.410368 0.0018238791 29.631315 -0.30095674 + 6300 5.9011035 -50.270159 -47.121537 34.005676 0.0019048302 27.500656 -0.31640935 + 6400 5.502422 -50.269086 -47.333186 32.779933 0.0019858256 25.642698 -0.33171137 + 6500 5.1522361 -50.267972 -47.518919 31.703747 0.0020667509 24.010742 -0.34682514 + 6600 4.8426527 -50.266817 -47.682947 30.753955 0.0021475225 22.568004 -0.36173006 + 6700 4.5674405 -50.265625 -47.828599 29.911814 0.0022280866 21.285445 -0.37640709 + 6800 4.3216522 -50.264395 -47.958513 29.163452 0.0023084174 20.140008 -0.39085666 + 6900 4.1013282 -50.26313 -48.074805 28.496518 0.0023885139 19.113242 -0.40506248 + 7000 3.9032702 -50.261831 -48.179183 27.90194 0.0024683969 18.19024 -0.41901469 + 7100 3.724868 -50.2605 -48.273041 27.371896 0.0025481062 17.35884 -0.43272933 + 7200 3.5639695 -50.259138 -48.357529 26.89966 0.0026276974 16.609012 -0.44620638 + 7300 3.4187816 -50.257743 -48.433601 26.480439 0.0027072396 15.932399 -0.45945212 + 7400 3.2877948 -50.256318 -48.502066 26.109145 0.0027868133 15.321967 -0.47246434 + 7500 3.1697267 -50.254865 -48.56361 25.781971 0.0028665077 14.77174 -0.48526006 + 7600 3.0634774 -50.25338 -48.618816 25.495767 0.0029464195 14.276591 -0.49784679 + 7700 2.9680959 -50.251868 -48.668196 25.247434 0.0030266508 13.832088 -0.51022378 + 7800 2.8827533 -50.250324 -48.712188 25.034584 0.0031073072 13.43437 -0.52242006 + 7900 2.8067218 -50.248752 -48.751183 24.854648 0.0031884966 13.080044 -0.53441576 + 8000 2.739358 -50.247146 -48.78552 24.705902 0.0032703269 12.766111 -0.54625728 + 8100 2.6800884 -50.245512 -48.815511 24.586269 0.003352905 12.4899 -0.55792685 + 8200 2.6283988 -50.243847 -48.841426 24.493934 0.0034363346 12.249013 -0.56944906 + 8300 2.5838233 -50.242148 -48.86351 24.42802 0.0035207151 12.041279 -0.58082697 + 8400 2.5459368 -50.240416 -48.881994 24.386467 0.0036061405 11.864719 -0.59207404 + 8500 2.5143471 -50.23866 -48.897093 24.367425 0.0036926982 11.717503 -0.6031939 + 8600 2.4886884 -50.236867 -48.90899 24.370737 0.0037804687 11.597926 -0.61420631 + 8700 2.4686158 -50.235045 -48.917878 24.393872 0.003869526 11.504383 -0.62511248 + 8800 2.4538005 -50.233192 -48.92393 24.436221 0.0039599381 11.43534 -0.63592614 + 8900 2.4439261 -50.231311 -48.927318 24.495987 0.0040517678 11.389323 -0.64665221 + 9000 2.4386859 -50.229399 -48.928202 24.571919 0.0041450744 11.364902 -0.65730127 + 9100 2.4377812 -50.227462 -48.926747 24.662499 0.0042399143 11.360686 -0.66787619 + 9200 2.4409216 -50.225498 -48.923108 24.766278 0.0043363422 11.375321 -0.67839903 + 9300 2.447826 -50.223507 -48.917432 24.882071 0.0044344105 11.407497 -0.68886647 + 9400 2.4582258 -50.22149 -48.909866 25.008577 0.0045341695 11.455963 -0.69927895 + 9500 2.471869 -50.219451 -48.900548 25.143849 0.0046356651 11.519544 -0.70966102 + 9600 2.4885255 -50.217386 -48.889596 25.286999 0.004738938 11.597167 -0.6940583 + 9700 2.5079938 -50.215302 -48.877125 25.436871 0.0048440213 11.687895 -0.70437543 + 9800 2.5301066 -50.213198 -48.863222 25.59205 0.0049509399 11.790946 -0.71464807 + 9900 2.5547371 -50.211072 -48.847954 25.752316 0.0050597095 11.90573 -0.72487926 + 10000 2.5818031 -50.208928 -48.831368 25.916904 0.0051703368 12.031865 -0.73506701 +Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms + +Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s +96.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.9104 | 2.9104 | 2.9104 | 0.0 | 19.81 +Bond | 0.00098079 | 0.00098079 | 0.00098079 | 0.0 | 0.01 +Neigh | 6.6139 | 6.6139 | 6.6139 | 0.0 | 45.02 +Comm | 0.55394 | 0.55394 | 0.55394 | 0.0 | 3.77 +Output | 0.0030074 | 0.0030074 | 0.0030074 | 0.0 | 0.02 +Modify | 4.5374 | 4.5374 | 4.5374 | 0.0 | 30.89 +Other | | 0.07132 | | | 0.49 + +Nlocal: 180 ave 180 max 180 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1510 ave 1510 max 1510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 13680 ave 13680 max 13680 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 13680 +Ave neighs/atom = 76 +Ave special neighs/atom = 0 +Neighbor list builds = 10000 +Dangerous builds not checked +Total wall time: 0:00:14 diff --git a/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.3 b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.3 new file mode 100644 index 0000000000..c105df63e9 --- /dev/null +++ b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.3 @@ -0,0 +1,197 @@ +LAMMPS (8 Feb 2023) +Processor partition = 3 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 32 pad +variable out_freq string 100 +variable job_name string H2 + +units real +atom_style full +pair_style table linear 10000 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no + +read_data H2.data +Reading data file ... + orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 180 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +pair_coeff 1 * pair.table PAIR_H2 +WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466) + +timestep 0.001 + +velocity all create 1.0 1985 rot yes dist gaussian + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4 + +thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +thermo ${out_freq} +thermo 100 + +#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd + +#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2 + +run 10000 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.55117 + ghost atom cutoff = 11.55117 + binsize = 5.775585, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes + Step Temp PotEng TotEng Pzz espring T_ring virial + 0 1 -50.292986 -49.759421 16.18218 0 0 4.331435e-14 + 100 0.99799183 -50.292972 -49.760479 16.176371 6.2763683e-07 15.879159 -0.0023935093 + 200 0.99208279 -50.292959 -49.763618 16.157336 2.500618e-06 15.785139 -0.0047805057 + 300 0.98260503 -50.292946 -49.768662 16.126279 5.5906177e-06 15.634338 -0.0071546335 + 400 0.97006821 -50.292934 -49.775339 16.085102 9.8548762e-06 15.434863 -0.0095106986 + 500 0.955104 -50.292922 -49.783311 16.036202 1.5241599e-05 15.196766 -0.011844212 + 600 0.93840578 -50.292908 -49.792208 15.982141 2.1695575e-05 14.931079 -0.014152859 + 700 0.92067359 -50.292894 -49.801655 15.925466 2.9163075e-05 14.64894 -0.016435757 + 800 0.90257158 -50.292879 -49.811298 15.868564 3.7595562e-05 14.360917 -0.018694156 + 900 0.88470062 -50.292862 -49.820817 15.813472 4.6952156e-05 14.07657 -0.020928907 + 1000 0.8675856 -50.292845 -49.829932 15.761951 5.7201072e-05 13.804251 -0.02314186 + 1100 0.85167476 -50.292826 -49.838402 15.715517 6.8320318e-05 13.551092 -0.025333843 + 1200 0.83734746 -50.292806 -49.846027 15.675218 8.0297954e-05 13.323129 -0.027508552 + 1300 0.8249274 -50.292785 -49.852632 15.642038 9.3132154e-05 13.125512 -0.0296698 + 1400 0.81469844 -50.292762 -49.858068 15.616792 0.00010683122 12.962757 -0.031821941 + 1500 0.80692178 -50.292739 -49.862194 15.600226 0.00012141373 12.839022 -0.033969494 + 1600 0.80185336 -50.292715 -49.864874 15.593117 0.0001369088 12.758378 -0.03611606 + 1700 0.79976156 -50.29269 -49.865965 15.596227 0.00015335664 12.725095 -0.038264652 + 1800 0.80094541 -50.292664 -49.865307 15.610404 0.00017080942 12.743931 -0.040416801 + 1900 0.80575383 -50.292637 -49.862715 15.636702 0.00018933238 12.820439 -0.042573524 + 2000 0.81460711 -50.292611 -49.857965 15.67644 0.00020900552 12.961304 -0.044736822 + 2100 0.82802133 -50.292583 -49.85078 15.731301 0.0002299256 13.174739 -0.046906382 + 2200 0.84663738 -50.292556 -49.84082 15.80341 0.00025220879 13.470941 -0.049081478 + 2300 0.87125571 -50.292527 -49.827656 15.895377 0.00027599404 13.862646 -0.051261652 + 2400 0.90287869 -50.292499 -49.810754 16.010541 0.00030144708 14.365803 -0.053443791 + 2500 0.94276179 -50.29247 -49.789446 16.15309 0.00032876555 15.000388 -0.055625674 + 2600 0.99247509 -50.292441 -49.762891 16.328426 0.00035818508 15.791381 -0.05780423 + 2700 1.0539754 -50.292412 -49.730048 16.543118 0.00038998665 16.76992 -0.059974442 + 2800 1.1296876 -50.292383 -49.689621 16.805367 0.00042450539 17.974586 -0.062128128 + 2900 1.2225906 -50.292352 -49.640021 17.125302 0.00046214072 19.452774 -0.064255792 + 3000 1.3362969 -50.292321 -49.57932 17.515126 0.000503368 21.261968 -0.066348705 + 3100 1.4751081 -50.292289 -49.505223 17.989435 0.0005487512 23.47061 -0.068394944 + 3200 1.6440125 -50.292255 -49.415068 18.56525 0.00059895625 26.158066 -0.070379528 + 3300 1.8485766 -50.292217 -49.305881 19.26156 0.00065476359 29.412908 -0.0722905 + 3400 2.0946636 -50.292172 -49.174533 20.098518 0.0007170785 33.328425 -0.070298499 + 3500 2.3878963 -50.292118 -49.01802 21.095116 0.00078693603 37.994084 -0.072718799 + 3600 2.7327825 -50.29205 -48.833933 22.267046 0.00086549715 43.481606 -0.071117313 + 3700 3.1314509 -50.291962 -48.621129 23.621508 0.00095403112 49.824863 -0.073902505 + 3800 3.5820285 -50.29185 -48.380605 25.151938 0.0010538788 56.994053 -0.082019029 + 3900 4.0768347 -50.291704 -48.116448 26.832847 0.0011663922 64.86697 -0.093365693 + 4000 4.6007622 -50.291519 -47.836714 28.612446 0.0012928467 73.203239 -0.10732489 + 4100 5.1304133 -50.29129 -47.553881 30.411364 0.0014343275 81.630577 -0.1197723 + 4200 5.6346502 -50.291011 -47.284558 32.123915 0.0015915962 89.653545 -0.13080997 + 4300 6.0770777 -50.290676 -47.04816 33.627475 0.0017649532 96.693059 -0.14165463 + 4400 6.4205234 -50.29029 -46.864523 34.796349 0.0019541156 102.15766 -0.15242678 + 4500 6.6328782 -50.28986 -46.750789 35.522716 0.0021581361 105.53646 -0.16280564 + 4600 6.692974 -50.289399 -46.718262 35.736356 0.0023753855 106.49265 -0.17244062 + 4700 6.5948627 -50.28892 -46.770133 35.418562 0.0026036121 104.93159 -0.18097864 + 4800 6.3491738 -50.288443 -46.900746 34.606797 0.0028400768 101.02241 -0.18808564 + 4900 5.981108 -50.287983 -47.096673 33.387033 0.0030817487 95.166073 -0.19348598 + 5000 5.5256727 -50.287549 -47.339243 31.878041 0.0033255323 87.919593 -0.19697013 + 5100 5.0215378 -50.287155 -47.607839 30.209726 0.0035684934 79.898246 -0.19841014 + 5200 4.5051017 -50.286803 -47.883038 28.504102 0.0038080527 71.681174 -0.19776394 + 5300 4.0060458 -50.286489 -48.149003 26.860164 0.0040421233 63.74064 -0.19507702 + 5400 3.5450327 -50.286205 -48.394699 25.34642 0.0042691817 56.405409 -0.17980245 + 5500 3.1335349 -50.28594 -48.613996 23.999815 0.0044882701 49.858022 -0.17499889 + 5600 2.7752591 -50.28568 -48.804899 22.832197 0.0046989433 44.157456 -0.1804676 + 5700 2.468384 -50.285415 -48.968371 21.836436 0.0049011768 39.274732 -0.17203381 + 5800 2.2078676 -50.285131 -49.10709 20.994608 0.0050952576 35.129626 -0.17967923 + 5900 1.9873283 -50.284819 -49.22445 20.285865 0.0052816779 31.620602 -0.18651596 + 6000 1.8003086 -50.284474 -49.323892 19.687668 0.0054610429 28.64491 -0.19262321 + 6100 1.640963 -50.284092 -49.408531 19.181029 0.0056340011 26.109545 -0.1982684 + 6200 1.50433 -50.283675 -49.481017 18.749125 0.0058011964 23.935562 -0.19911595 + 6300 1.3863531 -50.283219 -49.543509 18.379087 0.0059632392 22.058419 -0.20020649 + 6400 1.2837837 -50.28273 -49.597748 18.059898 0.0061206908 20.426426 -0.20439271 + 6500 1.1940433 -50.282206 -49.645106 17.783505 0.0062740588 18.998556 -0.19989782 + 6600 1.1150882 -50.281655 -49.686683 17.543117 0.0064237975 17.742293 -0.20427813 + 6700 1.0452925 -50.281076 -49.723345 17.333683 0.0065703119 16.631765 -0.20875566 + 6800 0.98335363 -50.28048 -49.755796 17.150648 0.0067139628 15.646249 -0.21165511 + 6900 0.92821916 -50.279858 -49.784593 16.991122 0.0068550735 14.768998 -0.21447191 + 7000 0.87903062 -50.279219 -49.810199 16.85215 0.0069939349 13.986354 -0.21690274 + 7100 0.83508106 -50.27857 -49.833 16.730809 0.0071308114 13.287068 -0.21879935 + 7200 0.79578318 -50.277905 -49.853302 16.625931 0.007265945 12.661795 -0.24086146 + 7300 0.76064516 -50.277227 -49.871373 16.535639 0.0073995599 12.10271 -0.24389998 + 7400 0.72925259 -50.27654 -49.887437 16.458538 0.0075318653 11.603219 -0.24724178 + 7500 0.70125479 -50.275848 -49.901683 16.39318 0.0076630586 11.157743 -0.24974257 + 7600 0.67635448 -50.275145 -49.914266 16.338958 0.0077933274 10.761551 -0.26938357 + 7700 0.65430014 -50.274434 -49.925322 16.294582 0.0079228516 10.410642 -0.27182741 + 7800 0.63488023 -50.273717 -49.934967 16.259573 0.0080518043 10.10165 -0.27327965 + 7900 0.61791898 -50.272993 -49.943293 16.233056 0.0081803536 9.8317776 -0.23270163 + 8000 0.60327334 -50.272261 -49.950375 16.214226 0.0083086629 9.5987492 -0.21174158 + 8100 0.59083054 -50.271521 -49.956274 16.203107 0.008436892 9.4007703 -0.20591477 + 8200 0.580506 -50.270774 -49.961036 16.198733 0.0085651973 9.2364955 -0.20633623 + 8300 0.57224102 -50.270016 -49.964688 16.201153 0.0086937323 9.1049904 -0.21200577 + 8400 0.56599941 -50.26925 -49.967252 16.209734 0.0088226478 9.0056795 -0.21499276 + 8500 0.56176264 -50.268474 -49.968737 16.224404 0.0089520921 8.9382678 -0.22565885 + 8600 0.55952259 -50.267687 -49.969145 16.244765 0.0090822109 8.9026261 -0.23453558 + 8700 0.55927158 -50.26689 -49.968482 16.270388 0.0092131476 8.8986323 -0.23126478 + 8800 0.56098987 -50.266078 -49.966754 16.301455 0.009345043 8.9259722 -0.23759225 + 8900 0.56463156 -50.265253 -49.963985 16.338219 0.0094780352 8.9839155 -0.25830691 + 9000 0.57011105 -50.264414 -49.960222 16.379852 0.0096122592 9.0711003 -0.24455142 + 9100 0.57729304 -50.263559 -49.955536 16.42695 0.0097478463 9.1853737 -0.25035816 + 9200 0.5859895 -50.262689 -49.950026 16.479216 0.0098849239 9.3237441 -0.2560083 + 9300 0.59596674 -50.261803 -49.943816 16.536984 0.010023615 9.482493 -0.26141076 + 9400 0.60696386 -50.2609 -49.937045 16.600194 0.010164037 9.6574694 -0.26654733 + 9500 0.61872142 -50.259982 -49.929854 16.669166 0.010306303 9.8445453 -0.2741745 + 9600 0.63101587 -50.259043 -49.922355 16.744325 0.010450522 10.040164 -0.27940426 + 9700 0.64369292 -50.258089 -49.914637 16.82549 0.010596798 10.24187 -0.28435931 + 9800 0.65669202 -50.257118 -49.906731 16.913131 0.010745233 10.4487 -0.28904477 + 9900 0.67005575 -50.256133 -49.898615 17.007446 0.01089593 10.661331 -0.29344272 + 10000 0.68392108 -50.25513 -49.890213 17.108905 0.011048996 10.881944 -0.29755711 +Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms + +Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s +98.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.8325 | 2.8325 | 2.8325 | 0.0 | 19.28 +Bond | 0.0010203 | 0.0010203 | 0.0010203 | 0.0 | 0.01 +Neigh | 6.5808 | 6.5808 | 6.5808 | 0.0 | 44.80 +Comm | 0.55003 | 0.55003 | 0.55003 | 0.0 | 3.74 +Output | 0.0030145 | 0.0030145 | 0.0030145 | 0.0 | 0.02 +Modify | 4.6599 | 4.6599 | 4.6599 | 0.0 | 31.72 +Other | | 0.06363 | | | 0.43 + +Nlocal: 180 ave 180 max 180 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1510 ave 1510 max 1510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 13680 ave 13680 max 13680 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 13680 +Ave neighs/atom = 76 +Ave special neighs/atom = 0 +Neighbor list builds = 10000 +Dangerous builds not checked +Total wall time: 0:00:14 diff --git a/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.4 b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.4 new file mode 100644 index 0000000000..cf64a9f262 --- /dev/null +++ b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.4 @@ -0,0 +1,197 @@ +LAMMPS (8 Feb 2023) +Processor partition = 4 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 32 pad +variable out_freq string 100 +variable job_name string H2 + +units real +atom_style full +pair_style table linear 10000 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no + +read_data H2.data +Reading data file ... + orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 180 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +pair_coeff 1 * pair.table PAIR_H2 +WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466) + +timestep 0.001 + +velocity all create 1.0 1985 rot yes dist gaussian + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4 + +thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +thermo ${out_freq} +thermo 100 + +#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd + +#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2 + +run 10000 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.55117 + ghost atom cutoff = 11.55117 + binsize = 5.775585, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes + Step Temp PotEng TotEng Pzz espring T_ring virial + 0 1 -50.292986 -49.759421 16.18218 0 0 4.331435e-14 + 100 0.99799183 -50.292972 -49.760479 16.17637 1.1826193e-13 15.879159 -0.0025913805 + 200 0.99208279 -50.292959 -49.763618 16.157337 7.489305e-12 15.785139 -0.0051808234 + 300 0.98260503 -50.292946 -49.768662 16.126285 8.3895453e-11 15.634338 -0.0077662384 + 400 0.97006821 -50.292933 -49.775339 16.085117 4.6129385e-10 15.434863 -0.010346287 + 500 0.955104 -50.292921 -49.783311 16.036242 1.7157587e-09 15.196766 -0.012920943 + 600 0.93840577 -50.292907 -49.792206 15.982224 4.9828406e-09 14.931079 -0.015491155 + 700 0.92067358 -50.292891 -49.801652 15.925608 1.2201305e-08 14.64894 -0.018055916 + 800 0.90257157 -50.292875 -49.811294 15.868782 2.6375763e-08 14.360917 -0.020616424 + 900 0.88470061 -50.292856 -49.820811 15.813794 5.1849593e-08 14.07657 -0.02317448 + 1000 0.86758559 -50.292836 -49.829923 15.762447 9.4579685e-08 13.804251 -0.025732882 + 1100 0.85167475 -50.292814 -49.83839 15.716171 1.6240678e-07 13.551092 -0.028294045 + 1200 0.83734745 -50.29279 -49.846011 15.676049 2.6532099e-07 13.323128 -0.030863385 + 1300 0.82492738 -50.292764 -49.852612 15.643102 4.1573034e-07 13.125511 -0.033446749 + 1400 0.81469842 -50.292737 -49.858042 15.618114 6.287493e-07 12.962757 -0.036050518 + 1500 0.80692176 -50.292706 -49.862161 15.601972 9.2253166e-07 12.839022 -0.038681006 + 1600 0.80185333 -50.292674 -49.864833 15.595319 1.3186783e-06 12.758377 -0.041346087 + 1700 0.79976154 -50.292639 -49.865914 15.598922 1.8427553e-06 12.725095 -0.044055451 + 1800 0.80094538 -50.2926 -49.865244 15.613674 2.524964e-06 12.743931 -0.046819731 + 1900 0.80575381 -50.292559 -49.862637 15.640669 3.4010112e-06 12.820438 -0.049651934 + 2000 0.81460709 -50.292514 -49.857868 15.681364 4.5132409e-06 12.961304 -0.052564979 + 2100 0.82802133 -50.292465 -49.850661 15.73743 5.9121027e-06 13.174739 -0.055577058 + 2200 0.84663739 -50.29241 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2.0946648 -50.290659 -49.17302 20.177003 0.00011076549 33.328444 -0.11794183 + 3500 2.3878978 -50.290296 -49.016197 21.189599 0.00013679846 37.994106 -0.12634541 + 3600 2.7327842 -50.289862 -48.831744 22.380493 0.0001689033 43.481633 -0.13563052 + 3700 3.1314527 -50.289342 -48.618508 23.757417 0.00020840179 49.824892 -0.1458703 + 3800 3.5820304 -50.288721 -48.377475 25.31432 0.00025679499 56.994084 -0.15714078 + 3900 4.0768367 -50.287983 -48.112726 27.026228 0.0003157187 64.867001 -0.1694959 + 4000 4.6007641 -50.287108 -47.832302 28.841926 0.0003868587 73.203268 -0.18296156 + 4100 5.1304148 -50.286087 -47.548677 30.682328 0.00047181946 81.6306 -0.19756083 + 4200 5.6346511 -50.284903 -47.278451 32.442736 0.00057194846 89.653559 -0.21328268 + 4300 6.0770778 -50.283545 -47.041029 33.999964 0.00068813116 96.69306 -0.23008376 + 4400 6.4205225 -50.282013 -46.856246 35.229403 0.00082058594 102.15765 -0.24791296 + 4500 6.6328762 -50.280301 -46.74123 36.023883 0.0009687004 105.53643 -0.26668503 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-0.75286641 + 7000 0.87904844 -50.210704 -49.741675 20.721268 0.0045481845 13.986637 -0.7692006 + 7100 0.83509929 -50.207463 -49.761883 20.757758 0.0046521178 13.287358 -0.78517926 + 7200 0.79580187 -50.204208 -49.779596 20.810709 0.0047552948 12.662092 -0.80082697 + 7300 0.76066442 -50.200945 -49.795082 20.878241 0.0048577976 12.103016 -0.8161606 + 7400 0.72927251 -50.197671 -49.808557 20.959362 0.0049596993 11.603536 -0.83120088 + 7500 0.70127548 -50.194387 -49.820211 21.052437 0.0050610673 11.158072 -0.84595004 + 7600 0.67637608 -50.191091 -49.830201 21.156826 0.005161965 10.761895 -0.86043159 + 7700 0.65432278 -50.187783 -49.838659 21.271416 0.0052624536 10.411002 -0.87466503 + 7800 0.63490405 -50.184459 -49.845696 21.395737 0.0053625933 10.102029 -0.88866261 + 7900 0.61794415 -50.181125 -49.851412 21.52846 0.0054624448 9.8321781 -0.90243744 + 8000 0.60330004 -50.177777 -49.855877 21.669443 0.0055620701 9.599174 -0.91600112 + 8100 0.59085898 -50.174411 -49.859149 21.81797 0.0056615336 9.4012229 -0.92936588 + 8200 0.58053641 -50.171025 -49.861271 21.974141 0.0057609033 9.2369793 -0.94255403 + 8300 0.57227364 -50.16762 -49.862274 22.13688 0.0058602524 9.1055094 -0.95557385 + 8400 0.5660345 -50.164193 -49.862177 22.306138 0.0059596607 9.0062378 -0.9684373 + 8500 0.56180048 -50.160744 -49.860987 22.48185 0.0060592167 8.9388698 -0.98115048 + 8600 0.55956345 -50.15727 -49.858706 22.663291 0.0061590199 8.9032763 -0.9937296 + 8700 0.55931575 -50.15377 -49.855339 22.850832 0.0062591826 8.899335 -1.0061868 + 8800 0.56103758 -50.150241 -49.850891 23.043918 0.006359832 8.9267313 -1.0185265 + 8900 0.564683 -50.146681 -49.845386 23.242887 0.0064611118 8.984734 -1.0307694 + 9000 0.57016633 -50.143095 -49.838874 23.44706 0.0065631821 9.0719798 -1.0429186 + 9100 0.57735215 -50.139473 -49.831418 23.657034 0.0066662188 9.1863142 -1.0549883 + 9200 0.58605231 -50.13582 -49.823123 23.872662 0.0067704103 9.3247434 -1.0669874 + 9300 0.59603298 -50.132131 -49.814109 24.094175 0.0068759533 9.483547 -1.078929 + 9400 0.60703315 -50.128412 -49.80452 24.321354 0.0069830466 9.6585719 -1.0908215 + 9500 0.61879332 -50.124656 -49.79449 24.554693 0.0070918841 9.8456893 -1.1026826 + 9600 0.63108995 -50.120866 -49.784139 24.794372 0.0072026473 10.041342 -1.1145246 + 9700 0.64376884 -50.117043 -49.773551 25.040354 0.0073154993 10.243078 -1.1263585 + 9800 0.6567696 -50.113185 -49.762755 25.293643 0.00743058 10.449934 -1.1381891 + 9900 0.67013503 -50.109296 -49.751736 25.553866 0.0075480045 10.662593 -1.150037 + 10000 0.68400233 -50.105373 -49.740413 25.821695 0.007667864 10.883237 -1.1619081 +Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms + +Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s +96.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.9541 | 2.9541 | 2.9541 | 0.0 | 20.11 +Bond | 0.00096595 | 0.00096595 | 0.00096595 | 0.0 | 0.01 +Neigh | 6.6965 | 6.6965 | 6.6965 | 0.0 | 45.58 +Comm | 0.55386 | 0.55386 | 0.55386 | 0.0 | 3.77 +Output | 0.0030352 | 0.0030352 | 0.0030352 | 0.0 | 0.02 +Modify | 4.4131 | 4.4131 | 4.4131 | 0.0 | 30.04 +Other | | 0.06945 | | | 0.47 + +Nlocal: 180 ave 180 max 180 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1510 ave 1510 max 1510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 13680 ave 13680 max 13680 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 13680 +Ave neighs/atom = 76 +Ave special neighs/atom = 0 +Neighbor list builds = 10000 +Dangerous builds not checked +Total wall time: 0:00:14 diff --git a/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.5 b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.5 new file mode 100644 index 0000000000..46e98fcbe1 --- /dev/null +++ b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.5 @@ -0,0 +1,197 @@ +LAMMPS (8 Feb 2023) +Processor partition = 5 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 32 pad +variable out_freq string 100 +variable job_name string H2 + +units real +atom_style full +pair_style table linear 10000 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no + +read_data H2.data +Reading data file ... + orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 180 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +pair_coeff 1 * pair.table PAIR_H2 +WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466) + +timestep 0.001 + +velocity all create 1.0 1985 rot yes dist gaussian + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4 + +thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +thermo ${out_freq} +thermo 100 + +#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd + +#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2 + +run 10000 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.55117 + ghost atom cutoff = 11.55117 + binsize = 5.775585, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes + Step Temp PotEng TotEng Pzz espring T_ring virial + 0 1 -50.292986 -49.759421 16.18218 0 0 4.331435e-14 + 100 0.9951423 -50.292972 -49.761999 16.167253 6.8948763e-13 27.030021 -0.0025924671 + 200 0.98099313 -50.292959 -49.769535 16.12199 4.364663e-11 26.645702 -0.0051895017 + 300 0.95873287 -50.292945 -49.781399 16.050646 4.8814317e-10 26.041069 -0.0077954546 + 400 0.93006021 -50.292933 -49.796685 15.959334 2.6734695e-09 25.262263 -0.010415337 + 500 0.89689329 -50.29292 -49.814369 15.854928 9.8711643e-09 24.361385 -0.013055676 + 600 0.86110024 -50.292904 -49.833451 15.743908 2.8339559e-08 23.389175 -0.015723485 + 700 0.82431428 -50.292887 -49.853062 15.63173 6.8290594e-08 22.389996 -0.018423373 + 800 0.78784526 -50.292868 -49.872501 15.522613 1.4463127e-07 21.399426 -0.021164155 + 900 0.7526687 -50.292845 -49.891248 15.419533 2.77427e-07 20.443961 -0.023953669 + 1000 0.71946253 -50.29282 -49.90894 15.324327 4.9211825e-07 19.542016 -0.026800589 + 1100 0.6886647 -50.29279 -49.925343 15.237994 8.1957891e-07 18.705487 -0.029714543 + 1200 0.66053403 -50.292757 -49.940319 15.160974 1.2961277e-06 17.941403 -0.032707733 + 1300 0.63520454 -50.292719 -49.953796 15.093459 1.963599e-06 17.253404 -0.035794247 + 1400 0.61273022 -50.292676 -49.965745 15.035373 2.869563e-06 16.642957 -0.03898766 + 1500 0.59312003 -50.292628 -49.976159 14.9866 4.0677665e-06 16.110306 -0.042305977 + 1600 0.57636482 -50.292572 -49.985044 14.947135 5.6188557e-06 15.655201 -0.045764398 + 1700 0.56245786 -50.292508 -49.992401 14.916846 7.5914412e-06 15.277461 -0.049383169 + 1800 0.55141125 -50.292438 -49.998224 14.895701 1.0063569e-05 14.977413 -0.053180653 + 1900 0.54326954 -50.292356 -50.002487 14.8841 1.3124682e-05 14.756269 -0.057185281 + 2000 0.53812235 -50.292262 -50.005139 14.882365 1.6878177e-05 14.616461 -0.06142508 + 2100 0.53611706 -50.292157 -50.006103 14.891003 2.1444699e-05 14.561993 -0.065932846 + 2200 0.5374728 -50.292036 -50.005259 14.911208 2.6966349e-05 14.598818 -0.070740681 + 2300 0.54249683 -50.291895 -50.002438 14.944078 3.3612057e-05 14.73528 -0.075893774 + 2400 0.55160424 -50.291734 -49.997418 14.991434 4.1584413e-05 14.982655 -0.081441387 + 2500 0.56534189 -50.291548 -49.989902 15.055565 5.1128356e-05 15.355797 -0.08743341 + 2600 0.58441729 -50.291332 -49.979508 15.139015 6.2542191e-05 15.873922 -0.093934223 + 2700 0.60973261 -50.291079 -49.965747 15.245349 7.6191529e-05 16.561536 -0.10101976 + 2800 0.64242331 -50.290782 -49.948007 15.379156 9.2526793e-05 17.44948 -0.10876973 + 2900 0.68389894 -50.290432 -49.925527 15.54557 0.00011210502 18.576039 -0.11728634 + 3000 0.7358813 -50.29002 -49.89738 15.751474 0.00013561664 19.987983 -0.12666711 + 3100 0.80043068 -50.289531 -49.862449 16.004894 0.00016391766 21.741271 -0.13702882 + 3200 0.87994476 -50.288947 -49.819439 16.314811 0.00019806723 23.901029 -0.14852041 + 3300 0.97710684 -50.288249 -49.766899 16.691936 0.00023936963 26.540142 -0.16126751 + 3400 1.0947513 -50.287415 -49.703294 17.14741 0.00028941795 29.735596 -0.17542667 + 3500 1.2356068 -50.286413 -49.627136 17.692223 0.00035013447 33.561511 -0.19115489 + 3600 1.401879 -50.285209 -49.537215 18.336419 0.00042379924 38.077789 -0.20858771 + 3700 1.5946465 -50.283764 -49.432917 19.085164 0.00051305445 43.313732 -0.22786881 + 3800 1.8130867 -50.282042 -49.314643 19.93789 0.00062086813 49.246998 -0.24911566 + 3900 2.0536114 -50.279989 -49.184254 20.885144 0.0007504384 55.780123 -0.27238956 + 4000 2.3090877 -50.277563 -49.045514 21.903844 0.00090502091 62.71936 -0.29774099 + 4100 2.5684074 -50.274725 -48.904312 22.957566 0.00108767 69.762993 -0.32513211 + 4200 2.8167154 -50.271434 -48.768533 23.996177 0.0013008998 76.507527 -0.35448596 + 4300 3.036538 -50.267666 -48.647475 24.959984 0.0015462956 82.478341 -0.38565277 + 4400 3.2098498 -50.263408 -48.550744 25.787127 0.0018241308 87.185831 -0.41841744 + 4500 3.3207993 -50.258668 -48.486806 26.421384 0.0021330655 90.199435 -0.45253018 + 4600 3.3584953 -50.253474 -48.461498 26.823507 0.0024700053 91.223334 -0.48770345 + 4700 3.3191098 -50.247864 -48.476903 26.979088 0.002830177 90.153547 -0.523627 + 4800 3.2066723 -50.24189 -48.530922 26.900395 0.0032074389 87.099523 -0.55998518 + 4900 3.032313 -50.235626 -48.61769 26.623396 0.0035947863 82.363581 -0.59650144 + 5000 2.8121843 -50.229136 -48.728653 26.202501 0.0039849754 76.384452 -0.63291394 + 5100 2.5646536 -50.222488 -48.854078 25.698898 0.0043711592 69.661033 -0.66900289 + 5200 2.3074927 -50.215744 -48.984547 25.172075 0.0047474367 62.676038 -0.70458409 + 5300 2.0556743 -50.208948 -49.112112 24.671889 0.0051092373 55.836155 -0.73953676 + 5400 1.8201204 -50.202145 -49.230993 24.233676 0.0054535012 49.438049 -0.77374738 + 5500 1.6074397 -50.195362 -49.337688 23.877579 0.0057786579 43.661222 -0.80716644 + 5600 1.4204402 -50.188613 -49.430716 23.612103 0.0060844379 38.581947 -0.83975723 + 5700 1.2590781 -50.181911 -49.510111 23.435375 0.0063715815 34.199035 -0.8715173 + 5800 1.1215024 -50.175255 -49.576861 23.340009 0.0066415095 30.462209 -0.90243963 + 5900 1.0049565 -50.168645 -49.632435 23.316226 0.0068960167 27.296594 -0.93254359 + 6000 0.90642655 -50.162073 -49.678436 23.35333 0.0071370232 24.620327 -0.96187362 + 6100 0.82303426 -50.15554 -49.716398 23.441044 0.0073664003 22.355228 -0.99044001 + 6200 0.75222945 -50.149036 -49.747672 23.571168 0.0075858646 20.432031 -1.0182716 + 6300 0.69185157 -50.142555 -49.773408 23.736184 0.0077969274 18.792049 -1.0454141 + 6400 0.64011849 -50.1361 -49.794555 23.930273 0.0080008828 17.386876 -1.0718977 + 6500 0.59558258 -50.129659 -49.811877 24.148617 0.0081988179 16.177194 -1.0977481 + 6600 0.55707711 -50.123229 -49.825992 24.387764 0.0083916354 15.131309 -1.1230042 + 6700 0.52366443 -50.11681 -49.837401 24.644278 0.0085800803 14.223755 -1.1476911 + 6800 0.49459087 -50.110398 -49.846502 24.915585 0.0087647672 13.43406 -1.1718456 + 6900 0.46924933 -50.103993 -49.853618 25.199975 0.0089462046 12.745734 -1.1954836 + 7000 0.44714908 -50.09759 -49.859007 25.495663 0.0091248169 12.145448 -1.2186489 + 7100 0.42789171 -50.09119 -49.862882 25.801204 0.0093009621 11.62238 -1.2413589 + 7200 0.41115213 -50.084791 -49.865415 26.115435 0.0094749465 11.1677 -1.2636357 + 7300 0.39666341 -50.078389 -49.866743 26.43778 0.0096470373 10.774158 -1.2855199 + 7400 0.38420469 -50.071981 -49.866983 26.767492 0.0098174711 10.435755 -1.3070246 + 7500 0.37359146 -50.065568 -49.866233 27.103933 0.0099864621 10.147478 -1.3281809 + 7600 0.36466763 -50.059148 -49.864574 27.446285 0.010154207 9.9050896 -1.3490095 + 7700 0.35729911 -50.052716 -49.862074 27.794551 0.010320892 9.7049462 -1.3695395 + 7800 0.35136861 -50.046271 -49.858793 28.148371 0.010486691 9.5438621 -1.3897895 + 7900 0.34677153 -50.039813 -49.854788 28.507205 0.010651775 9.4189963 -1.4097881 + 8000 0.34341297 -50.033336 -49.850103 28.870887 0.010816309 9.3277714 -1.4295506 + 8100 0.34120579 -50.026841 -49.844785 29.238802 0.010980456 9.2678199 -1.4491058 + 8200 0.3400696 -50.020321 -49.838872 29.611242 0.011144377 9.2369587 -1.4684765 + 8300 0.33993073 -50.013777 -49.832402 29.987651 0.011308235 9.2331869 -1.4876802 + 8400 0.34072278 -50.007208 -49.82541 30.367811 0.011472193 9.2547003 -1.5067423 + 8500 0.34238718 -50.000608 -49.817922 30.75172 0.011636417 9.2999089 -1.5256766 + 8600 0.34487349 -49.993976 -49.809964 31.138912 0.011801076 9.3674418 -1.5445114 + 8700 0.34813839 -49.987308 -49.801554 31.529558 0.011966343 9.4561231 -1.5632615 + 8800 0.35214326 -49.980605 -49.792714 31.923412 0.012132398 9.5649031 -1.5819515 + 8900 0.35684992 -49.973862 -49.783459 32.320438 0.012299427 9.6927453 -1.6005873 + 9000 0.36221521 -49.967079 -49.773813 32.720589 0.012467623 9.8384771 -1.6191906 + 9100 0.36818518 -49.96025 -49.763799 33.12412 0.012637186 10.000633 -1.6377754 + 9200 0.3746904 -49.953378 -49.753456 33.530521 0.012808324 10.177328 -1.6563518 + 9300 0.3816439 -49.946457 -49.742826 33.940033 0.01298125 10.366198 -1.6749285 + 9400 0.3889426 -49.939487 -49.73196 34.352706 0.013156185 10.564445 -1.6935206 + 9500 0.39647284 -49.932468 -49.720924 34.768109 0.01333335 10.768982 -1.712126 + 9600 0.40411904 -49.925391 -49.709767 35.186397 0.013512971 10.976668 -1.7307508 + 9700 0.41177414 -49.918266 -49.698558 35.606965 0.013695276 11.184595 -1.7493922 + 9800 0.41934973 -49.911084 -49.687333 36.03058 0.013880493 11.390363 -1.7680484 + 9900 0.42678411 -49.903846 -49.676129 36.456503 0.014068856 11.592295 -1.7867244 + 10000 0.43404714 -49.896555 -49.664963 36.884919 0.014260602 11.789574 -1.8054063 +Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms + +Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s +98.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.9459 | 2.9459 | 2.9459 | 0.0 | 20.05 +Bond | 0.0010983 | 0.0010983 | 0.0010983 | 0.0 | 0.01 +Neigh | 6.4646 | 6.4646 | 6.4646 | 0.0 | 44.00 +Comm | 0.54538 | 0.54538 | 0.54538 | 0.0 | 3.71 +Output | 0.0030317 | 0.0030317 | 0.0030317 | 0.0 | 0.02 +Modify | 4.662 | 4.662 | 4.662 | 0.0 | 31.73 +Other | | 0.06897 | | | 0.47 + +Nlocal: 180 ave 180 max 180 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1510 ave 1510 max 1510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 13680 ave 13680 max 13680 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 13680 +Ave neighs/atom = 76 +Ave special neighs/atom = 0 +Neighbor list builds = 10000 +Dangerous builds not checked +Total wall time: 0:00:14 diff --git a/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.6 b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.6 new file mode 100644 index 0000000000..ae27b84d32 --- /dev/null +++ b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.6 @@ -0,0 +1,197 @@ +LAMMPS (8 Feb 2023) +Processor partition = 6 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 32 pad +variable out_freq string 100 +variable job_name string H2 + +units real +atom_style full +pair_style table linear 10000 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no + +read_data H2.data +Reading data file ... + orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 180 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds + +pair_coeff 1 * pair.table PAIR_H2 +WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466) + +timestep 0.001 + +velocity all create 1.0 1985 rot yes dist gaussian + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4 + +thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +thermo ${out_freq} +thermo 100 + +#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd + +#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2 + +run 10000 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.55117 + ghost atom cutoff = 11.55117 + binsize = 5.775585, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes + Step Temp PotEng TotEng Pzz espring T_ring virial + 0 1 -50.292986 -49.759421 16.18218 0 0 4.331435e-14 + 100 0.9951423 -50.292972 -49.761999 16.167254 3.663073e-06 27.030021 -0.0025950927 + 200 0.98099313 -50.292958 -49.769535 16.121999 1.4652294e-05 26.645702 -0.0052104718 + 300 0.95873287 -50.292945 -49.781399 16.050672 3.2966429e-05 26.041069 -0.0078660339 + 400 0.93006021 -50.292932 -49.796684 15.959387 5.8599875e-05 25.262263 -0.010582044 + 500 0.89689329 -50.292917 -49.814366 15.855074 9.1539141e-05 24.361385 -0.013380753 + 600 0.86110024 -50.292898 -49.833445 15.744205 0.00013176059 23.389175 -0.016282487 + 700 0.82431428 -50.292877 -49.853052 15.632253 0.00017923062 22.389996 -0.019305323 + 800 0.78784526 -50.29285 -49.872483 15.523595 0.00023390859 21.399426 -0.022473781 + 900 0.7526687 -50.292816 -49.891219 15.421094 0.00029575217 20.443961 -0.025805439 + 1000 0.71946253 -50.292776 -49.908896 15.326586 0.0003647244 19.542016 -0.029318877 + 1100 0.6886647 -50.292726 -49.925279 15.241234 0.00044080156 18.705487 -0.033035613 + 1200 0.66053404 -50.292668 -49.94023 15.165485 0.00052398138 17.941403 -0.036980816 + 1300 0.63520455 -50.292595 -49.953672 15.099745 0.00061429107 17.253404 -0.041183239 + 1400 0.61273022 -50.292511 -49.965579 15.043883 0.00071179519 16.642957 -0.045662316 + 1500 0.59312004 -50.29241 -49.975942 14.99787 0.00081660341 16.110306 -0.050440479 + 1600 0.57636482 -50.292289 -49.984761 14.961722 0.00092887845 15.655202 -0.055550832 + 1700 0.56245787 -50.292149 -49.992041 14.935319 0.0010488445 15.277461 -0.061027295 + 1800 0.55141126 -50.291984 -49.99777 14.919091 0.0011767964 14.977414 -0.066900795 + 1900 0.54326956 -50.291792 -50.001923 14.913094 0.0013131107 14.756269 -0.073216193 + 2000 0.53812238 -50.29157 -50.004447 14.917947 0.0014582582 14.616462 -0.080017237 + 2100 0.53611709 -50.291312 -50.005259 14.934473 0.0016128191 14.561994 -0.087363239 + 2200 0.53747284 -50.291009 -50.004233 14.964038 0.0017775021 14.598819 -0.095297839 + 2300 0.54249688 -50.290657 -50.001199 15.008081 0.0019531669 14.735282 -0.10390758 + 2400 0.5516043 -50.290246 -49.995929 15.068555 0.0021408527 14.982657 -0.11326027 + 2500 0.56534197 -50.289766 -49.988119 15.147769 0.0023418123 15.355799 -0.12345646 + 2600 0.58441738 -50.289207 -49.977382 15.249155 0.0025575544 15.873925 -0.13459188 + 2700 0.60973272 -50.28855 -49.963218 15.376625 0.0027898943 16.561539 -0.14680402 + 2800 0.64242344 -50.287778 -49.945003 15.535379 0.0030410156 17.449483 -0.16021499 + 2900 0.68389909 -50.286869 -49.921964 15.731194 0.003313542 18.576043 -0.1749965 + 3000 0.73588147 -50.28579 -49.893149 15.972304 0.0036106211 19.987987 -0.19131687 + 3100 0.80043087 -50.284508 -49.857426 16.267625 0.0039360184 21.741276 -0.20938994 + 3200 0.87994497 -50.282984 -49.813476 16.627323 0.0042942181 23.901035 -0.229419 + 3300 0.97710707 -50.281162 -49.759812 17.064318 0.0046905236 26.540149 -0.25165651 + 3400 1.0947515 -50.278979 -49.694858 17.591402 0.0051311469 29.735603 -0.27634359 + 3500 1.2356071 -50.276358 -49.617081 18.222808 0.0056232657 33.561517 -0.30373125 + 3600 1.4018792 -50.273211 -49.525217 18.97057 0.0061750242 38.077795 -0.33406344 + 3700 1.5946467 -50.269438 -49.41859 19.844391 0.0067954397 43.313738 -0.36756248 + 3800 1.8130868 -50.264926 -49.297526 20.847335 0.0074941739 49.247003 -0.4044001 + 3900 2.0536116 -50.259558 -49.163823 21.972799 0.0082811282 55.780127 -0.44468343 + 4000 2.3090877 -50.253214 -49.021165 23.203274 0.0091658295 62.719362 -0.48844585 + 4100 2.5684074 -50.245778 -48.875365 24.50535 0.010156603 69.762993 -0.53559997 + 4200 2.8167153 -50.237155 -48.734254 25.832794 0.011259571 76.507524 -0.58595872 + 4300 3.0365377 -50.22728 -48.607089 27.128084 0.012477576 82.478334 -0.63920669 + 4400 3.2098494 -50.216129 -48.503465 28.32938 0.013809186 87.18582 -0.69492156 + 4500 3.3207987 -50.203729 -48.431867 29.380289 0.015247971 90.19942 -0.75258375 + 4600 3.3584946 -50.190151 -48.398176 30.239405 0.016782256 91.223315 -0.81162394 + 4700 3.319109 -50.175529 -48.404569 30.887433 0.01839546 90.153525 -0.87142276 + 4800 3.2066714 -50.160034 -48.449067 31.329923 0.020067061 87.099499 -0.93139568 + 4900 3.0323121 -50.14386 -48.525924 31.596801 0.021774071 82.363558 -0.99098372 + 5000 2.8121835 -50.127216 -48.626733 31.734704 0.02349282 76.384432 -1.04971 + 5100 2.5646531 -50.11031 -48.741901 31.798135 0.025200765 69.661019 -1.1071803 + 5200 2.3074925 -50.093317 -48.86212 31.840218 0.026878076 62.676032 -1.16309 + 5300 2.0556744 -50.076391 -48.979555 31.905031 0.028508785 55.836159 -1.217247 + 5400 1.820121 -50.059654 -49.088501 32.023732 0.030081384 49.438064 -1.2695269 + 5500 1.6074407 -50.04318 -49.185506 32.214415 0.031588873 43.661248 -1.319891 + 5600 1.4204416 -50.02701 -49.269112 32.484092 0.033028319 38.581985 -1.3683615 + 5700 1.2590798 -50.011162 -49.339361 32.830285 0.034400107 34.199083 -1.4149934 + 5800 1.1215045 -49.995631 -49.397236 33.245821 0.035707041 30.462267 -1.4598878 + 5900 1.0049589 -49.980399 -49.444188 33.721747 0.03695346 27.29666 -1.5031416 + 6000 0.90642926 -49.965438 -49.4818 34.248321 0.038144494 24.620401 -1.5448741 + 6100 0.82303723 -49.950718 -49.511574 34.817039 0.039285497 22.355309 -1.585191 + 6200 0.75223267 -49.936211 -49.534846 35.419814 0.040381668 20.432118 -1.6242074 + 6300 0.69185501 -49.921889 -49.552739 36.050843 0.041437835 18.792142 -1.6620216 + 6400 0.64012215 -49.907725 -49.566179 36.704661 0.042458347 17.386976 -1.6987306 + 6500 0.59558646 -49.893699 -49.575915 37.378286 0.04344705 16.177299 -1.7344148 + 6600 0.55708121 -49.879794 -49.582555 38.067181 0.044407312 15.131421 -1.7691453 + 6700 0.52366875 -49.865988 -49.586576 38.769884 0.045342063 14.223873 -1.8030059 + 6800 0.49459542 -49.852276 -49.588377 39.48355 0.046253857 13.434184 -1.8360506 + 6900 0.46925412 -49.838637 -49.58826 40.206955 0.047144922 12.745864 -1.8683386 + 7000 0.44715411 -49.825066 -49.58648 40.938794 0.048017218 12.145585 -1.8999205 + 7100 0.427897 -49.811553 -49.583243 41.677982 0.048872484 11.622524 -1.9308529 + 7200 0.4111577 -49.798086 -49.578707 42.423605 0.049712274 11.167851 -1.9611851 + 7300 0.39666926 -49.784662 -49.573013 43.175155 0.050538 10.774317 -1.9909515 + 7400 0.38421083 -49.771272 -49.56627 43.931762 0.051350953 10.435921 -2.0202015 + 7500 0.37359789 -49.757907 -49.558568 44.69348 0.052152332 10.147653 -2.0489622 + 7600 0.36467436 -49.744563 -49.549985 45.459725 0.052943262 9.9052723 -2.0772881 + 7700 0.35730613 -49.731235 -49.540589 46.229921 0.053724811 9.7051368 -2.1052027 + 7800 0.3513759 -49.717911 -49.530429 47.004627 0.054498005 9.54406 -2.1327445 + 7900 0.34677906 -49.704589 -49.51956 47.78318 0.055263836 9.419201 -2.1599468 + 8000 0.34342073 -49.691262 -49.508025 48.565675 0.056023277 9.327982 -2.1868375 + 8100 0.34121371 -49.677922 -49.495862 49.351802 0.056777286 9.2680351 -2.2134444 + 8200 0.34007764 -49.664566 -49.483112 50.141603 0.057526819 9.2371771 -2.2397997 + 8300 0.33993883 -49.651181 -49.469802 50.935241 0.05827283 9.2334067 -2.2659331 + 8400 0.34073085 -49.637766 -49.455963 51.732654 0.059016284 9.2549196 -2.2918688 + 8500 0.34239516 -49.62431 -49.441619 52.534019 0.059758157 9.3001256 -2.317626 + 8600 0.3448813 -49.610812 -49.426796 53.338612 0.060499441 9.367654 -2.3432261 + 8700 0.34814597 -49.597265 -49.411506 54.147073 0.061241149 9.4563288 -2.3686991 + 8800 0.35215054 -49.583658 -49.395763 54.959512 0.061984314 9.5651009 -2.3940587 + 8900 0.35685687 -49.569985 -49.379579 55.776434 0.062729991 9.692934 -2.419329 + 9000 0.36222181 -49.556241 -49.362972 56.597626 0.063479254 9.8386562 -2.4445253 + 9100 0.36819143 -49.54242 -49.345966 57.423306 0.064233198 10.000803 -2.469667 + 9200 0.37469636 -49.528518 -49.328593 58.253634 0.064992931 10.17749 -2.4947681 + 9300 0.38164964 -49.514521 -49.310886 59.088869 0.065759574 10.366354 -2.5198522 + 9400 0.38894823 -49.500427 -49.292898 59.929378 0.066534253 10.564598 -2.5449285 + 9500 0.3964785 -49.486229 -49.274681 60.775174 0.067318101 10.769135 -2.5700196 + 9600 0.4041249 -49.471917 -49.25629 61.626259 0.068112253 10.976827 -2.5951326 + 9700 0.41178035 -49.457494 -49.237782 62.482132 0.06891785 11.184764 -2.6202815 + 9800 0.41935645 -49.44294 -49.219186 63.343831 0.069736042 11.390545 -2.6454805 + 9900 0.42679147 -49.428257 -49.200536 64.211037 0.070567996 11.592495 -2.670741 + 10000 0.43405521 -49.413432 -49.181835 65.08463 0.071414903 11.789793 -2.6960774 +Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms + +Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s +95.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.1084 | 3.1084 | 3.1084 | 0.0 | 21.16 +Bond | 0.0010414 | 0.0010414 | 0.0010414 | 0.0 | 0.01 +Neigh | 6.6306 | 6.6306 | 6.6306 | 0.0 | 45.13 +Comm | 0.56093 | 0.56093 | 0.56093 | 0.0 | 3.82 +Output | 0.002951 | 0.002951 | 0.002951 | 0.0 | 0.02 +Modify | 4.3177 | 4.3177 | 4.3177 | 0.0 | 29.39 +Other | | 0.06942 | | | 0.47 + +Nlocal: 180 ave 180 max 180 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1510 ave 1510 max 1510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 13680 ave 13680 max 13680 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 13680 +Ave neighs/atom = 76 +Ave special neighs/atom = 0 +Neighbor list builds = 10000 +Dangerous builds not checked +Total wall time: 0:00:14 diff --git a/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.7 b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.7 new file mode 100644 index 0000000000..ac54d52847 --- /dev/null +++ b/examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.7 @@ -0,0 +1,197 @@ +LAMMPS (8 Feb 2023) +Processor partition = 7 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 32 pad +variable out_freq string 100 +variable job_name string H2 + +units real +atom_style full +pair_style table linear 10000 + +neighbor 2.0 bin +neigh_modify every 1 delay 0 check no + +read_data H2.data +Reading data file ... + orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 180 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.002 seconds + +pair_coeff 1 * pair.table PAIR_H2 +WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr. +WARNING: Should only be flagged at inflection points (src/pair_table.cpp:466) + +timestep 0.001 + +velocity all create 1.0 1985 rot yes dist gaussian + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4 + +thermo_style custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +thermo ${out_freq} +thermo 100 + +#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd + +#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2 + +run 10000 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 11.55117 + ghost atom cutoff = 11.55117 + binsize = 5.775585, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes + Step Temp PotEng TotEng Pzz espring T_ring virial + 0 1 -50.292986 -49.759421 16.18218 0 0 4.331435e-14 + 100 0.99396717 -50.292908 -49.762562 16.16754 3.6546345e-06 31.630244 -0.01511026 + 200 0.97647843 -50.292785 -49.77177 16.117482 1.4519126e-05 31.073714 -0.030258999 + 300 0.94920978 -50.292584 -49.786119 16.040198 3.2307193e-05 30.205965 -0.045469889 + 400 0.91451321 -50.292301 -49.804349 15.94486 5.6578376e-05 29.101843 -0.060775514 + 500 0.87495051 -50.291935 -49.825092 15.839811 8.6783378e-05 27.84287 -0.07621024 + 600 0.83290521 -50.291484 -49.847075 15.733867 0.00012231241 26.504895 -0.091795014 + 700 0.79035049 -50.290943 -49.869239 15.633262 0.0001625386 25.150709 -0.10756384 + 800 0.74877056 -50.29031 -49.890792 15.542706 0.00020685191 23.827543 -0.12353621 + 900 0.70918842 -50.289582 -49.911184 15.465561 0.00025468227 22.567951 -0.13974782 + 1000 0.67224667 -50.288756 -49.930069 15.403036 0.00030551305 21.392383 -0.15621567 + 1100 0.63830199 -50.287828 -49.947252 15.356514 0.00035888685 20.312188 -0.17298512 + 1200 0.60751172 -50.286791 -49.962644 15.325845 0.0004144061 19.332373 -0.19008041 + 1300 0.57990404 -50.285641 -49.976225 15.311509 0.00047173031 18.453835 -0.20753645 + 1400 0.5554312 -50.284374 -49.988015 15.313263 0.00053057146 17.675055 -0.22539174 + 1500 0.53400813 -50.282975 -49.998047 15.33133 0.00059068877 16.993325 -0.24369544 + 1600 0.51553984 -50.281444 -50.00637 15.365561 0.00065188331 16.405623 -0.26248285 + 1700 0.49994085 -50.279767 -50.013016 15.416271 0.00071399304 15.909229 -0.28182209 + 1800 0.48714931 -50.277932 -50.018006 15.48387 0.00077688833 15.502174 -0.30176215 + 1900 0.47713797 -50.275928 -50.021344 15.569019 0.00084046832 15.183591 -0.32238808 + 2000 0.46992375 -50.273735 -50.023 15.673314 0.00090465799 14.954018 -0.3437631 + 2100 0.46557711 -50.271332 -50.022917 15.797801 0.00096940607 14.815698 -0.36598703 + 2200 0.46423244 -50.2687 -50.021002 15.944553 0.0010346838 14.772908 -0.38915619 + 2300 0.46610038 -50.26581 -50.017115 16.115839 0.0011004847 14.83235 -0.41338963 + 2400 0.47148286 -50.262625 -50.011058 16.314677 0.0011668255 15.003632 -0.43882597 + 2500 0.48079165 -50.259109 -50.002575 16.545079 0.0012337477 15.299859 -0.46562537 + 2600 0.49457102 -50.255212 -49.991327 16.811386 0.0013013219 15.738349 -0.49395245 + 2700 0.51352449 -50.250875 -49.976877 17.11979 0.0013696525 16.341491 -0.52401609 + 2800 0.53854543 -50.246032 -49.958683 17.477089 0.0014388859 17.137712 -0.55604082 + 2900 0.57074936 -50.240596 -49.936064 17.892199 0.0015092207 18.162513 -0.59030618 + 3000 0.61150422 -50.234467 -49.90819 18.375616 0.001580922 19.459423 -0.62708735 + 3100 0.66245096 -50.227523 -49.874062 18.939819 0.0016543394 21.080662 -0.66672955 + 3200 0.72550205 -50.219616 -49.832514 19.60023 0.0017299293 23.087088 -0.70958417 + 3300 0.80279929 -50.210579 -49.782233 20.37383 0.0018082826 25.546857 -0.75603924 + 3400 0.89660476 -50.200203 -49.721806 21.28012 0.0018901552 28.531956 -0.80651501 + 3500 1.0090938 -50.188252 -49.649835 22.340233 0.0019765002 32.111606 -0.86141363 + 3600 1.1420183 -50.174459 -49.565118 23.57558 0.0020684981 36.34156 -0.92115194 + 3700 1.2962221 -50.158518 -49.466899 25.006266 0.0021675754 41.248667 -0.98609175 + 3800 1.4710194 -50.140107 -49.355223 26.648455 0.0022754045 46.811106 -1.0565325 + 3900 1.6635051 -50.118886 -49.231298 28.511102 0.0023938687 52.936429 -1.1326688 + 4000 1.8679372 -50.094526 -49.097861 30.592386 0.0025249809 59.441913 -1.214555 + 4100 2.075405 -50.066723 -48.95936 32.878933 0.0026707445 66.044 -1.3020682 + 4200 2.2740293 -50.035234 -48.821891 35.342354 0.0028329538 72.364666 -1.394874 + 4300 2.449883 -49.999912 -48.69274 37.94169 0.0030129483 77.96072 -1.4924536 + 4400 2.5886538 -49.960721 -48.579506 40.62924 0.0032113484 82.376716 -1.5940701 + 4500 2.6778127 -49.917775 -48.488988 43.35421 0.0034278221 85.21395 -1.6987968 + 4600 2.7088053 -49.871336 -48.426012 46.071925 0.0036609337 86.200203 -1.8055903 + 4700 2.6786752 -49.821807 -48.39256 48.749456 0.0039081229 85.241397 -1.9133555 + 4800 2.5906421 -49.769708 -48.387433 51.369043 0.0041658356 82.439989 -2.0209603 + 4900 2.4534656 -49.71564 -48.406557 53.929171 0.0044297991 78.074727 -2.1273728 + 5000 2.2797967 -49.660246 -48.443826 56.439389 0.0046953978 72.548196 -2.2316692 + 5100 2.0839917 -49.60414 -48.492195 58.917167 0.0049580886 66.317246 -2.3330819 + 5200 1.8799454 -49.547898 -48.544825 61.38072 0.0052137855 59.824039 -2.4310487 + 5300 1.6794028 -49.492001 -48.59593 63.845702 0.0054591569 53.442329 -2.5251887 + 5400 1.4910004 -49.436812 -48.641266 66.323664 0.0056917984 47.446947 -2.6153153 + 5500 1.3200581 -49.382602 -48.678265 68.81759 0.0059102724 42.007182 -2.7013892 + 5600 1.1689597 -49.32954 -48.705824 71.326608 0.0061140319 37.198896 -2.7834961 + 5700 1.0378669 -49.277687 -48.723917 73.847293 0.0063032634 33.027232 -2.8618238 + 5800 0.92551081 -49.227051 -48.733231 76.373912 0.0064786911 29.451811 -2.9366159 + 5900 0.82988009 -49.177354 -48.734559 78.907054 0.0066413821 26.408629 -3.0079862 + 6000 0.74872148 -49.128988 -48.729496 81.429069 0.0067925784 23.825981 -3.0765541 + 6100 0.6798481 -49.081399 -48.718656 83.949013 0.0069335708 21.634277 -3.1425093 + 6200 0.62129621 -49.034965 -48.703463 86.450184 0.0070656124 19.771026 -3.2059256 + 6300 0.5713815 -48.989354 -48.684484 88.938306 0.0071898691 18.182629 -3.2671248 + 6400 0.52869861 -48.944483 -48.662388 91.411964 0.0073073957 16.824365 -3.326325 + 6500 0.49209369 -48.900284 -48.63772 93.869881 0.00741913 15.659515 -3.383704 + 6600 0.4606278 -48.85645 -48.610675 96.319181 0.0075258972 14.6582 -3.4393879 + 6700 0.4335401 -48.813153 -48.581831 98.754093 0.0076284202 13.796209 -3.4935699 + 6800 0.41021495 -48.770575 -48.551698 101.16784 0.0077273325 13.053951 -3.546418 + 6900 0.39015391 -48.728202 -48.520029 103.57385 0.0078231904 12.415565 -3.5980989 + 7000 0.37295279 -48.686464 -48.487469 105.95986 0.0079164859 11.868187 -3.6485312 + 7100 0.35828286 -48.645075 -48.453908 108.33347 0.008007657 11.401357 -3.6979091 + 7200 0.34587564 -48.603786 -48.419239 110.70102 0.0080970974 11.006532 -3.7462688 + 7300 0.33551045 -48.563011 -48.383994 113.05147 0.0081851643 10.676688 -3.7937749 + 7400 0.32700405 -48.5225 -48.348023 115.39114 0.008272185 10.405996 -3.8404567 + 7500 0.32020193 -48.481991 -48.311143 117.72756 0.0083584619 10.189537 -3.8863461 + 7600 0.31497086 -48.441913 -48.273856 120.0495 0.008444277 10.023073 -3.9315862 + 7700 0.31119256 -48.401778 -48.235736 122.37022 0.0085298943 9.9028389 -3.9761586 + 7800 0.30875834 -48.362027 -48.197284 124.67777 0.0086155626 9.8253766 -4.020194 + 7900 0.30756489 -48.322398 -48.158292 126.9798 0.0087015164 9.7873982 -4.0637137 + 8000 0.30751134 -48.282865 -48.118788 129.27742 0.0087879767 9.7856943 -4.1067668 + 8100 0.30849789 -48.243167 -48.078563 131.57737 0.0088751511 9.8170884 -4.1492332 + 8200 0.31042593 -48.203515 -48.037882 133.87491 0.0089632335 9.8784428 -4.1915847 + 8300 0.31319977 -48.163874 -47.996762 136.17056 0.0090524039 9.9667128 -4.2336145 + 8400 0.3167294 -48.124228 -47.955232 138.46555 0.0091428273 10.079033 -4.2753558 + 8500 0.32093339 -48.084773 -47.913534 140.75426 0.0092346543 10.212814 -4.3167737 + 8600 0.32574097 -48.045251 -47.871447 143.04447 0.0093280205 10.365802 -4.3579897 + 8700 0.33109202 -48.005633 -47.828974 145.33751 0.0094230472 10.536084 -4.3990428 + 8800 0.33693414 -47.965895 -47.786118 147.63516 0.0095198428 10.721993 -4.4399711 + 8900 0.34321684 -47.926004 -47.742875 149.9379 0.009618504 10.921922 -4.4808086 + 9000 0.34988367 -47.885934 -47.699248 152.24678 0.0097191181 11.134076 -4.5215921 + 9100 0.35686443 -47.845658 -47.655247 154.56358 0.0098217652 11.356219 -4.5623394 + 9200 0.3640698 -47.805147 -47.610893 156.88915 0.0099265208 11.58551 -4.6030874 + 9300 0.37139091 -47.764138 -47.565977 159.23099 0.010033457 11.818484 -4.6439479 + 9400 0.37870543 -47.722844 -47.52078 161.5788 0.010142648 12.051248 -4.6846276 + 9500 0.38588975 -47.68146 -47.475562 163.93728 0.010254165 12.279869 -4.7255143 + 9600 0.39283543 -47.639735 -47.430132 166.30871 0.010368088 12.500896 -4.7664862 + 9700 0.39946605 -47.597406 -47.384265 168.70114 0.010484497 12.711897 -4.8075181 + 9800 0.40575037 -47.55491 -47.338416 171.10373 0.010603483 12.911878 -4.848721 + 9900 0.41170816 -47.511756 -47.292083 173.53055 0.010725141 13.101469 -4.8900195 + 10000 0.41740707 -47.468384 -47.245671 175.97095 0.010849577 13.282821 -4.9315123 +Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms + +Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s +97.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.9822 | 2.9822 | 2.9822 | 0.0 | 20.30 +Bond | 0.00090722 | 0.00090722 | 0.00090722 | 0.0 | 0.01 +Neigh | 6.5119 | 6.5119 | 6.5119 | 0.0 | 44.33 +Comm | 0.55377 | 0.55377 | 0.55377 | 0.0 | 3.77 +Output | 0.0024523 | 0.0024523 | 0.0024523 | 0.0 | 0.02 +Modify | 4.5713 | 4.5713 | 4.5713 | 0.0 | 31.12 +Other | | 0.06845 | | | 0.47 + +Nlocal: 180 ave 180 max 180 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1510 ave 1510 max 1510 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 13712 ave 13712 max 13712 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 13712 +Ave neighs/atom = 76.177778 +Ave special neighs/atom = 0 +Neighbor list builds = 10000 +Dangerous builds not checked +Total wall time: 0:00:14 From 3e2b5dd9d30acef544af055c588cab71ef689312 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 25 Feb 2023 23:47:11 -0500 Subject: [PATCH 018/109] small cleanup --- src/REPLICA/fix_pimd_nvt.cpp | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/src/REPLICA/fix_pimd_nvt.cpp b/src/REPLICA/fix_pimd_nvt.cpp index 89d9a4127f..8f34df0b83 100644 --- a/src/REPLICA/fix_pimd_nvt.cpp +++ b/src/REPLICA/fix_pimd_nvt.cpp @@ -29,6 +29,7 @@ #include "error.h" #include "force.h" #include "math_const.h" +#include "math_special.h" #include "memory.h" #include "universe.h" #include "update.h" @@ -40,6 +41,8 @@ using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; +using MathSpecial::powint; + enum { PIMD, NMPIMD, CMD }; /* ---------------------------------------------------------------------- */ @@ -234,7 +237,7 @@ void FixPIMDNVT::init() if (method == CMD || method == NMPIMD) nmpimd_init(); else - for (int i = 1; i <= atom->ntypes; i++) mass[i] = atom->mass[i] / np * fmass; + for (int i = 1; i <= atom->ntypes; i++) mass[i] = atom->mass[i] * inverse_np * fmass; if (!nhc_ready) nhc_init(); } @@ -468,8 +471,8 @@ void FixPIMDNVT::nmpimd_init() // Set up eigenvectors for non-degenerated modes for (int i = 0; i < np; i++) { - M_x2xp[0][i] = 1.0 / np; - if (np % 2 == 0) M_x2xp[np - 1][i] = 1.0 / np * pow(-1.0, i); + M_x2xp[0][i] = inverse_np; + if (np % 2 == 0) M_x2xp[np - 1][i] = inverse_np * powint(-1.0, i); } // Set up eigenvectors for degenerated modes @@ -880,8 +883,8 @@ int FixPIMDNVT::size_restart(int /*nlocal*/) double FixPIMDNVT::compute_vector(int n) { - if (n == 0) { return spring_energy; } - if (n == 1) { return t_sys; } - if (n == 2) { return virial; } + if (n == 0) return spring_energy; + if (n == 1) return t_sys; + if (n == 2) return virial; return 0.0; } From 76c879c388c32e2bc62d879c9496a77c6c27c177 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 26 Feb 2023 00:16:03 -0500 Subject: [PATCH 019/109] make sure that output variables are initialized --- src/REPLICA/fix_pimd_nvt.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/REPLICA/fix_pimd_nvt.cpp b/src/REPLICA/fix_pimd_nvt.cpp index 8f34df0b83..1f2f29f35c 100644 --- a/src/REPLICA/fix_pimd_nvt.cpp +++ b/src/REPLICA/fix_pimd_nvt.cpp @@ -72,6 +72,8 @@ FixPIMDNVT::FixPIMDNVT(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) nhc_eta_dotdot = nullptr; nhc_eta_mass = nullptr; + spring_energy = t_sys = virial = 0.0; + method = PIMD; fmass = 1.0; nhc_temp = 298.15; From 2bd6cde4e822b51af6e6e4d796cffb8a8fff2f65 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 26 Feb 2023 00:19:39 -0500 Subject: [PATCH 020/109] add reference output --- .../pimd/prot-hairpin/log.25Feb23.scp.g++.8 | 2 + .../pimd/prot-hairpin/log.25Feb23.scp.g++.8.0 | 148 ++++++++++++++++++ .../pimd/prot-hairpin/log.25Feb23.scp.g++.8.1 | 146 +++++++++++++++++ .../pimd/prot-hairpin/log.25Feb23.scp.g++.8.2 | 146 +++++++++++++++++ .../pimd/prot-hairpin/log.25Feb23.scp.g++.8.3 | 146 +++++++++++++++++ .../pimd/prot-hairpin/log.25Feb23.scp.g++.8.4 | 146 +++++++++++++++++ .../pimd/prot-hairpin/log.25Feb23.scp.g++.8.5 | 146 +++++++++++++++++ .../pimd/prot-hairpin/log.25Feb23.scp.g++.8.6 | 146 +++++++++++++++++ .../pimd/prot-hairpin/log.25Feb23.scp.g++.8.7 | 146 +++++++++++++++++ 9 files changed, 1172 insertions(+) create mode 100644 examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8 create mode 100644 examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.0 create mode 100644 examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.1 create mode 100644 examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.2 create mode 100644 examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.3 create mode 100644 examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.4 create mode 100644 examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.5 create mode 100644 examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.6 create mode 100644 examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.7 diff --git a/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8 b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8 new file mode 100644 index 0000000000..14b41c14f3 --- /dev/null +++ b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8 @@ -0,0 +1,2 @@ +LAMMPS (8 Feb 2023) +Running on 8 partitions of processors diff --git a/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.0 b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.0 new file mode 100644 index 0000000000..873d412bf1 --- /dev/null +++ b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.0 @@ -0,0 +1,148 @@ +LAMMPS (8 Feb 2023) +Processor partition = 0 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 8 pad + +units real +neigh_modify delay 2 every 1 + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic + +pair_style lj/charmm/coul/long 11 12 +pair_modify mix arithmetic +kspace_style pppm 1e-4 + +read_data system.data +Reading data file ... + orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8674 atoms + reading velocities ... + 8674 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 5869 bonds + reading angles ... + 3264 angles + reading dihedrals ... + 708 dihedrals + reading impropers ... + 38 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 9 = max # of 1-3 neighbors + 17 = max # of 1-4 neighbors + 21 = max # of special neighbors + special bonds CPU = 0.004 seconds + read_data CPU = 0.138 seconds +#read_restart system_${ibead}.rest1 +special_bonds charmm + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0 + +thermo 10 +thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +timestep 0.08 + +# restart 100 system_${ibead}.rest1 system_${ibead}.rest2 + +group prot id <= 256 +256 atoms in group prot +# dump 1 prot dcd 100 prot_${ibead}.dcd + +run 200 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.22071363 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.024910591 + estimated relative force accuracy = 7.5017505e-05 + using double precision KISS FFT + 3d grid and FFT values/proc = 15625 8000 +Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule +Fix pimd/nvt -P/(beta^2 * hbar^2) = -2.9535019e+01 (kcal/mol/A^2) + +Neighbor list info ... + update: every = 1 steps, delay = 2 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Inconsistent image flags (src/domain.cpp:815) +Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes + Step Temp PotEng TotEng espring T_ring virial + 0 306.20099 -26166.171 -18250.089 0 0 -676.31071 + 10 131.27164 -24353.129 -20959.421 307.69774 131.25651 -622.84631 + 20 173.87922 -20639.595 -16144.371 903.19698 173.85917 -146.32235 + 30 174.36894 -14805.957 -10298.072 2123.5094 174.34883 1001.9707 + 40 209.39721 -9107.42 -3693.9648 3643.8992 209.37307 2169.6179 + 50 224.56543 -4755.7551 1049.8374 5433.6153 224.53954 3077.7538 + 60 236.84365 -1848.0123 4275.0036 7420.6008 236.81634 3690.4423 + 70 251.60145 -545.63452 5958.9084 9472.1666 251.57244 3930.8483 + 80 259.97884 -310.2814 6410.8387 11592.586 259.94887 4052.0897 + 90 266.56259 -619.03771 6272.2892 13763.979 266.53186 3895.0106 + 100 277.74387 -1327.8055 5852.5862 15788.989 277.71185 3691.775 + 110 278.73044 -1998.5 5207.397 17723.605 278.69831 2838.6857 + 120 286.74106 -2688.0018 4724.9903 19437.173 286.70801 2354.3367 + 130 284.45763 -3484.7277 3869.2319 20933.859 284.42484 2037.2135 + 140 290.24681 -4412.7819 3090.8428 22113.049 290.21335 1802.8857 + 150 294.32521 -5490.1829 2118.8788 23005.855 294.29127 1927.3626 + 160 293.9109 -6586.1293 1012.2214 23597.9 293.87701 2198.3058 + 170 290.52772 -7737.8309 -226.94392 23882.219 290.49423 2454.2765 + 180 289.91516 -8766.2419 -1271.1912 23875.129 289.88174 2549.258 + 190 292.57992 -9618.0848 -2054.1432 23580.482 292.54619 2605.4823 + 200 295.4078 -10200.536 -2563.4865 23028.461 295.37374 2587.5531 +Loop time of 35.3333 on 1 procs for 200 steps with 8674 atoms + +Performance: 0.039 ns/day, 613.425 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.689 | 27.689 | 27.689 | 0.0 | 78.37 +Bond | 0.1312 | 0.1312 | 0.1312 | 0.0 | 0.37 +Kspace | 2.4446 | 2.4446 | 2.4446 | 0.0 | 6.92 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.12014 | 0.12014 | 0.12014 | 0.0 | 0.34 +Output | 0.0020193 | 0.0020193 | 0.0020193 | 0.0 | 0.01 +Modify | 4.886 | 4.886 | 4.886 | 0.0 | 13.83 +Other | | 0.05992 | | | 0.17 + +Nlocal: 8674 ave 8674 max 8674 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 27366 ave 27366 max 27366 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4485849 +Ave neighs/atom = 517.16036 +Ave special neighs/atom = 2.2573207 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:35 diff --git a/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.1 b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.1 new file mode 100644 index 0000000000..51a69030c2 --- /dev/null +++ b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.1 @@ -0,0 +1,146 @@ +LAMMPS (8 Feb 2023) +Processor partition = 1 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 8 pad + +units real +neigh_modify delay 2 every 1 + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic + +pair_style lj/charmm/coul/long 11 12 +pair_modify mix arithmetic +kspace_style pppm 1e-4 + +read_data system.data +Reading data file ... + orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8674 atoms + reading velocities ... + 8674 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 5869 bonds + reading angles ... + 3264 angles + reading dihedrals ... + 708 dihedrals + reading impropers ... + 38 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 9 = max # of 1-3 neighbors + 17 = max # of 1-4 neighbors + 21 = max # of special neighbors + special bonds CPU = 0.004 seconds + read_data CPU = 0.139 seconds +#read_restart system_${ibead}.rest1 +special_bonds charmm + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0 + +thermo 10 +thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +timestep 0.08 + +# restart 100 system_${ibead}.rest1 system_${ibead}.rest2 + +group prot id <= 256 +256 atoms in group prot +# dump 1 prot dcd 100 prot_${ibead}.dcd + +run 200 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.22071363 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.024910591 + estimated relative force accuracy = 7.5017505e-05 + using double precision KISS FFT + 3d grid and FFT values/proc = 15625 8000 +Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 2 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Inconsistent image flags (src/domain.cpp:815) +Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes + Step Temp PotEng TotEng espring T_ring virial + 0 306.20099 -26166.171 -18250.089 0 0 -676.31071 + 10 64.17217 -26206.83 -24547.814 19.798491 300.69483 -715.39964 + 20 68.220475 -26516.716 -24753.042 40.042407 319.66418 -514.11207 + 30 57.966715 -26566.219 -25067.631 92.36071 271.61761 32.199121 + 40 49.627434 -26115.147 -24832.15 156.77313 232.54181 589.56751 + 50 50.238512 -24830.72 -23531.926 251.81147 235.40517 1098.4708 + 60 56.338925 -22753.456 -21296.951 361.53524 263.99019 1897.4199 + 70 54.380851 -19964.7 -18558.815 512.1854 254.81514 2327.9231 + 80 56.718808 -16822.195 -15355.868 692.48978 265.77022 2784.4839 + 90 57.350586 -13726.44 -12243.78 926.0914 268.73058 3260.3863 + 100 57.262365 -11280.793 -9800.4136 1186.0078 268.3172 3554.7754 + 110 58.507688 -9681.3843 -8168.8105 1483.328 274.15247 3368.3688 + 120 58.690757 -9008.7198 -7491.4132 1803.3617 275.01029 2974.5497 + 130 58.623212 -9097.3273 -7581.7669 2143.6544 274.69379 2535.9822 + 140 59.453502 -9689.6967 -8152.6711 2490.8635 278.58432 1947.3155 + 150 59.231787 -10601.929 -9070.635 2837.9543 277.54542 1774.9432 + 160 58.39319 -11413.85 -9904.2362 3183.3024 273.61596 1744.3579 + 170 60.201493 -12074.462 -10518.099 3515.6508 282.08922 1744.1497 + 180 59.592955 -12415.79 -10875.16 3827.6991 279.23776 1935.0884 + 190 59.698333 -12625.161 -11081.806 4120.4275 279.73154 1962.5444 + 200 59.87495 -12794.677 -11246.756 4387.202 280.55912 1854.7836 +Loop time of 35.3334 on 1 procs for 200 steps with 8674 atoms + +Performance: 0.039 ns/day, 613.427 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s +97.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.948 | 27.948 | 27.948 | 0.0 | 79.10 +Bond | 0.12842 | 0.12842 | 0.12842 | 0.0 | 0.36 +Kspace | 2.4577 | 2.4577 | 2.4577 | 0.0 | 6.96 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.11986 | 0.11986 | 0.11986 | 0.0 | 0.34 +Output | 0.0021166 | 0.0021166 | 0.0021166 | 0.0 | 0.01 +Modify | 4.617 | 4.617 | 4.617 | 0.0 | 13.07 +Other | | 0.06042 | | | 0.17 + +Nlocal: 8674 ave 8674 max 8674 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 27366 ave 27366 max 27366 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4485849 +Ave neighs/atom = 517.16036 +Ave special neighs/atom = 2.2573207 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:35 diff --git a/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.2 b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.2 new file mode 100644 index 0000000000..03d6c04804 --- /dev/null +++ b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.2 @@ -0,0 +1,146 @@ +LAMMPS (8 Feb 2023) +Processor partition = 2 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 8 pad + +units real +neigh_modify delay 2 every 1 + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic + +pair_style lj/charmm/coul/long 11 12 +pair_modify mix arithmetic +kspace_style pppm 1e-4 + +read_data system.data +Reading data file ... + orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8674 atoms + reading velocities ... + 8674 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 5869 bonds + reading angles ... + 3264 angles + reading dihedrals ... + 708 dihedrals + reading impropers ... + 38 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 9 = max # of 1-3 neighbors + 17 = max # of 1-4 neighbors + 21 = max # of special neighbors + special bonds CPU = 0.004 seconds + read_data CPU = 0.139 seconds +#read_restart system_${ibead}.rest1 +special_bonds charmm + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0 + +thermo 10 +thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +timestep 0.08 + +# restart 100 system_${ibead}.rest1 system_${ibead}.rest2 + +group prot id <= 256 +256 atoms in group prot +# dump 1 prot dcd 100 prot_${ibead}.dcd + +run 200 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.22071363 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.024910591 + estimated relative force accuracy = 7.5017505e-05 + using double precision KISS FFT + 3d grid and FFT values/proc = 15625 8000 +Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 2 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Inconsistent image flags (src/domain.cpp:815) +Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes + Step Temp PotEng TotEng espring T_ring virial + 0 306.20099 -26166.171 -18250.089 0 0 -676.31071 + 10 64.17182 -26152.123 -24493.117 2.6867435 300.69318 -871.30328 + 20 68.223719 -26376.797 -24613.039 8.6943178 319.67938 -734.6258 + 30 57.962426 -26437.775 -24939.297 20.196606 271.59751 -442.97527 + 40 49.527052 -26345.74 -25065.339 36.486067 232.07145 -109.57718 + 50 50.00573 -26013.669 -24720.893 64.828577 234.31441 90.23132 + 60 56.176816 -25453.583 -24001.268 104.35099 263.23058 350.85294 + 70 54.335616 -24764.408 -23359.692 168.84911 254.60318 370.58559 + 80 56.386432 -24068.851 -22611.117 255.96556 264.21279 359.85013 + 90 57.394261 -23487.859 -22004.071 377.57122 268.93523 350.57006 + 100 56.595909 -23070.567 -21607.418 531.24569 265.19435 380.72648 + 110 56.785626 -22692.803 -21224.749 716.4839 266.08332 119.53289 + 120 57.068588 -22142.475 -20667.105 936.74977 267.4092 53.114976 + 130 57.211273 -21289.908 -19810.849 1184.7712 268.0778 165.3536 + 140 58.110208 -20136.125 -18633.827 1461.5509 272.28998 268.40059 + 150 57.980844 -18752.784 -17253.831 1762.042 271.68381 732.81511 + 160 58.120526 -17237.742 -15735.177 2083.496 272.33833 1353.819 + 170 58.192327 -15808.132 -14303.711 2418.0799 272.67477 1963.8895 + 180 59.169638 -14676.59 -13146.903 2755.6611 277.2542 2483.717 + 190 60.190674 -13997.692 -12441.609 3096.3553 282.03852 2865.7644 + 200 60.619191 -13706.35 -12139.188 3426.2396 284.04645 2830.1842 +Loop time of 35.3333 on 1 procs for 200 steps with 8674 atoms + +Performance: 0.039 ns/day, 613.425 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s +99.2% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.558 | 27.558 | 27.558 | 0.0 | 77.99 +Bond | 0.1313 | 0.1313 | 0.1313 | 0.0 | 0.37 +Kspace | 2.4344 | 2.4344 | 2.4344 | 0.0 | 6.89 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.11913 | 0.11913 | 0.11913 | 0.0 | 0.34 +Output | 0.0022372 | 0.0022372 | 0.0022372 | 0.0 | 0.01 +Modify | 5.0291 | 5.0291 | 5.0291 | 0.0 | 14.23 +Other | | 0.05932 | | | 0.17 + +Nlocal: 8674 ave 8674 max 8674 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 27366 ave 27366 max 27366 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4485849 +Ave neighs/atom = 517.16036 +Ave special neighs/atom = 2.2573207 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:35 diff --git a/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.3 b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.3 new file mode 100644 index 0000000000..5e15398b16 --- /dev/null +++ b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.3 @@ -0,0 +1,146 @@ +LAMMPS (8 Feb 2023) +Processor partition = 3 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 8 pad + +units real +neigh_modify delay 2 every 1 + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic + +pair_style lj/charmm/coul/long 11 12 +pair_modify mix arithmetic +kspace_style pppm 1e-4 + +read_data system.data +Reading data file ... + orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8674 atoms + reading velocities ... + 8674 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 5869 bonds + reading angles ... + 3264 angles + reading dihedrals ... + 708 dihedrals + reading impropers ... + 38 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 9 = max # of 1-3 neighbors + 17 = max # of 1-4 neighbors + 21 = max # of special neighbors + special bonds CPU = 0.015 seconds + read_data CPU = 0.153 seconds +#read_restart system_${ibead}.rest1 +special_bonds charmm + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0 + +thermo 10 +thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +timestep 0.08 + +# restart 100 system_${ibead}.rest1 system_${ibead}.rest2 + +group prot id <= 256 +256 atoms in group prot +# dump 1 prot dcd 100 prot_${ibead}.dcd + +run 200 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.22071363 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.024910591 + estimated relative force accuracy = 7.5017505e-05 + using double precision KISS FFT + 3d grid and FFT values/proc = 15625 8000 +Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 2 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Inconsistent image flags (src/domain.cpp:815) +Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes + Step Temp PotEng TotEng espring T_ring virial + 0 306.20099 -26166.171 -18250.089 0 0 -676.31071 + 10 23.892089 -26194.747 -25577.075 6.0651132 382.22935 -806.80519 + 20 27.051257 -26510.555 -25811.21 19.798054 432.77021 -722.7628 + 30 27.053581 -26558.283 -25858.879 46.409761 432.8074 -314.77439 + 40 19.1336 -26301.271 -25806.618 80.715535 306.1023 33.240778 + 50 19.277021 -25564.199 -25065.839 122.0411 308.39678 420.32166 + 60 20.762569 -24490.516 -23953.751 171.68786 332.16281 922.0134 + 70 18.895283 -23277.775 -22789.283 228.13302 302.28967 1340.4892 + 80 20.103678 -22119.758 -21600.026 293.69148 321.62176 1692.277 + 90 18.733051 -21236.09 -20751.793 371.14173 299.69426 2111.5887 + 100 18.287299 -20684.674 -20211.9 458.53118 292.56305 2434.0418 + 110 18.012563 -20345.727 -19880.056 560.10663 288.16778 2560.064 + 120 17.92092 -19998.225 -19534.923 676.3247 286.70167 2752.7643 + 130 17.494577 -19524.549 -19072.269 808.35795 279.88096 3081.7784 + 140 17.122298 -18815.761 -18373.106 957.14076 273.92518 3209.6451 + 150 17.447826 -17981.659 -17530.588 1123.5613 279.13303 3627.9284 + 160 17.6202 -17066.393 -16610.866 1310.1872 281.8907 4230.0427 + 170 17.370561 -16269.055 -15819.981 1507.5411 277.89693 4602.925 + 180 17.444401 -15692.511 -15241.529 1720.5033 279.07824 5000.4081 + 190 17.587192 -15476.239 -15021.565 1938.8703 281.36263 5063.6159 + 200 18.000638 -15470.948 -15005.586 2164.2187 287.977 4707.0585 +Loop time of 35.3335 on 1 procs for 200 steps with 8674 atoms + +Performance: 0.039 ns/day, 613.428 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.094 | 27.094 | 27.094 | 0.0 | 76.68 +Bond | 0.1276 | 0.1276 | 0.1276 | 0.0 | 0.36 +Kspace | 2.3873 | 2.3873 | 2.3873 | 0.0 | 6.76 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.11312 | 0.11312 | 0.11312 | 0.0 | 0.32 +Output | 0.0020657 | 0.0020657 | 0.0020657 | 0.0 | 0.01 +Modify | 5.5507 | 5.5507 | 5.5507 | 0.0 | 15.71 +Other | | 0.05892 | | | 0.17 + +Nlocal: 8674 ave 8674 max 8674 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 27366 ave 27366 max 27366 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4485849 +Ave neighs/atom = 517.16036 +Ave special neighs/atom = 2.2573207 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:35 diff --git a/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.4 b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.4 new file mode 100644 index 0000000000..997a4c1acd --- /dev/null +++ b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.4 @@ -0,0 +1,146 @@ +LAMMPS (8 Feb 2023) +Processor partition = 4 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 8 pad + +units real +neigh_modify delay 2 every 1 + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic + +pair_style lj/charmm/coul/long 11 12 +pair_modify mix arithmetic +kspace_style pppm 1e-4 + +read_data system.data +Reading data file ... + orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8674 atoms + reading velocities ... + 8674 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 5869 bonds + reading angles ... + 3264 angles + reading dihedrals ... + 708 dihedrals + reading impropers ... + 38 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 9 = max # of 1-3 neighbors + 17 = max # of 1-4 neighbors + 21 = max # of special neighbors + special bonds CPU = 0.004 seconds + read_data CPU = 0.138 seconds +#read_restart system_${ibead}.rest1 +special_bonds charmm + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0 + +thermo 10 +thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +timestep 0.08 + +# restart 100 system_${ibead}.rest1 system_${ibead}.rest2 + +group prot id <= 256 +256 atoms in group prot +# dump 1 prot dcd 100 prot_${ibead}.dcd + +run 200 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.22071363 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.024910591 + estimated relative force accuracy = 7.5017505e-05 + using double precision KISS FFT + 3d grid and FFT values/proc = 15625 8000 +Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 2 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Inconsistent image flags (src/domain.cpp:815) +Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes + Step Temp PotEng TotEng espring T_ring virial + 0 306.20099 -26166.171 -18250.089 0 0 -676.31071 + 10 23.892095 -26119.899 -25502.227 4.2771563 382.22944 -813.96512 + 20 27.051103 -26287.602 -25588.262 15.607084 432.76775 -745.77933 + 30 27.042026 -26290.973 -25591.867 35.550734 432.62253 -326.69805 + 40 19.133546 -26173.654 -25679.002 70.11544 306.10144 -11.324153 + 50 19.302675 -25883.61 -25384.586 121.68648 308.8072 290.09295 + 60 20.704866 -25425.468 -24890.194 201.50535 331.23967 650.74045 + 70 18.95281 -24809.575 -24319.596 321.84847 303.21 967.87686 + 80 20.178541 -24115.258 -23593.591 491.86818 322.81943 1230.7506 + 90 18.755289 -23448.841 -22963.969 726.07287 300.05003 1426.7932 + 100 18.159265 -22868.418 -22398.954 1013.598 290.51475 1609.3405 + 110 17.922985 -22283.38 -21820.025 1355.5366 286.7347 1483.5981 + 120 17.617358 -21583.469 -21128.015 1747.6539 281.84524 1444.208 + 130 17.233206 -20748.165 -20302.643 2173.0115 275.6995 1597.8139 + 140 17.06066 -19726.034 -19284.972 2629.6918 272.9391 1704.3744 + 150 17.004216 -18648.306 -18208.703 3099.2098 272.0361 2025.6026 + 160 17.414218 -17588.638 -17138.435 3580.8838 278.59537 2747.2565 + 170 17.295959 -16669.449 -16222.304 4058.5589 276.70344 3432.2976 + 180 17.706054 -15991.367 -15533.62 4524.6837 283.26421 4008.5413 + 190 17.649786 -15623.329 -15167.037 4968.3076 282.36402 4251.4209 + 200 17.914982 -15484.434 -15021.286 5382.5961 286.60667 4187.5146 +Loop time of 35.3335 on 1 procs for 200 steps with 8674 atoms + +Performance: 0.039 ns/day, 613.428 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s +98.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.644 | 27.644 | 27.644 | 0.0 | 78.24 +Bond | 0.1292 | 0.1292 | 0.1292 | 0.0 | 0.37 +Kspace | 2.4108 | 2.4108 | 2.4108 | 0.0 | 6.82 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.12913 | 0.12913 | 0.12913 | 0.0 | 0.37 +Output | 0.0021704 | 0.0021704 | 0.0021704 | 0.0 | 0.01 +Modify | 4.959 | 4.959 | 4.959 | 0.0 | 14.03 +Other | | 0.05951 | | | 0.17 + +Nlocal: 8674 ave 8674 max 8674 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 27366 ave 27366 max 27366 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4485849 +Ave neighs/atom = 517.16036 +Ave special neighs/atom = 2.2573207 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:35 diff --git a/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.5 b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.5 new file mode 100644 index 0000000000..840f0e9011 --- /dev/null +++ b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.5 @@ -0,0 +1,146 @@ +LAMMPS (8 Feb 2023) +Processor partition = 5 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 8 pad + +units real +neigh_modify delay 2 every 1 + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic + +pair_style lj/charmm/coul/long 11 12 +pair_modify mix arithmetic +kspace_style pppm 1e-4 + +read_data system.data +Reading data file ... + orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8674 atoms + reading velocities ... + 8674 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 5869 bonds + reading angles ... + 3264 angles + reading dihedrals ... + 708 dihedrals + reading impropers ... + 38 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 9 = max # of 1-3 neighbors + 17 = max # of 1-4 neighbors + 21 = max # of special neighbors + special bonds CPU = 0.004 seconds + read_data CPU = 0.139 seconds +#read_restart system_${ibead}.rest1 +special_bonds charmm + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0 + +thermo 10 +thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +timestep 0.08 + +# restart 100 system_${ibead}.rest1 system_${ibead}.rest2 + +group prot id <= 256 +256 atoms in group prot +# dump 1 prot dcd 100 prot_${ibead}.dcd + +run 200 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.22071363 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.024910591 + estimated relative force accuracy = 7.5017505e-05 + using double precision KISS FFT + 3d grid and FFT values/proc = 15625 8000 +Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 2 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Inconsistent image flags (src/domain.cpp:815) +Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes + Step Temp PotEng TotEng espring T_ring virial + 0 306.20099 -26166.171 -18250.089 0 0 -676.31071 + 10 14.020019 -26051.605 -25689.152 7.3596437 382.89455 -789.8534 + 20 15.752865 -25975.95 -25568.698 25.331469 430.21956 -594.00538 + 30 17.181375 -25873.108 -25428.926 57.426817 469.23297 -181.78718 + 40 11.772036 -25785.82 -25481.483 101.0172 321.50089 318.12089 + 50 11.907234 -25813.038 -25505.205 157.46734 325.19321 630.72419 + 60 12.407378 -25738.74 -25417.978 232.72881 338.85245 1042.2805 + 70 11.569463 -25485.646 -25186.546 331.59654 315.9685 1219.4474 + 80 12.423569 -25007.927 -24686.746 455.84829 339.29462 1585.4189 + 90 11.222078 -24360.128 -24070.009 610.51406 306.48124 1770.0165 + 100 10.746584 -23649.481 -23371.654 794.88729 293.49524 1751.0868 + 110 10.688659 -22906.499 -22630.17 1011.4935 291.91326 1164.4167 + 120 10.413653 -22131.25 -21862.03 1258.7802 284.40268 494.75639 + 130 10.207431 -21354.621 -21090.733 1532.012 278.77066 -85.33744 + 140 9.9484212 -20506.422 -20249.23 1833.2006 271.69695 -582.25635 + 150 9.8592991 -19641.288 -19386.399 2150.5002 269.26298 -860.97106 + 160 9.9476229 -18750.371 -18493.199 2484.32 271.67515 -781.67257 + 170 9.9050652 -17855.648 -17599.576 2822.3305 270.51287 -564.01235 + 180 9.9461836 -17049.565 -16792.431 3164.947 271.63584 -414.44888 + 190 9.9650455 -16346.398 -16088.776 3500.8641 272.15097 -250.509 + 200 10.114117 -15721.822 -15460.346 3824.3372 276.22219 -539.50977 +Loop time of 35.3336 on 1 procs for 200 steps with 8674 atoms + +Performance: 0.039 ns/day, 613.431 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.569 | 27.569 | 27.569 | 0.0 | 78.03 +Bond | 0.13166 | 0.13166 | 0.13166 | 0.0 | 0.37 +Kspace | 2.4398 | 2.4398 | 2.4398 | 0.0 | 6.91 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.12114 | 0.12114 | 0.12114 | 0.0 | 0.34 +Output | 0.0022707 | 0.0022707 | 0.0022707 | 0.0 | 0.01 +Modify | 5.0103 | 5.0103 | 5.0103 | 0.0 | 14.18 +Other | | 0.05914 | | | 0.17 + +Nlocal: 8674 ave 8674 max 8674 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 27366 ave 27366 max 27366 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4485849 +Ave neighs/atom = 517.16036 +Ave special neighs/atom = 2.2573207 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:35 diff --git a/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.6 b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.6 new file mode 100644 index 0000000000..a98694339b --- /dev/null +++ b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.6 @@ -0,0 +1,146 @@ +LAMMPS (8 Feb 2023) +Processor partition = 6 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 8 pad + +units real +neigh_modify delay 2 every 1 + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic + +pair_style lj/charmm/coul/long 11 12 +pair_modify mix arithmetic +kspace_style pppm 1e-4 + +read_data system.data +Reading data file ... + orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8674 atoms + reading velocities ... + 8674 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 5869 bonds + reading angles ... + 3264 angles + reading dihedrals ... + 708 dihedrals + reading impropers ... + 38 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 9 = max # of 1-3 neighbors + 17 = max # of 1-4 neighbors + 21 = max # of special neighbors + special bonds CPU = 0.004 seconds + read_data CPU = 0.139 seconds +#read_restart system_${ibead}.rest1 +special_bonds charmm + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0 + +thermo 10 +thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +timestep 0.08 + +# restart 100 system_${ibead}.rest1 system_${ibead}.rest2 + +group prot id <= 256 +256 atoms in group prot +# dump 1 prot dcd 100 prot_${ibead}.dcd + +run 200 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.22071363 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.024910591 + estimated relative force accuracy = 7.5017505e-05 + using double precision KISS FFT + 3d grid and FFT values/proc = 15625 8000 +Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 2 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Inconsistent image flags (src/domain.cpp:815) +Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes + Step Temp PotEng TotEng espring T_ring virial + 0 306.20099 -26166.171 -18250.089 0 0 -676.31071 + 10 14.02002 -25861.333 -25498.879 45.268744 382.8946 -722.47561 + 20 15.752886 -25289.441 -24882.188 135.42322 430.22014 -482.48877 + 30 17.181691 -24659.071 -24214.881 316.76011 469.24159 115.80651 + 40 11.76983 -24165.345 -23861.065 544.21259 321.44065 710.32531 + 50 11.904289 -24034.29 -23726.534 812.12301 325.1128 1057.7309 + 60 12.409559 -23964.986 -23644.167 1115.614 338.91201 1490.6948 + 70 11.53241 -23718.204 -23420.061 1442.0767 314.95657 1654.3805 + 80 12.377693 -23123.366 -22803.371 1794.1167 338.04173 2019.537 + 90 11.21341 -22129.26 -21839.365 2172.5974 306.24451 2037.5349 + 100 10.778526 -20922.126 -20643.474 2553.3173 294.36759 1922.6067 + 110 10.656113 -19666.579 -19391.091 2944.1884 291.02442 1115.4533 + 120 10.374573 -18508.305 -18240.096 3331.7564 283.3354 401.15223 + 130 10.057534 -17613.953 -17353.939 3714.254 274.67688 -248.49945 + 140 9.7972276 -16953.726 -16700.443 4076.4386 267.56777 -841.79062 + 150 9.8266474 -16502.516 -16248.472 4422.7241 268.37124 -1155.8854 + 160 9.9655308 -16127.142 -15869.507 4748.4514 272.16422 -1094.1994 + 170 9.9292831 -15818.923 -15562.225 5045.9331 271.17428 -884.00102 + 180 10.157102 -15473.205 -15210.618 5313.5511 277.39613 -553.25499 + 190 10.068063 -15095.751 -14835.466 5545.0144 274.96443 -237.36247 + 200 10.155151 -14754.017 -14491.48 5742.1288 277.34285 -332.89648 +Loop time of 35.3338 on 1 procs for 200 steps with 8674 atoms + +Performance: 0.039 ns/day, 613.434 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s +97.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.875 | 27.875 | 27.875 | 0.0 | 78.89 +Bond | 0.12707 | 0.12707 | 0.12707 | 0.0 | 0.36 +Kspace | 2.4348 | 2.4348 | 2.4348 | 0.0 | 6.89 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.11906 | 0.11906 | 0.11906 | 0.0 | 0.34 +Output | 0.0021503 | 0.0021503 | 0.0021503 | 0.0 | 0.01 +Modify | 4.7164 | 4.7164 | 4.7164 | 0.0 | 13.35 +Other | | 0.05955 | | | 0.17 + +Nlocal: 8674 ave 8674 max 8674 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 27366 ave 27366 max 27366 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4485849 +Ave neighs/atom = 517.16036 +Ave special neighs/atom = 2.2573207 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:35 diff --git a/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.7 b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.7 new file mode 100644 index 0000000000..55f561c6ec --- /dev/null +++ b/examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.7 @@ -0,0 +1,146 @@ +LAMMPS (8 Feb 2023) +Processor partition = 7 +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +variable ibead uloop 8 pad + +units real +neigh_modify delay 2 every 1 + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic + +pair_style lj/charmm/coul/long 11 12 +pair_modify mix arithmetic +kspace_style pppm 1e-4 + +read_data system.data +Reading data file ... + orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 8674 atoms + reading velocities ... + 8674 velocities + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 5869 bonds + reading angles ... + 3264 angles + reading dihedrals ... + 708 dihedrals + reading impropers ... + 38 impropers +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 4 = max # of 1-2 neighbors + 9 = max # of 1-3 neighbors + 17 = max # of 1-4 neighbors + 21 = max # of special neighbors + special bonds CPU = 0.004 seconds + read_data CPU = 0.138 seconds +#read_restart system_${ibead}.rest1 +special_bonds charmm + +fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0 + +thermo 10 +thermo_style custom step temp pe etotal f_1[1] f_1[2] f_1[3] +thermo_modify colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial +timestep 0.08 + +# restart 100 system_${ibead}.rest1 system_${ibead}.rest2 + +group prot id <= 256 +256 atoms in group prot +# dump 1 prot dcd 100 prot_${ibead}.dcd + +run 200 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.22071363 + grid = 20 20 20 + stencil order = 5 + estimated absolute RMS force accuracy = 0.024910591 + estimated relative force accuracy = 7.5017505e-05 + using double precision KISS FFT + 3d grid and FFT values/proc = 15625 8000 +Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule +Neighbor list info ... + update: every = 1 steps, delay = 2 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d + bin: standard +WARNING: Inconsistent image flags (src/domain.cpp:815) +Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes + Step Temp PotEng TotEng espring T_ring virial + 0 306.20099 -26166.171 -18250.089 0 0 -676.31071 + 10 11.858328 -24949.912 -24643.343 11.21746 379.42274 -589.42772 + 20 13.313433 -22332.782 -21988.595 25.891404 425.98075 -189.42618 + 30 14.492332 -18605.094 -18230.43 60.87232 463.70115 853.22726 + 40 10.100576 -15158.156 -14897.03 103.87947 323.18115 1870.5664 + 50 10.437976 -12976.762 -12706.913 161.50852 333.97672 2649.3283 + 60 10.544993 -11868.561 -11595.946 225.58416 337.40089 3264.9267 + 70 9.756396 -11851.23 -11599.002 303.66274 312.16868 3549.9084 + 80 10.642372 -12316.225 -12041.092 392.92619 340.51663 3853.3301 + 90 9.3834726 -12853.33 -12610.744 501.5373 300.2365 3943.7218 + 100 8.9858656 -13254.517 -13022.21 619.67563 287.51455 3852.5038 + 110 8.9674385 -13407.55 -13175.719 752.87088 286.92495 3047.0516 + 120 8.7200626 -13430.184 -13204.748 897.34682 279.00983 2614.6547 + 130 8.4404226 -13413.462 -13195.256 1051.1979 270.06239 2361.7563 + 140 8.1867868 -13405.663 -13194.013 1215.2723 261.94697 2042.4666 + 150 8.26024 -13427.11 -13213.561 1389.0864 264.29721 2179.5219 + 160 8.2139102 -13403.956 -13191.605 1573.9454 262.81482 2489.6486 + 170 8.2258918 -13367.291 -13154.631 1768.2198 263.19819 2793.6911 + 180 8.4548603 -13245.62 -13027.04 1968.4468 270.52434 3070.2942 + 190 8.4589955 -12920.954 -12702.268 2174.1321 270.65665 3360.4993 + 200 8.537811 -12448.973 -12228.248 2382.746 273.17846 3370.2077 +Loop time of 35.3334 on 1 procs for 200 steps with 8674 atoms + +Performance: 0.039 ns/day, 613.428 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s +99.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 27.709 | 27.709 | 27.709 | 0.0 | 78.42 +Bond | 0.13165 | 0.13165 | 0.13165 | 0.0 | 0.37 +Kspace | 2.4416 | 2.4416 | 2.4416 | 0.0 | 6.91 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.12826 | 0.12826 | 0.12826 | 0.0 | 0.36 +Output | 0.002116 | 0.002116 | 0.002116 | 0.0 | 0.01 +Modify | 4.863 | 4.863 | 4.863 | 0.0 | 13.76 +Other | | 0.05754 | | | 0.16 + +Nlocal: 8674 ave 8674 max 8674 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 27366 ave 27366 max 27366 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 4485849 +Ave neighs/atom = 517.16036 +Ave special neighs/atom = 2.2573207 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:35 From 0b5acdca51fe8f1de48914ee0a6fd6831ff49fe4 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 26 Feb 2023 13:47:11 -0500 Subject: [PATCH 021/109] convert hard error about invalid atom masses from EAM potentials to warning --- src/atom.cpp | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/src/atom.cpp b/src/atom.cpp index 32285758c0..610ac809fe 100644 --- a/src/atom.cpp +++ b/src/atom.cpp @@ -1914,11 +1914,15 @@ void Atom::set_mass(const char *file, int line, const char *str, int type_offset void Atom::set_mass(const char *file, int line, int itype, double value) { - if (mass == nullptr) error->all(file,line, "Cannot set mass for atom style {}", atom_style); + if (mass == nullptr) + error->all(file,line, "Cannot set per-type mass for atom style {}", atom_style); if (itype < 1 || itype > ntypes) error->all(file,line,"Invalid type {} for atom mass {}", itype, value); - if (value <= 0.0) error->all(file,line,"Invalid atom mass value {}", value); - + if (value <= 0.0) { + if (comm->me == 0) + error->warning(file,line,"Ignoring invalid mass value {} for atom type {}", value, itype); + return; + } mass[itype] = value; mass_setflag[itype] = 1; } From 8368b78f23d25ba6643684c8fd8d11aea0501bc0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 26 Feb 2023 13:52:31 -0500 Subject: [PATCH 022/109] document the change in mass handling --- doc/src/pair_eam.rst | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/doc/src/pair_eam.rst b/doc/src/pair_eam.rst index 27347b77f0..654f49c166 100644 --- a/doc/src/pair_eam.rst +++ b/doc/src/pair_eam.rst @@ -116,11 +116,12 @@ are parameterized in terms of LAMMPS :doc:`metal units `. .. note:: - Note that unlike for other potentials, cutoffs for EAM - potentials are not set in the pair_style or pair_coeff command; they - are specified in the EAM potential files themselves. Likewise, the - EAM potential files list atomic masses; thus you do not need to use - the :doc:`mass ` command to specify them. + Note that unlike for other potentials, cutoffs for EAM potentials are not + set in the pair_style or pair_coeff command; they are specified in the EAM + potential files themselves. Likewise, valid EAM potential files usually + contain atomic masses; thus you may not need to use the :doc:`mass ` + command to specify them, unless the potential file uses a dummy value (e.g. + 0.0). LAMMPS will print a warning, if this is the case. There are web sites that distribute and document EAM potentials stored in DYNAMO or other formats: From 095f1d328e15993cff962163a1be5371ef5e5ae0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 24 Feb 2023 12:05:14 -0500 Subject: [PATCH 023/109] make non-polymorph functions and all data members protected. --- src/REPLICA/fix_pimd_nvt.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/REPLICA/fix_pimd_nvt.h b/src/REPLICA/fix_pimd_nvt.h index 6f1321bbda..2cd1397562 100644 --- a/src/REPLICA/fix_pimd_nvt.h +++ b/src/REPLICA/fix_pimd_nvt.h @@ -52,6 +52,8 @@ class FixPIMDNVT : public Fix { int pack_forward_comm(int, int *, double *, int, int *) override; void unpack_forward_comm(int, int, double *) override; + protected: + int method; int np; double inverse_np; From 22998f43ae085090e345f58f7e316fe4d2e85ef4 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Tue, 28 Feb 2023 11:59:06 +0200 Subject: [PATCH 024/109] Include method declaration in bond_morse.h --- src/MOLECULE/bond_morse.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/MOLECULE/bond_morse.h b/src/MOLECULE/bond_morse.h index 5515ea023e..4d0e8e359c 100644 --- a/src/MOLECULE/bond_morse.h +++ b/src/MOLECULE/bond_morse.h @@ -35,6 +35,7 @@ class BondMorse : public Bond { void read_restart(FILE *) override; void write_data(FILE *) override; double single(int, double, int, int, double &) override; + void born_matrix(int, double, int, int, double &, double &) override; void *extract(const char *, int &) override; protected: From 3ab4735aa44189e4276ba99221dc30dda2f5b632 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Tue, 28 Feb 2023 12:00:31 +0200 Subject: [PATCH 025/109] Implement born_matrix in bond_morse.cpp --- src/MOLECULE/bond_morse.cpp | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/src/MOLECULE/bond_morse.cpp b/src/MOLECULE/bond_morse.cpp index e9555698da..b7020b0441 100644 --- a/src/MOLECULE/bond_morse.cpp +++ b/src/MOLECULE/bond_morse.cpp @@ -30,7 +30,10 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -BondMorse::BondMorse(LAMMPS *_lmp) : Bond(_lmp) {} +BondMorse::BondMorse(LAMMPS *_lmp) : Bond(_lmp) +{ + born_matrix_enable = 1; +} /* ---------------------------------------------------------------------- */ @@ -209,6 +212,18 @@ double BondMorse::single(int type, double rsq, int /*i*/, int /*j*/, double &ffo /* ---------------------------------------------------------------------- */ +void BondMorse::born_matrix(int type, double rsq, int /*i*/, int /*j*/, double &du, double &du2) +{ + double r = sqrt(rsq); + double dr = r - r0[type]; + double ralpha = exp(-alpha[type] * dr); + + du = 2.0 * d0[type] * alpha[type] * (1.0 - ralpha) * ralpha; + du2 = -2.0 * d0[type] * alpha[type] * alpha[type] * (1.0 - 2.0 * ralpha) * ralpha; +} + +/* ---------------------------------------------------------------------- */ + void *BondMorse::extract(const char *str, int &dim) { dim = 1; From 7aeccd9a6df6a24d064f505cdea8b8baad6c9240 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Tue, 28 Feb 2023 17:28:02 +0200 Subject: [PATCH 026/109] Include method declaration in bond_nonlinear.h --- src/EXTRA-MOLECULE/bond_nonlinear.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/EXTRA-MOLECULE/bond_nonlinear.h b/src/EXTRA-MOLECULE/bond_nonlinear.h index 3023add89d..f092643662 100644 --- a/src/EXTRA-MOLECULE/bond_nonlinear.h +++ b/src/EXTRA-MOLECULE/bond_nonlinear.h @@ -35,6 +35,7 @@ class BondNonlinear : public Bond { void read_restart(FILE *) override; void write_data(FILE *) override; double single(int, double, int, int, double &) override; + void born_matrix(int, double, int, int, double &, double &) override; void *extract(const char *, int &) override; protected: From 3cd881f0b95e63989e8498ca22c78da470a6d5a3 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Tue, 28 Feb 2023 17:29:50 +0200 Subject: [PATCH 027/109] Implement born_matrix in bond_nonlinear.cpp --- src/EXTRA-MOLECULE/bond_nonlinear.cpp | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/src/EXTRA-MOLECULE/bond_nonlinear.cpp b/src/EXTRA-MOLECULE/bond_nonlinear.cpp index 873c54e917..a2955b7d2e 100644 --- a/src/EXTRA-MOLECULE/bond_nonlinear.cpp +++ b/src/EXTRA-MOLECULE/bond_nonlinear.cpp @@ -28,7 +28,10 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -BondNonlinear::BondNonlinear(LAMMPS *lmp) : Bond(lmp) {} +BondNonlinear::BondNonlinear(LAMMPS *lmp) : Bond(lmp) +{ + born_matrix_enable = 1; +} /* ---------------------------------------------------------------------- */ @@ -207,6 +210,21 @@ double BondNonlinear::single(int type, double rsq, int /*i*/, int /*j*/, /* ---------------------------------------------------------------------- */ +void BondNonlinear::born_matrix(int type, double rsq, int /*i*/, int /*j*/, double &du, double &du2) +{ + double r = sqrt(rsq); + double dr = r - r0[type]; + double drsq = dr * dr; + double lamdasq = lamda[type] * lamda[type]; + double denom = lamdasq - drsq; + double denomsq = denom * denom; + + du = 2.0 * epsilon[type] * lamdasq * dr / denomsq; + du2 = 2.0 * epsilon[type] * lamdasq * (lamdasq + 3.0 * drsq)/ (denomsq * denom); +} + +/* ---------------------------------------------------------------------- */ + void *BondNonlinear::extract(const char *str, int &dim) { dim = 1; From a6eac92cd59016f72d71a95626bbce39d69f12a1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 28 Feb 2023 11:20:33 -0500 Subject: [PATCH 028/109] update list of pair styles that support fix adapt --- doc/src/fix_adapt.rst | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index a3e851faf0..8dda1b3bb6 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -139,7 +139,7 @@ formulas for the meaning of these parameters: +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`buck/mdf ` | a,c | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`coul/cut ` | scale | type pairs | +| :doc:`coul/cut, coul/cut/global ` | scale | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`coul/cut/soft ` | lambda | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ @@ -151,10 +151,16 @@ formulas for the meaning of these parameters: +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`coul/long/soft ` | scale, lambda, coulombic_cutoff | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`coul/slater/long ` | scale | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`coul/streitz ` | scale | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`eam, eam/alloy, eam/fs ` | scale | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`gauss ` | a | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`harmonic/cut ` | k, cutoff | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lennard/mdf ` | A,B | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lj/class2 ` | epsilon,sigma | type pairs | @@ -181,6 +187,8 @@ formulas for the meaning of these parameters: +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`lubricate ` | mu | global | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`meam ` | scale | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`mie/cut ` | epsilon,sigma,gamma_repulsive,gamma_attractive | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`morse, morse/smooth/linear ` | D0,R0,alpha | type pairs | @@ -191,7 +199,7 @@ formulas for the meaning of these parameters: +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`nm/cut/coul/cut, nm/cut/coul/long ` | E0,R0,m,n,coulombic_cutoff | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`reaxff ` | chi, eta, gamma | type global | +| :doc:`pace, pace/extrapolation ` | scale | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`snap ` | scale | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ @@ -203,11 +211,13 @@ formulas for the meaning of these parameters: +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`spin/neel ` | coulombic_cutoff | type global | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ +| :doc:`soft ` | a | type pairs | ++------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`table ` | table_cutoff | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`ufm ` | epsilon,sigma | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`soft ` | a | type pairs | +| :doc:`wf/cut ` | epsilon,sigma,nu,mu | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ .. note:: From 02190b82c2dbec001731a7b8668e3583d3b4bfe0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 28 Feb 2023 11:22:14 -0500 Subject: [PATCH 029/109] link pair style hybrid/scaled to fix adapt and fix alchemy --- doc/src/pair_hybrid.rst | 3 ++- src/ML-SNAP/pair_snap.cpp | 2 ++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/doc/src/pair_hybrid.rst b/doc/src/pair_hybrid.rst index 5ba5fb51d2..a33991e43e 100644 --- a/doc/src/pair_hybrid.rst +++ b/doc/src/pair_hybrid.rst @@ -91,7 +91,8 @@ contributions from sub-styles are weighted by their scale factors, which may be fractional or even negative. Furthermore the scale factors may be variables that may change during a simulation. This enables switching smoothly between two different pair styles or two different -parameter sets during a run. +parameter sets during a run in a similar fashion as could be done +with :doc:`fix adapt ` or :doc:`fix alchemy `. All pair styles that will be used are listed as "sub-styles" following the *hybrid* or *hybrid/overlay* keyword, in any order. In case of the diff --git a/src/ML-SNAP/pair_snap.cpp b/src/ML-SNAP/pair_snap.cpp index 034f76b13a..3029e9212d 100644 --- a/src/ML-SNAP/pair_snap.cpp +++ b/src/ML-SNAP/pair_snap.cpp @@ -796,6 +796,8 @@ double PairSNAP::memory_usage() return bytes; } +/* ---------------------------------------------------------------------- */ + void *PairSNAP::extract(const char *str, int &dim) { dim = 2; From a98c497dbb282fe1b0b73c5b9ca96f81a743985a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 28 Feb 2023 18:10:45 -0500 Subject: [PATCH 030/109] redesign the Howto pages on water models and add inputs and molecule files --- doc/src/Howto.rst | 1 + doc/src/Howto_spc.rst | 114 ++++++- doc/src/Howto_tip3p.rst | 244 ++++++++++++--- doc/src/Howto_tip4p.rst | 325 +++++++++++++++----- doc/src/Howto_tip5p.rst | 161 ++++++++++ doc/utils/sphinx-config/false_positives.txt | 3 + 6 files changed, 718 insertions(+), 130 deletions(-) create mode 100644 doc/src/Howto_tip5p.rst diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index f229deafb3..1366ecb839 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -70,6 +70,7 @@ Force fields howto Howto_amoeba Howto_tip3p Howto_tip4p + Howto_tip5p Howto_spc Packages howto diff --git a/doc/src/Howto_spc.rst b/doc/src/Howto_spc.rst index 520942547e..6414d3b846 100644 --- a/doc/src/Howto_spc.rst +++ b/doc/src/Howto_spc.rst @@ -20,7 +20,6 @@ atoms and the water molecule to run a rigid SPC model. | LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0 | :math:`r_0` of OH bond = 1.0 | :math:`\theta_0` of HOH angle = 109.47\ :math:`^{\circ}` -| Note that as originally proposed, the SPC model was run with a 9 Angstrom cutoff for both LJ and Coulomb terms. It can also be used @@ -33,16 +32,123 @@ the partial charge assignments change: | O charge = -0.8476 | H charge = 0.4238 -| See the :ref:`(Berendsen) ` reference for more details on both the SPC and SPC/E models. +Below is the code for a LAMMPS input file and a molecule file +(``spce.mol``) of SPC/E water for use with the :doc:`molecule command +` demonstrating how to set up a small bulk water system for +SPC/E with rigid bonds. + +.. code-block:: LAMMPS + + units real + atom_style full + region box block -5 5 -5 5 -5 5 + create_box 2 box bond/types 1 angle/types 1 & + extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 + + mass 1 15.9994 + mass 2 1.008 + + pair_style lj/cut/coul/cut 10.0 + pair_coeff 1 1 0.1553 3.166 + pair_coeff 1 2 0.0 1.0 + pair_coeff 2 2 0.0 1.0 + + bond_style zero + bond_coeff 1 1.0 + + angle_style zero + angle_coeff 1 109.47 + + molecule water spce.mol + create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33 + + timestep 1.0 + fix rigid all shake 0.0001 10 10000 b 1 a 1 + minimize 0.0 0.0 1000 10000 + run 0 post no + reset_timestep 0 + velocity all create 300.0 5463576 + fix integrate all nvt temp 300.0 300.0 1.0 + + thermo_style custom step temp press etotal density pe ke + thermo 1000 + run 20000 upto + write_data tip4p.data nocoeff + +.. _spce_molecule: +.. code-block:: + + # Water molecule. SPC/E geometry + + 3 atoms + 2 bonds + 1 angles + + Coords + + 1 0.00000 -0.06461 0.00000 + 2 0.81649 0.51275 0.00000 + 3 -0.81649 0.51275 0.00000 + + Types + + 1 1 # O + 2 2 # H + 3 2 # H + + Charges + + 1 -0.8476 + 2 0.4238 + 3 0.4238 + + Bonds + + 1 1 1 2 + 2 1 1 3 + + Angles + + 1 1 2 1 3 + + Shake Flags + + 1 1 + 2 1 + 3 1 + + Shake Atoms + + 1 1 2 3 + 2 1 2 3 + 3 1 2 3 + + Shake Bond Types + + 1 1 1 1 + 2 1 1 1 + 3 1 1 1 + + Special Bond Counts + + 1 2 0 0 + 2 1 1 0 + 3 1 1 0 + + Special Bonds + + 1 2 3 + 2 1 3 + 3 1 2 + Wikipedia also has a nice article on `water models `_. ---------- .. _howto-Berendsen: -**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, -6269-6271 (1987). +**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987). diff --git a/doc/src/Howto_tip3p.rst b/doc/src/Howto_tip3p.rst index 5571b3291a..682c7f2640 100644 --- a/doc/src/Howto_tip3p.rst +++ b/doc/src/Howto_tip3p.rst @@ -1,53 +1,211 @@ TIP3P water model ================= -The TIP3P water model as implemented in CHARMM -:ref:`(MacKerell) ` specifies a 3-site rigid water molecule with -charges and Lennard-Jones parameters assigned to each of the 3 atoms. -In LAMMPS the :doc:`fix shake ` command can be used to hold -the two O-H bonds and the H-O-H angle rigid. A bond style of -*harmonic* and an angle style of *harmonic* or *charmm* should also be -used. +The TIP3P water model as implemented in CHARMM :ref:`(MacKerell) +` specifies a 3-site rigid water molecule with charges and +Lennard-Jones parameters assigned to each of the 3 atoms. -These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid TIP3P-CHARMM model with a -cutoff. The K values can be used if a flexible TIP3P model (without -fix shake) is desired. If the LJ epsilon and sigma for HH and OH are -set to 0.0, it corresponds to the original 1983 TIP3P model -:ref:`(Jorgensen) `. +A suitable pair style with cutoff Coulomb would be: -| O mass = 15.9994 -| H mass = 1.008 -| O charge = -0.834 -| H charge = 0.417 -| LJ :math:`\epsilon` of OO = 0.1521 -| LJ :math:`\sigma` of OO = 3.1507 -| LJ :math:`\epsilon` of HH = 0.0460 -| LJ :math:`\sigma` of HH = 0.4000 -| LJ :math:`\epsilon` of OH = 0.0836 -| LJ :math:`\sigma` of OH = 1.7753 -| K of OH bond = 450 -| :math:`r_0` of OH bond = 0.9572 -| K of HOH angle = 55 -| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` -| +* :doc:`pair_style lj/cut/coul/cut ` -These are the parameters to use for TIP3P with a long-range Coulomb -solver (e.g. Ewald or PPPM in LAMMPS), see :ref:`(Price) ` for -details: +or these commands for a long-range Coulomb model: + +* :doc:`pair_style lj/cut/coul/long ` +* :doc:`pair_style lj/cut/coul/long/soft ` +* :doc:`kspace_style pppm ` +* :doc:`kspace_style pppm/disp ` + +In LAMMPS the :doc:`fix shake or fix rattle ` command can be +used to hold the two O-H bonds and the H-O-H angle rigid. A bond style +of :doc:`harmonic ` and an angle style of :doc:`harmonic +` or :doc:`charmm ` should also be used. +In case of rigid bonds also bond style :doc:`zero ` and angle +style :doc:`zero ` can be used. + +The table below lists the force field parameters (in real :doc:`units +`) to for the water molecule atoms to run a rigid or flexible +TIP3P-CHARMM model with a cutoff, the original 1983 TIP3P model +:ref:`(Jorgensen) `, or a TIP3P model with parameters +optimized for a long-range Coulomb solver (e.g. Ewald or PPPM in LAMMPS) +:ref:`(Price) `. The K values can be used if a flexible TIP3P +model (without fix shake) is desired, for rigid bonds/angles they are +ignored. + + .. list-table:: + :header-rows: 1 + :widths: auto + + * - Parameter + - TIP3P-CHARMM + - TIP3P (original) + - TIP3P (Ewald) + * - O mass (amu) + - 15.9994 + - 15.9994 + - 15.9994 + * - H mass (amu) + - 1.008 + - 1.008 + - 1.008 + * - O charge (:math:`e`) + - -0.834 + - -0.834 + - -0.834 + * - H charge (:math:`e`) + - 0.417 + - 0.417 + - 0.417 + * - LJ :math:`\epsilon` of OO (kcal/mole) + - 0.1521 + - 0.1521 + - 0.1020 + * - LJ :math:`\sigma` of OO (:math:`\AA`) + - 3.1507 + - 3.1507 + - 3.188 + * - LJ :math:`\epsilon` of HH (kcal/mole) + - 0.0460 + - 0.0 + - 0.0 + * - LJ :math:`\sigma` of HH (:math:`\AA`) + - 0.4 + - 1.0 + - 1.0 + * - LJ :math:`\epsilon` of OH (kcal/mole) + - 0.0836 + - 0.0 + - 0.0 + * - LJ :math:`\sigma` of OH (:math:`\AA`) + - 1.7753 + - 1.0 + - 1.0 + * - K of OH bond (kcal/mole/:math:`\AA^2`) + - 450 + - 450 + - 450 + * - :math:`r_0` of OH bond (:math:`\AA`) + - 0.9572 + - 0.9572 + - 0.9572 + * - K of HOH angle (kcal/mole) + - 55.0 + - 55.0 + - 55.0 + * - :math:`\theta_0` of HOH angle + - 104.52\ :math:`^{\circ}` + - 104.52\ :math:`^{\circ}` + - 104.52\ :math:`^{\circ}` + +Below is the code for a LAMMPS input file and a molecule file +(``tip3p.mol``) of TIP3P water for use with the :doc:`molecule command +` demonstrating how to set up a small bulk water system for +TIP3P with rigid bonds. + +.. code-block:: LAMMPS + + units real + atom_style full + region box block -5 5 -5 5 -5 5 + create_box 2 box bond/types 1 angle/types 1 & + extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 + + mass 1 15.9994 + mass 2 1.008 + + pair_style lj/cut/coul/cut 8.0 + pair_coeff 1 1 0.1521 3.1507 + pair_coeff 2 2 0.0 1.0 + + bond_style zero + bond_coeff 1 0.9574 + + angle_style zero + angle_coeff 1 104.52 + + molecule water tip3p.mol + create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33 + + fix rigid all shake 0.001 10 10000 b 1 a 1 + minimize 0.0 0.0 1000 10000 + run 0 post no + + reset_timestep 0 + velocity all create 300.0 5463576 + fix integrate all nvt temp 300 300 1.0 + + thermo_style custom step temp press etotal pe + + thermo 1000 + run 20000 + write_data tip3p.data nocoeff + +.. _tip3p_molecule: +.. code-block:: + + # Water molecule. TIP3P geometry + + 3 atoms + 2 bonds + 1 angles + + Coords + + 1 0.00000 -0.06556 0.00000 + 2 0.75695 0.52032 0.00000 + 3 -0.75695 0.52032 0.00000 + + Types + + 1 1 # O + 2 2 # H + 3 2 # H + + Charges + + 1 -0.834 + 2 0.417 + 3 0.417 + + Bonds + + 1 1 1 2 + 2 1 1 3 + + Angles + + 1 1 2 1 3 + + Shake Flags + + 1 1 + 2 1 + 3 1 + + Shake Atoms + + 1 1 2 3 + 2 1 2 3 + 3 1 2 3 + + Shake Bond Types + + 1 1 1 1 + 2 1 1 1 + 3 1 1 1 + + Special Bond Counts + + 1 2 0 0 + 2 1 1 0 + 3 1 1 0 + + Special Bonds + + 1 2 3 + 2 1 3 + 3 1 2 -| O mass = 15.9994 -| H mass = 1.008 -| O charge = -0.830 -| H charge = 0.415 -| LJ :math:`\epsilon` of OO = 0.102 -| LJ :math:`\sigma` of OO = 3.188 -| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0 -| K of OH bond = 450 -| :math:`r_0` of OH bond = 0.9572 -| K of HOH angle = 55 -| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` -| Wikipedia also has a nice article on `water models `_. diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index 19b811a282..7912557e61 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -2,100 +2,138 @@ TIP4P water model ================= The four-point TIP4P rigid water model extends the traditional -three-point TIP3P model by adding an additional site, usually -massless, where the charge associated with the oxygen atom is placed. -This site M is located at a fixed distance away from the oxygen along -the bisector of the HOH bond angle. A bond style of *harmonic* and an -angle style of *harmonic* or *charmm* should also be used. +:doc:`three-point TIP3P ` model by adding an additional +site M, usually massless, where the charge associated with the oxygen +atom is placed. This site M is located at a fixed distance away from +the oxygen along the bisector of the HOH bond angle. A bond style of +:doc:`harmonic ` and an angle style of :doc:`harmonic +` or :doc:`charmm ` should also be used. +In case of rigid bonds also bond style :doc:`zero ` and angle +style :doc:`zero ` can be used. -A TIP4P model is run with LAMMPS using either these commands -for a cutoff model: +There are two ways to implement TIP4P water in LAMMPS: -* :doc:`pair_style tip4p/cut ` -* :doc:`pair_style lj/cut/tip4p/cut ` +#. Use a specially written pair style that uses the :ref:`TIP3P geometry + ` without the point M. The point M location is then + implicitly derived from the other atoms or each water molecule and + used during the force computation. The forces on M are then + projected on the oxygen and the two hydrogen atoms. This is + computationally very efficient, but the charge distribution in space + is only correct within the tip4p labeled styles. So all other + computations using charges will "see" the negative charge incorrectly + on the oxygen atom. -or these commands for a long-range model: + This can be done with the following pair styles for Coulomb with a cutoff: -* :doc:`pair_style tip4p/long ` -* :doc:`pair_style lj/cut/tip4p/long ` -* :doc:`pair_style lj/long/tip4p/long ` -* :doc:`pair_style tip4p/long/soft ` -* :doc:`pair_style lj/cut/tip4p/long/soft ` -* :doc:`kspace_style pppm/tip4p ` -* :doc:`kspace_style pppm/disp/tip4p ` + * :doc:`pair_style tip4p/cut ` + * :doc:`pair_style lj/cut/tip4p/cut ` -The bond lengths and bond angles should be held fixed using the -:doc:`fix shake ` or :doc:`fix rattle ` command, -unless a parameterization for a flexible TIP4P model is used. The -parameter sets listed below are all for rigid TIP4P model variants and -thus the bond and angle force constants are not used and can be set to -any legal value; only equilibrium length and angle are used. + or these commands for a long-range Coulomb treatment: -These are the additional parameters (in real units) to set for O and H -atoms and the water molecule to run a rigid TIP4P model with a cutoff -:ref:`(Jorgensen) `. Note that the OM distance is specified in -the :doc:`pair_style ` command, not as part of the pair -coefficients. + * :doc:`pair_style tip4p/long ` + * :doc:`pair_style lj/cut/tip4p/long ` + * :doc:`pair_style lj/long/tip4p/long ` + * :doc:`pair_style tip4p/long/soft ` + * :doc:`pair_style lj/cut/tip4p/long/soft ` + * :doc:`kspace_style pppm/tip4p ` + * :doc:`kspace_style pppm/disp/tip4p ` -| O mass = 15.9994 -| H mass = 1.008 -| O charge = -1.040 -| H charge = 0.520 -| :math:`r_0` of OH bond = 0.9572 -| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` -| OM distance = 0.15 -| LJ :math:`\epsilon` of O-O = 0.1550 -| LJ :math:`\sigma` of O-O = 3.1536 -| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0 -| Coulomb cutoff = 8.5 -| + The bond lengths and bond angles should be held fixed using the + :doc:`fix shake ` or :doc:`fix rattle ` command, + unless a parameterization for a flexible TIP4P model is used. The + parameter sets listed below are all for rigid TIP4P model variants and + thus the bond and angle force constants are not used and can be set to + any legal value; only equilibrium length and angle are used. -For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005); -https://doi.org/10.1063/1.1931662) these values can be used: +#. Use an :ref:`explicit 4 point TIP4P geometry ` where + the oxygen atom carries no charge and the M point no Lennard-Jones + interactions. Since :doc:`fix shake ` or :doc:`fix rattle + ` may not be applied to this kind of geometry, :doc:`fix + rigid or fix rigid/small ` or its thermostatted variants + are required to maintain a rigid geometry. This avoids some of the + issues with respect to analysis and non-tip4p styles, but it is a + more costly force computation (more atoms in the same volume and thus + more neighbors in the neighbor lists) and requires a much shorter + timestep for stable integration of the rigid body motion. Since no + bonds or angles are required, they do not need to be defined and atom + style charge would be sufficient for a bulk TIP4P water system. In + order to avoid that LAMMPS produces an error due to the massless M + site a tiny non-zero mass needs to be assigned. -| O mass = 15.9994 -| H mass = 1.008 -| O charge = -1.1794 -| H charge = 0.5897 -| :math:`r_0` of OH bond = 0.9572 -| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` -| OM distance = 0.1577 -| LJ :math:`\epsilon` of O-O = 0.21084 -| LJ :math:`\sigma` of O-O = 3.1668 -| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0 -| Coulomb cutoff = 8.5 -| +The table below lists the force field parameters (in real :doc:`units +`) to for a selection of popular variants of the TIP4P model. +There is the rigid TIP4P model with a cutoff :ref:`(Jorgensen) +`, the TIP4/Ice model :ref:`(Abascal1) `, the +TIP4P/2005 model :ref:`(Abascal2) ` and a version of TIP4P +parameters adjusted for use with a long-range Coulombic solver +(e.g. Ewald or PPPM in LAMMPS). Note that for implicit TIP4P models the +OM distance is specified in the :doc:`pair_style ` command, +not as part of the pair coefficients. -For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005); -https://doi.org/10.1063/1.2121687), these values can be used: + .. list-table:: + :header-rows: 1 + :widths: auto -| O mass = 15.9994 -| H mass = 1.008 -| O charge = -1.1128 -| H charge = 0.5564 -| :math:`r_0` of OH bond = 0.9572 -| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` -| OM distance = 0.1546 -| LJ :math:`\epsilon` of O-O = 0.1852 -| LJ :math:`\sigma` of O-O = 3.1589 -| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0 -| Coulomb cutoff = 8.5 -| - -These are the parameters to use for TIP4P with a long-range Coulombic -solver (e.g. Ewald or PPPM in LAMMPS): - -| O mass = 15.9994 -| H mass = 1.008 -| O charge = -1.0484 -| H charge = 0.5242 -| :math:`r_0` of OH bond = 0.9572 -| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}` -| OM distance = 0.1250 -| LJ :math:`\epsilon` of O-O = 0.16275 -| LJ :math:`\sigma` of O-O = 3.16435 -| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0 -| + * - Parameter + - TIP4P (original) + - TIP4P/Ice + - TIP4P/2005 + - TIP4P (Ewald) + * - O mass (amu) + - 15.9994 + - 15.9994 + - 15.9994 + - 15.9994 + * - H mass (amu) + - 1.008 + - 1.008 + - 1.008 + - 1.008 + * - O or M charge (:math:`e`) + - -1.040 + - -1.1794 + - -1.1128 + - -1.04844 + * - H charge (:math:`e`) + - 0.520 + - 0.5897 + - 0.5564 + - 0.52422 + * - LJ :math:`\epsilon` of OO (kcal/mole) + - 0.1550 + - 0.1577 + - 0.1852 + - 0.16275 + * - LJ :math:`\sigma` of OO (:math:`\AA`) + - 3.1536 + - 3.1668 + - 3.1589 + - 3.16435 + * - LJ :math:`\epsilon` of HH, MM, OH, OM, HM (kcal/mole) + - 0.0 + - 0.0 + - 0.0 + - 0.0 + * - LJ :math:`\sigma` of HH, MM, OH, OM, HM (:math:`\AA`) + - 1.0 + - 1.0 + - 1.0 + - 1.0 + * - :math:`r_0` of OH bond (:math:`\AA`) + - 0.9572 + - 0.9572 + - 0.9572 + - 0.9572 + * - :math:`\theta_0` of HOH angle + - 104.52\ :math:`^{\circ}` + - 104.52\ :math:`^{\circ}` + - 104.52\ :math:`^{\circ}` + - 104.52\ :math:`^{\circ}` + * - OM distance (:math:`\AA`) + - 0.15 + - 0.1577 + - 0.1546 + - 0.1250 Note that the when using the TIP4P pair style, the neighbor list cutoff for Coulomb interactions is effectively extended by a distance 2 \* (OM @@ -108,6 +146,117 @@ trade-off for your model. The OM distance and the LJ and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long ` command. +Below is the code for a LAMMPS input file using the implicit method and +the :ref:`TIP3P molecule file `. Because the TIP4P +charges are different from TIP3P they need to be reset (or the molecule +file changed): + +.. code-block:: LAMMPS + + units real + atom_style full + region box block -5 5 -5 5 -5 5 + create_box 2 box bond/types 1 angle/types 1 & + extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2 + + mass 1 15.9994 + mass 2 1.008 + + pair_style lj/cut/tip4p/cut 1 2 1 1 0.15 8.0 + pair_coeff 1 1 0.1550 3.1536 + pair_coeff 2 2 0.0 1.0 + + bond_style zero + bond_coeff 1 0.9574 + + angle_style zero + angle_coeff 1 104.52 + + molecule water tip3p.mol # this uses the TIP3P geometry + create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33 + # must change charges for TIP4P + set type 1 charge -1.040 + set type 2 charge 0.520 + + fix rigid all shake 0.001 10 10000 b 1 a 1 + minimize 0.0 0.0 1000 10000 + run 0 post no + + reset_timestep 0 + velocity all create 300.0 5463576 + fix integrate all nvt temp 300 300 1.0 + + thermo_style custom step temp press etotal pe + + thermo 1000 + run 20000 + write_data tip3p.data nocoeff + +Below is the code for a LAMMPS input file using the explicit method and +a TIP4P molecule file. Because of using :doc:`fix rigid/nvt/small +` no bonds need to be defined and thus no extra storage needs +to be reserved for them, but we need to switch to atom style full or use +:doc:`fix property/atom mol ` so that fix +rigid/nvt/small can identify rigid bodies by their molecule ID: + +.. code-block:: LAMMPS + + units real + atom_style charge + region box block -5 5 -5 5 -5 5 + create_box 3 box + + mass 1 15.9994 + mass 2 1.008 + mass 3 1.0e-100 + + pair_style lj/cut/coul/cut 8.0 + pair_coeff 1 1 0.1550 3.1536 + pair_coeff 2 2 0.0 1.0 + pair_coeff 3 3 0.0 1.0 + + fix mol all property/atom mol + molecule water tip4p.mol + create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33 + + timestep 0.1 + fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0 + velocity all create 300.0 5463576 + + thermo_style custom step temp press etotal density pe ke + thermo 1000 + run 20000 + write_data tip4p.data nocoeff + +.. _tip4p_molecule: +.. code-block:: + + # Water molecule. Explicit TIP4P geometry for use with fix rigid + + 4 atoms + + Coords + + 1 0.00000 -0.06556 0.00000 + 2 0.75695 0.52032 0.00000 + 2 -0.75695 0.52032 0.00000 + 4 0.00000 0.08444 0.00000 + + Types + + 1 1 # O + 2 2 # H + 3 2 # H + 4 3 # M + + Charges + + 1 0.000 + 2 0.520 + 3 0.520 + 4 -1.040 + + Wikipedia also has a nice article on `water models `_. ---------- @@ -116,3 +265,13 @@ Wikipedia also has a nice article on `water models ` by adding two additional sites L, usually +massless, where the charge associated with the oxygen atom is placed. +These sites L are located at a fixed distance away from the oxygen atom, +forming a tetrahedral angle that is rotated by 90 degrees from the HOH +plane. Those sites thus somewhat approximate lone pairs of the oxygen +and consequently improve the water structure to become even more +"tetrahedral" in comparison to the :doc:`four-point TIP4P model +`. + +A suitable pair style with cutoff Coulomb would be: + +* :doc:`pair_style lj/cut/coul/cut ` + +or these commands for a long-range model: + +* :doc:`pair_style lj/cut/coul/long ` +* :doc:`pair_style lj/cut/coul/long/soft ` +* :doc:`kspace_style pppm ` +* :doc:`kspace_style pppm/disp ` + +A TIP5P model *must* be run using a :doc:`rigid fix ` since +there is no other option to keep this kind of structure rigid in LAMMPS. +In order to avoid that LAMMPS produces an error due to the massless L +sites, those need to be assigned a tiny non-zero mass. + +The table below lists the force field parameters (in real :doc:`units +`) to for a the TIP5P model with a cutoff :ref:`(Mahoney) +` and the TIP5P-E model :ref:`(Rick) ` for use with a +long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS). + + .. list-table:: + :header-rows: 1 + :widths: auto + + * - Parameter + - TIP5P + - TIP5P-E + * - O mass (amu) + - 15.9994 + - 15.9994 + * - H mass (amu) + - 1.008 + - 1.008 + * - O charge (:math:`e`) + - 0.0 + - 0.0 + * - L charge (:math:`e`) + - -0.241 + - -0.241 + * - H charge (:math:`e`) + - 0.241 + - 0.241 + * - LJ :math:`\epsilon` of OO (kcal/mole) + - 0.1600 + - 0.1780 + * - LJ :math:`\sigma` of OO (:math:`\AA`) + - 3.1200 + - 3.0970 + * - LJ :math:`\epsilon` of HH, LL, OH, OL, HL (kcal/mole) + - 0.0 + - 0.0 + * - LJ :math:`\sigma` of HH, LL, OH, OL, HL (:math:`\AA`) + - 1.0 + - 1.0 + * - :math:`r_0` of OH bond (:math:`\AA`) + - 0.9572 + - 0.9572 + * - :math:`\theta_0` of HOH angle + - 104.52\ :math:`^{\circ}` + - 104.52\ :math:`^{\circ}` + * - OL distance (:math:`\AA`) + - 0.70 + - 0.70 + * - :math:`\theta_0` of LOL angle + - 109.47\ :math:`^{\circ}` + - 109.47\ :math:`^{\circ}` + +Below is the code for a LAMMPS input file for setting up a simulation of +TIP5P water with a molecule file. Because of using :doc:`fix +rigid/nvt/small ` no bonds need to be defined and thus no +extra storage needs to be reserved for them, but we need to switch to +atom style full or use :doc:`fix property/atom mol ` +so that fix rigid/nvt/small can identify rigid bodies by their molecule +ID: + +.. code-block:: LAMMPS + + units real + atom_style charge + region box block -5 5 -5 5 -5 5 + create_box 3 box + + mass 1 15.9994 + mass 2 1.008 + mass 3 1.0e-100 + + pair_style lj/cut/coul/cut 8.0 + pair_coeff 1 1 0.160 3.12 + pair_coeff 2 2 0.0 1.0 + pair_coeff 3 3 0.0 1.0 + + fix mol all property/atom mol + molecule water tip5p.mol + create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33 + + timestep 0.20 + fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0 + reset_timestep 0 + velocity all create 300.0 5463576 + + thermo_style custom step temp press etotal density pe ke + thermo 1000 + run 20000 + write_data tip5p.data nocoeff + +.. _tip5p_molecule: +.. code-block:: + + # Water molecule. Explicit TIP5P geometry for use with fix rigid + + 5 atoms + + Coords + + 1 0.00000 -0.06556 0.00000 + 2 0.75695 0.52032 0.00000 + 3 -0.75695 0.52032 0.00000 + 4 0.00000 -0.46971 0.57154 + 5 0.00000 -0.46971 -0.57154 + + Types + + 1 1 # O + 2 2 # H + 3 2 # H + 4 3 # L + 5 3 # L + + Charges + + 1 0.000 + 2 0.241 + 3 0.241 + 4 -0.241 + 5 -0.241 + +Wikipedia also has a nice article on `water models `_. + +---------- + +.. _Mahoney: + +**(Mahoney)** Mahoney, Jorgensen, J Chem Phys 112, 8910 (2000) + +.. _Rick: + +**(Rick)** Rick, J Chem Phys 120, 6085 (2004) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index fdacbf9c4c..0349c894a2 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1,5 +1,6 @@ aa aat +Abascal abc abf ABI @@ -1985,6 +1986,7 @@ magelec Maginn magneton magnetons +Mahoney mainboard mainboards makefile @@ -3186,6 +3188,7 @@ Sandia sandybrown sanitizer Sanyal +Sanz Sarath sc scafacos From 2507e414d9e4c38f4c7d0bc9cfdee4daf51c5538 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 28 Feb 2023 18:11:05 -0500 Subject: [PATCH 031/109] fix broken link --- doc/src/fix_adapt.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_adapt.rst b/doc/src/fix_adapt.rst index 8dda1b3bb6..926b8ed0c6 100644 --- a/doc/src/fix_adapt.rst +++ b/doc/src/fix_adapt.rst @@ -153,7 +153,7 @@ formulas for the meaning of these parameters: +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`coul/slater/long ` | scale | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ -| :doc:`coul/streitz ` | scale | type pairs | +| :doc:`coul/streitz ` | scale | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ | :doc:`eam, eam/alloy, eam/fs ` | scale | type pairs | +------------------------------------------------------------------------------+--------------------------------------------------+-------------+ From 103e63eca532476df63abb586ca4b716aaf1aa35 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 28 Feb 2023 18:58:57 -0500 Subject: [PATCH 032/109] more careful checks and print error messages to global root. --- src/REPLICA/fix_alchemy.cpp | 83 +++++++++++++++++++++++++------------ src/variable.cpp | 2 +- 2 files changed, 58 insertions(+), 27 deletions(-) diff --git a/src/REPLICA/fix_alchemy.cpp b/src/REPLICA/fix_alchemy.cpp index 2f99f667b6..c6617c4600 100644 --- a/src/REPLICA/fix_alchemy.cpp +++ b/src/REPLICA/fix_alchemy.cpp @@ -35,12 +35,12 @@ using namespace FixConst; FixAlchemy::FixAlchemy(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), commbuf(nullptr) { - if (narg != 4) error->all(FLERR, "Incorrect number of arguments for fix alchemy"); - if (universe->nworlds != 2) error->all(FLERR, "Must use exactly two partitions"); + if (narg != 4) error->universe_all(FLERR, "Incorrect number of arguments for fix alchemy"); + if (universe->nworlds != 2) error->universe_all(FLERR, "Must use exactly two partitions"); if (utils::strmatch(arg[3], "^v_")) id_lambda = arg[3] + 2; else - error->all(FLERR, "Must use variable as lambda argument to fix alchemy"); + error->universe_all(FLERR, "Must use variable as lambda argument to fix alchemy"); lambda = epot[0] = epot[1] = epot[2] = 0.0; progress = 0; @@ -73,7 +73,9 @@ FixAlchemy::FixAlchemy(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), int allfail = 0; MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld); if (allfail) - error->all(FLERR, "Number of atoms and domain decomposition must match for both partitions"); + error->universe_all(FLERR, + "Number of atoms and domain decomposition must be the same " + "on all partitions"); id_pe = std::string(id) + "_pe"; pe = modify->add_compute(id_pe + " all pe"); @@ -130,17 +132,19 @@ void FixAlchemy::init() memory->create(commbuf, sizeof(double) * nmax, "alchemy:nmax"); if (modify->get_fix_by_style("^balance").size() > 0) - error->all(FLERR, "Fix alchemy is not compatible with load balancing"); + error->universe_all(FLERR, "Fix alchemy is not compatible with load balancing"); if (modify->get_fix_by_style("^alchemy").size() > 1) - error->all(FLERR, "There may only one fix alchemy at a time"); + error->universe_all(FLERR, "There may only one fix alchemy at a time"); + + if (utils::strmatch(update->integrate_style, "^respa")) + error->universe_all(FLERR, "Must not use run style respa with fix alchemy"); ivar = input->variable->find(id_lambda.c_str()); if (ivar < 0) - error->universe_one(FLERR, fmt::format("Variable {} for fix alchemy does not exist", id_lambda)); + error->universe_one(FLERR, fmt::format("Fix alchemy variable {} does not exist", id_lambda)); if (!input->variable->equalstyle(ivar)) - error->universe_one(FLERR, - fmt::format("Variable {} for fix alchemy is invalid style", id_lambda)); + error->universe_one(FLERR, fmt::format("Fix alchemy variable {} is invalid style", id_lambda)); lambda = input->variable->compute_equal(ivar); // synchronize box dimensions, determine if resync during run will be needed. @@ -156,33 +160,60 @@ void FixAlchemy::init() void FixAlchemy::setup(int vflag) { - if (utils::strmatch(update->integrate_style, "^respa")) { - auto respa = dynamic_cast(update->integrate); - respa->copy_flevel_f(ilevel_respa); - post_force_respa(vflag, ilevel_respa, 0); - respa->copy_f_flevel(ilevel_respa); - } else { - post_force(vflag); - } - if (universe->me == 0) { - double delta = update->ntimestep - update->beginstep; - if ((delta != 0.0) && (update->beginstep != update->endstep)) - delta /= update->endstep - update->beginstep; - progress = static_cast(delta*100.0); - auto msg = fmt::format("Starting alchemical transformation at {:>3d}%\n", progress); + progress = 0; + auto msg = fmt::format("Starting alchemical run\n"); if (universe->uscreen) fmt::print(universe->uscreen, msg); if (universe->ulogfile) fmt::print(universe->ulogfile, msg); } + + // recheck domain decomposition, atom ordering, and synchronize positions + + post_integrate(); + + // mix initial forces + + post_force(vflag); } /* ---------------------------------------------------------------------- */ void FixAlchemy::post_integrate() { + // re-check that we have the same domain decomposition on all ranks + const int nlocal = atom->nlocal; + int my_nlocal[2] = {0, 0}; + int all_nlocal[2] = {0, 0}; + my_nlocal[universe->iworld] = nlocal; + MPI_Allreduce(my_nlocal, all_nlocal, 2, MPI_INT, MPI_SUM, samerank); + int fail = (all_nlocal[0] == all_nlocal[1]) ? 0 : 1; + int allfail = 0; + MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld); + if (allfail) + error->universe_all(FLERR, + "Number of atoms and domain decomposition must be the same on " + "all partitions"); + + // check that we have the same atom order on all ranks + // re-use communication buffer for positions and forces + + tagint *tagbuf = (tagint *) commbuf; + tagint *tag = atom->tag; + if (universe->iworld == 0) { + for (int i = 0; i < nlocal; ++i) tagbuf[i] = tag[i]; + } + MPI_Bcast(tagbuf, nlocal, MPI_LMP_TAGINT, 0, samerank); + fail = allfail = 0; + if (universe->iworld > 0) { + for (int i = 0; i < nlocal; ++i) + if (tag[i] != tagbuf[i]) fail = 1; + } + MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld); + if (allfail) error->universe_all(FLERR, "Atoms must have the same order on all partitions"); + // synchronize atom positions - const int nall = atom->nlocal + atom->nghost; + const int nall = atom->nlocal; MPI_Bcast(&atom->x[0][0], 3 * nall, MPI_DOUBLE, 0, samerank); // synchronize box dimensions, if needed @@ -228,10 +259,10 @@ void FixAlchemy::post_force(int /*vflag*/) double delta = update->ntimestep - update->beginstep; if ((delta != 0.0) && (update->beginstep != update->endstep)) delta /= update->endstep - update->beginstep; - int status = static_cast(delta*100.0); + int status = static_cast(delta * 100.0); if ((status / 10) > (progress / 10)) { progress = status; - auto msg = fmt::format(" Alchemical transformation progress: {:>3d}%\n", progress); + auto msg = fmt::format(" Alchemical run progress: {:>3d}%\n", progress); if (universe->uscreen) fmt::print(universe->uscreen, msg); if (universe->ulogfile) fmt::print(universe->ulogfile, msg); } diff --git a/src/variable.cpp b/src/variable.cpp index 2ac9bd0364..fffd9b35c3 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -239,7 +239,7 @@ void Variable::set(int narg, char **arg) style[nvar] = WORLD; num[nvar] = narg - 2; if (num[nvar] != universe->nworlds) - error->all(FLERR,"World variable count doesn't match # of partitions"); + error->universe_all(FLERR,"World variable count doesn't match # of partitions"); which[nvar] = universe->iworld; pad[nvar] = 0; data[nvar] = new char*[num[nvar]]; From bc4da2afef42a5c9d23d87cf22422cd3ec81f115 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 28 Feb 2023 19:26:18 -0500 Subject: [PATCH 033/109] roll back change causing unittest failures --- src/variable.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/variable.cpp b/src/variable.cpp index fffd9b35c3..2ac9bd0364 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -239,7 +239,7 @@ void Variable::set(int narg, char **arg) style[nvar] = WORLD; num[nvar] = narg - 2; if (num[nvar] != universe->nworlds) - error->universe_all(FLERR,"World variable count doesn't match # of partitions"); + error->all(FLERR,"World variable count doesn't match # of partitions"); which[nvar] = universe->iworld; pad[nvar] = 0; data[nvar] = new char*[num[nvar]]; From e59d08ee8b61f9d6a5cfe4fd83d2d4049389bdf8 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Wed, 1 Mar 2023 10:22:07 +0200 Subject: [PATCH 034/109] Include method declaration in pair_lj_class2_coul_cut.h --- src/CLASS2/pair_lj_class2_coul_cut.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/CLASS2/pair_lj_class2_coul_cut.h b/src/CLASS2/pair_lj_class2_coul_cut.h index ca5d6830f5..c4e9ba2ec9 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.h +++ b/src/CLASS2/pair_lj_class2_coul_cut.h @@ -40,6 +40,7 @@ class PairLJClass2CoulCut : public Pair { void write_data(FILE *) override; void write_data_all(FILE *) override; double single(int, int, int, int, double, double, double, double &) override; + void born_matrix(int, int, int, int, double, double, double, double &, double &) override; void *extract(const char *, int &) override; protected: From 85f3d6eaef260a47d118f1aa5737e2819116f61c Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Wed, 1 Mar 2023 10:24:22 +0200 Subject: [PATCH 035/109] Implement born_matrix in pair_lj_class2_coul_cut.cpp --- src/CLASS2/pair_lj_class2_coul_cut.cpp | 32 ++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) diff --git a/src/CLASS2/pair_lj_class2_coul_cut.cpp b/src/CLASS2/pair_lj_class2_coul_cut.cpp index d05eb9acae..3f66f1550f 100644 --- a/src/CLASS2/pair_lj_class2_coul_cut.cpp +++ b/src/CLASS2/pair_lj_class2_coul_cut.cpp @@ -32,6 +32,7 @@ using namespace MathConst; PairLJClass2CoulCut::PairLJClass2CoulCut(LAMMPS *lmp) : Pair(lmp) { + born_matrix_enable = 1; writedata = 1; centroidstressflag = CENTROID_SAME; } @@ -470,6 +471,37 @@ double PairLJClass2CoulCut::single(int i, int j, int itype, int jtype, double rs /* ---------------------------------------------------------------------- */ +void PairLJClass2CoulCut::born_matrix(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, double &dupair, + double &du2pair) +{ + double rinv, r2inv, r3inv, r7inv, r8inv; + double du_lj, du2_lj, du_coul, du2_coul; + + double *q = atom->q; + double qqrd2e = force->qqrd2e; + + r2inv = 1.0 / rsq; + rinv = sqrt(r2inv); + r3inv = r2inv * rinv; + r7inv = r3inv * r3inv * rinv; + r8inv = r7inv * rinv; + + // Reminder: lj1[i][j] = 18.0 * epsilon[i][j] * pow(sigma[i][j], 9.0); + // Reminder: lj2[i][j] = 18.0 * epsilon[i][j] * pow(sigma[i][j], 6.0); + du_lj = r7inv * (lj2[itype][jtype] - lj1[itype][jtype] * r3inv); + du2_lj = r8inv * (10 * lj1[itype][jtype] * r3inv - 7 * lj2[itype][jtype]); + + // Reminder: qqrd2e converts q^2/r to energy w/ dielectric constant + du_coul = -qqrd2e * q[i] * q[j] * r2inv; + du2_coul = 2.0 * qqrd2e * q[i] * q[j] * r3inv; + + dupair = factor_lj * du_lj + factor_coul * du_coul; + du2pair = factor_lj * du2_lj + factor_coul * du2_coul; +} + +/* ---------------------------------------------------------------------- */ + void *PairLJClass2CoulCut::extract(const char *str, int &dim) { dim = 2; From e0cc7aad97325d4bd11dc39242289121eeb5e666 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Wed, 1 Mar 2023 12:36:35 +0200 Subject: [PATCH 036/109] Include method declaration in pair_buck_coul_cut.h --- src/pair_buck_coul_cut.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/pair_buck_coul_cut.h b/src/pair_buck_coul_cut.h index b5f19def38..3b13cb46b3 100644 --- a/src/pair_buck_coul_cut.h +++ b/src/pair_buck_coul_cut.h @@ -40,6 +40,7 @@ class PairBuckCoulCut : public Pair { void write_data(FILE *) override; void write_data_all(FILE *) override; double single(int, int, int, int, double, double, double, double &) override; + void born_matrix(int, int, int, int, double, double, double, double &, double &) override; void *extract(const char *, int &) override; protected: From 45009c8c66d6bf183b5be870a4d0d8a8e7d069c4 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Wed, 1 Mar 2023 12:38:23 +0200 Subject: [PATCH 037/109] Implement born_matrix in pair_buck_coul_cut.cpp --- src/pair_buck_coul_cut.cpp | 38 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) diff --git a/src/pair_buck_coul_cut.cpp b/src/pair_buck_coul_cut.cpp index 4f85ccd430..369b77474f 100644 --- a/src/pair_buck_coul_cut.cpp +++ b/src/pair_buck_coul_cut.cpp @@ -36,6 +36,7 @@ using namespace MathConst; PairBuckCoulCut::PairBuckCoulCut(LAMMPS *lmp) : Pair(lmp) { + born_matrix_enable = 1; writedata = 1; } @@ -475,6 +476,43 @@ double PairBuckCoulCut::single(int i, int j, int itype, int jtype, double rsq, d /* ---------------------------------------------------------------------- */ +void PairBuckCoulCut::born_matrix(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, double &dupair, + double &du2pair) +{ + double rinv, r2inv, r3inv, r6inv, r7inv, r8inv, r, rexp; + double du_lj, du2_lj, du_coul, du2_coul; + + double *q = atom->q; + double qqrd2e = force->qqrd2e; + + r = sqrt(rsq); + rexp = exp(-r*rhoinv[itype][jtype]); + + r2inv = 1.0 / rsq; + rinv = sqrt(r2inv); + r3inv = r2inv * rinv; + r6inv = r2inv * r2inv * r2inv; + r7inv = r6inv * rinv; + r8inv = r6inv * r2inv; + + // Reminder: buck1[itype][jtype] = a[itype][jtype]/rho[itype][jtype]; + // Reminder: buck2[itype][jtype] = 6.0*c[itype][jtype]; + + du_lj = buck2[itype][jtype] * r7inv - buck1[itype][jtype] * rexp; + du2_lj = (buck1[itype][jtype] / rho[itype][jtype]) * rexp - 7 * buck2[itype][jtype] * r8inv; + + // Reminder: qqrd2e converts q^2/r to energy w/ dielectric constant + + du_coul = -qqrd2e * q[i] * q[j] * r2inv; + du2_coul = 2.0 * qqrd2e * q[i] * q[j] * r3inv; + + dupair = factor_lj * du_lj + factor_coul * du_coul; + du2pair = factor_lj * du2_lj + factor_coul * du2_coul; +} + +/* ---------------------------------------------------------------------- */ + void *PairBuckCoulCut::extract(const char *str, int &dim) { dim = 2; From 060976bb262a559cb7d311e819e101985ea0154e Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Wed, 1 Mar 2023 18:29:56 +0200 Subject: [PATCH 038/109] Include method declaration in pair_coul_cut.h --- src/pair_coul_cut.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/pair_coul_cut.h b/src/pair_coul_cut.h index dc3a3df64f..0890a7da33 100644 --- a/src/pair_coul_cut.h +++ b/src/pair_coul_cut.h @@ -40,6 +40,7 @@ class PairCoulCut : public Pair { void write_data(FILE *) override; void write_data_all(FILE *) override; double single(int, int, int, int, double, double, double, double &) override; + void born_matrix(int, int, int, int, double, double, double, double &, double &) override; void *extract(const char *, int &) override; protected: From b8922ffe07451907179321c64879e4c6ef249326 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Wed, 1 Mar 2023 18:30:51 +0200 Subject: [PATCH 039/109] Include method declaration in pair_coul_debye.h --- src/pair_coul_debye.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/pair_coul_debye.h b/src/pair_coul_debye.h index 0f28efb46a..1d8b5760fa 100644 --- a/src/pair_coul_debye.h +++ b/src/pair_coul_debye.h @@ -32,6 +32,7 @@ class PairCoulDebye : public PairCoulCut { void write_restart_settings(FILE *) override; void read_restart_settings(FILE *) override; double single(int, int, int, int, double, double, double, double &) override; + void born_matrix(int, int, int, int, double, double, double, double &, double &) override; protected: double kappa; From fa57857cc0d67744847166a3c572454ff1755ac7 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Wed, 1 Mar 2023 18:32:11 +0200 Subject: [PATCH 040/109] Implement born_matrix in pair_coul_cut.cpp --- src/pair_coul_cut.cpp | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index 9246e535fe..f0a749baa8 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -30,6 +30,7 @@ using namespace LAMMPS_NS; PairCoulCut::PairCoulCut(LAMMPS *lmp) : Pair(lmp) { + born_matrix_enable = 1; writedata = 1; } @@ -329,6 +330,31 @@ double PairCoulCut::single(int i, int j, int /*itype*/, int /*jtype*/, double rs /* ---------------------------------------------------------------------- */ +void PairCoulCut::born_matrix(int i, int j, int /*itype*/, int /*jtype*/, double rsq, + double factor_coul, double /*factor_lj*/, double &dupair, + double &du2pair) +{ + double rinv, r2inv, r3inv; + double du_coul, du2_coul; + + double *q = atom->q; + double qqrd2e = force->qqrd2e; + + r2inv = 1.0 / rsq; + rinv = sqrt(r2inv); + r3inv = r2inv * rinv; + + // Reminder: qqrd2e converts q^2/r to energy w/ dielectric constant + + du_coul = -qqrd2e * q[i] * q[j] * r2inv; + du2_coul = 2.0 * qqrd2e * q[i] * q[j] * r3inv; + + dupair = factor_coul * du_coul; + du2pair = factor_coul * du2_coul; +} + +/* ---------------------------------------------------------------------- */ + void *PairCoulCut::extract(const char *str, int &dim) { dim = 2; From 35a9771e235123c8be6124816d9377b1da3bf56b Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Wed, 1 Mar 2023 18:33:37 +0200 Subject: [PATCH 041/109] Implement born_matrix in pair_coul_debye.cpp --- src/pair_coul_debye.cpp | 31 ++++++++++++++++++++++++++++++- 1 file changed, 30 insertions(+), 1 deletion(-) diff --git a/src/pair_coul_debye.cpp b/src/pair_coul_debye.cpp index 0f375f6e00..285b742074 100644 --- a/src/pair_coul_debye.cpp +++ b/src/pair_coul_debye.cpp @@ -26,7 +26,10 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairCoulDebye::PairCoulDebye(LAMMPS *lmp) : PairCoulCut(lmp) {} +PairCoulDebye::PairCoulDebye(LAMMPS *lmp) : PairCoulCut(lmp) +{ + born_matrix_enable = 1; +} /* ---------------------------------------------------------------------- */ @@ -177,3 +180,29 @@ double PairCoulDebye::single(int i, int j, int /*itype*/, int /*jtype*/, phicoul = force->qqrd2e * atom->q[i]*atom->q[j] * rinv * screening; return factor_coul*phicoul; } + +/* ---------------------------------------------------------------------- */ + +void PairCoulDebye::born_matrix(int i, int j, int /*itype*/, int /*jtype*/, double rsq, + double factor_coul, double /*factor_lj*/, double &dupair, + double &du2pair) +{ + double r, rinv, r2inv, r3inv, screening; + double du_coul, du2_coul; + + double *q = atom->q; + double qqrd2e = force->qqrd2e; + + r = sqrt(rsq); + r2inv = 1.0 / rsq; + rinv = sqrt(r2inv); + r3inv = r2inv * rinv; + screening = exp(-kappa*r); + + // Reminder: qqrd2e converts q^2/r to energy w/ dielectric constant + du_coul = -qqrd2e * q[i] * q[j] * r2inv * (1 + kappa * r) * screening; + du2_coul = qqrd2e * q[i] * q[j] * r3inv * (2 + 2 * kappa * r + kappa * kappa * rsq) * screening; + + dupair = factor_coul * du_coul; + du2pair = factor_coul * du2_coul; +} From a715a56afebcd35a7548ee6f1afd0f520ca2596e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Mar 2023 20:41:00 -0500 Subject: [PATCH 042/109] fix typo --- doc/src/fix_wall.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index 7b38b6035c..2ca215bf71 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -371,7 +371,7 @@ is *no*, which means the system must be non-periodic when using a wall. But you may wish to use a periodic box. E.g. to allow some particles to interact with the wall via the fix group-ID, and others to pass through it and wrap around a periodic box. In this case you should ensure that -the wall if sufficiently far enough away from the box boundary. If you +the wall is sufficiently far enough away from the box boundary. If you do not, then particles may interact with both the wall and with periodic images on the other side of the box, which is probably not what you want. From 04d30329145047c0df69573a1ecd9ba35ef09cdb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Mar 2023 20:41:13 -0500 Subject: [PATCH 043/109] improve error messages --- src/read_data.cpp | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/src/read_data.cpp b/src/read_data.cpp index 59db1b6937..6785e51ecc 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -1985,7 +1985,8 @@ void ReadData::paircoeffs() next = strchr(buf, '\n'); *next = '\0'; parse_coeffs(buf, nullptr, 1, 2, toffset, tlabelflag, lmap->lmap2lmap.atom); - if (ncoeffarg == 0) error->all(FLERR, "Unexpected empty line in PairCoeffs section"); + if (ncoeffarg == 0) + error->all(FLERR, "Unexpected empty line in PairCoeffs section. Expected {} lines.", ntypes); force->pair->coeff(ncoeffarg, coeffarg); buf = next + 1; } @@ -2016,7 +2017,9 @@ void ReadData::pairIJcoeffs() next = strchr(buf, '\n'); *next = '\0'; parse_coeffs(buf, nullptr, 0, 2, toffset, tlabelflag, lmap->lmap2lmap.atom); - if (ncoeffarg == 0) error->all(FLERR, "Unexpected empty line in PairCoeffs section"); + if (ncoeffarg == 0) + error->all(FLERR, "Unexpected empty line in PairIJCoeffs section. " + "Expected {} lines.", (ntypes-1)*ntypes); force->pair->coeff(ncoeffarg, coeffarg); buf = next + 1; } @@ -2045,7 +2048,8 @@ void ReadData::bondcoeffs() next = strchr(buf, '\n'); *next = '\0'; parse_coeffs(buf, nullptr, 0, 1, boffset, blabelflag, lmap->lmap2lmap.bond); - if (ncoeffarg == 0) error->all(FLERR, "Unexpected empty line in BondCoeffs section"); + if (ncoeffarg == 0) + error->all(FLERR, "Unexpected empty line in BondCoeffs section. Expected {} lines.", nbondtypes); force->bond->coeff(ncoeffarg, coeffarg); buf = next + 1; } From c5c787ca5c04075507de7c0c8bc9d99baea9b00f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Mar 2023 20:41:36 -0500 Subject: [PATCH 044/109] better align with docs bundled with the MSCG library --- doc/src/fix_mscg.rst | 66 ++++++++++++++++++++++---------------------- 1 file changed, 33 insertions(+), 33 deletions(-) diff --git a/doc/src/fix_mscg.rst b/doc/src/fix_mscg.rst index 5e9bc520b5..3255f3fbe9 100644 --- a/doc/src/fix_mscg.rst +++ b/doc/src/fix_mscg.rst @@ -40,15 +40,15 @@ Description This fix applies the Multi-Scale Coarse-Graining (MSCG) method to snapshots from a dump file to generate potentials for coarse-grained -simulations from all-atom simulations, using a force-matching -technique (:ref:`Izvekov `, :ref:`Noid `). +simulations from all-atom simulations, using a force-matching technique +(:ref:`Izvekov `, :ref:`Noid `). -It makes use of the MS-CG library, written and maintained by Greg -Voth's group at the University of Chicago, which is freely available -on their `MS-CG GitHub site `_. See instructions -on obtaining and installing the MS-CG library in the src/MSCG/README -file, which must be done before you build LAMMPS with this fix command -and use the command in a LAMMPS input script. +It makes use of the MS-CG library, written and maintained by Greg Voth's +group at the University of Chicago, which is freely available on their +`MS-CG GitHub site `_. +See instructions on obtaining and installing the MS-CG library in the +src/MSCG/README file, which must be done before you build LAMMPS with +this fix command and use the command in a LAMMPS input script. An example script using this fix is provided the examples/mscg directory. @@ -65,15 +65,18 @@ simulations is as follows: 6. Check the results of the force matching. 7. Run coarse-grained simulations using the new coarse-grained potentials. -This fix can perform the range finding and force matching steps 4 and -5 of the above workflow when used in conjunction with the -:doc:`rerun ` command. It does not perform steps 1-3 and 6-7. +This fix can perform the range finding and force matching steps 4 and 5 +of the above workflow when used in conjunction with the :doc:`rerun +` command. It does not perform steps 1-3 and 6-7. -Step 2 can be performed using a Python script (what is the name?) -provided with the MS-CG library which defines the coarse-grained model -and converts a standard LAMMPS dump file for an all-atom simulation -(step 1) into a LAMMPS dump file which has the positions of and forces -on the coarse-grained beads. +Step 2 can be performed using a Python script (cgmap), which defines the +coarse-grained model and converts a standard LAMMPS dump file for an +all-atom simulation (step 1) into a LAMMPS dump file which has the +positions of and forces on the coarse-grained beads. To use cgmap the +following repositories need to be downloaded and installed. + +#. The custom lammpsdata branch of mdtraj from https://github.com/hockyg/mdtraj/tree/lammpsdata +#. The master branch of cgmap from https://github.com/uchicago-voth/cgmap In step 3, an input file named "control.in" is needed by the MS-CG library which sets parameters for the range finding and force matching @@ -83,12 +86,12 @@ info on this file. When this fix is used to perform steps 4 and 5, the MS-CG library also produces additional output files. The range finder functionality -(step 4) outputs files defining pair and bonded interaction ranges. -The force matching functionality (step 5) outputs tabulated force -files for every interaction in the system. Other diagnostic files can -also be output depending on the parameters in the MS-CG library input -script. Again, see the documentation provided with the MS-CG library -for more info. +(step 4) outputs files defining pair and bonded interaction ranges. The +force matching functionality (step 5) outputs tabulated force files for +every interaction in the system. Other diagnostic files can also be +output depending on the parameters in the MS-CG library input script. +Again, see the documentation provided with the MS-CG library for more +info. ---------- @@ -97,8 +100,8 @@ be invoked. If *on*, the step 4 range finder functionality is invoked. *off*, the step 5 force matching functionality is invoked. If the *name* keyword is used, string names are defined to associate -with the integer atom types in LAMMPS. *Ntype* names must be -provided, one for each atom type (1-Ntype). +with the integer atom types in LAMMPS. *Ntype* names must be provided, +one for each atom type (1-Ntype). The *max* keyword specifies the maximum number of bonds, angles, and dihedrals a bead can have in the coarse-grained model. @@ -107,16 +110,13 @@ Restrictions """""""""""" This fix is part of the MSCG package. It is only enabled if LAMMPS was -built with that package. See the :doc:`Build package ` -doc page for more info. +built with that package. Building the MSCG package also requires +external libraries. See the :doc:`Build_package` and :doc:`Build_extras` +pages for more info. -The MS-CG library uses C++11, which may not be supported by older -compilers. The MS-CG library also has some additional numeric library -dependencies, which are described in its documentation. - -Currently, the MS-CG library is not setup to run in parallel with MPI, -so this fix can only be used in a serial LAMMPS build and run -on a single processor. +Currently, the MS-CG library is not set up to run in parallel with MPI, +so this fix can only be used in a serial LAMMPS build and run on a +single processor. Related commands """""""""""""""" From 8a1771aa61011195e14f8e1c6b640b1159cc6310 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Mar 2023 20:52:15 -0500 Subject: [PATCH 045/109] implement documented pair style requirements for DPD-MESO intgreation fixes --- doc/src/fix_mvv_dpd.rst | 30 +++++++++++++++++------------- doc/src/pair_mesodpd.rst | 2 +- src/DPD-MESO/fix_mvv_dpd.cpp | 9 +++++++-- src/DPD-MESO/fix_mvv_edpd.cpp | 9 +++++++-- src/DPD-MESO/fix_mvv_tdpd.cpp | 8 ++++++-- 5 files changed, 38 insertions(+), 20 deletions(-) diff --git a/doc/src/fix_mvv_dpd.rst b/doc/src/fix_mvv_dpd.rst index efabab2183..c2f8a50391 100644 --- a/doc/src/fix_mvv_dpd.rst +++ b/doc/src/fix_mvv_dpd.rst @@ -65,33 +65,37 @@ a default value of 0.5 is used, which effectively reproduces the standard velocity-Verlet (VV) scheme. For more details, see :ref:`Groot `. -Fix *mvv/dpd* updates the position and velocity of each atom. It can -be used with the :doc:`pair_style mdpd ` command or other +Fix *mvv/dpd* updates the position and velocity of each atom. It can be +used with the :doc:`pair_style mdpd ` command or other pair styles such as :doc:`pair dpd `. -Fix *mvv/edpd* updates the per-atom temperature, in addition to -position and velocity, and must be used with the :doc:`pair_style edpd ` command. +Fix *mvv/edpd* updates the per-atom temperature, in addition to position +and velocity, and must be used with the :doc:`pair_style edpd +` command. -Fix *mvv/tdpd* updates the per-atom chemical concentration, in -addition to position and velocity, and must be used with the -:doc:`pair_style tdpd ` command. +Fix *mvv/tdpd* updates the per-atom chemical concentration, in addition +to position and velocity, and must be used with the :doc:`pair_style +tdpd ` command. ---------- Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about this fix is written to :doc:`binary restart files `. None of the :doc:`fix_modify ` options -are relevant to this fix. No global or per-atom quantities are stored -by this fix for access by various :doc:`output commands `. +No information about this fix is written to :doc:`binary restart files +`. None of the :doc:`fix_modify ` options are +relevant to this fix. No global or per-atom quantities are stored by +this fix for access by various :doc:`output commands `. No parameter of this fix can be used with the *start/stop* keywords of -the :doc:`run ` command. This fix is not invoked during :doc:`energy minimization `. +the :doc:`run ` command. This fix is not invoked during +:doc:`energy minimization `. Restrictions """""""""""" -This fix is part of the DPD-MESO package. It is only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` page for more info. +These fixes are part of the DPD-MESO package. They are only enabled if +LAMMPS was built with that package. See the :doc:`Build package +` page for more info. Related commands """""""""""""""" diff --git a/doc/src/pair_mesodpd.rst b/doc/src/pair_mesodpd.rst index e5cd2643dd..5d244f3b1d 100644 --- a/doc/src/pair_mesodpd.rst +++ b/doc/src/pair_mesodpd.rst @@ -299,7 +299,7 @@ Restrictions """""""""""" The pair styles *edpd*, *mdpd*, *mdpd/rhosum* and *tdpd* are part of -the DPD-MESO package. It is only enabled if LAMMPS was built with +the DPD-MESO package. They are only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. diff --git a/src/DPD-MESO/fix_mvv_dpd.cpp b/src/DPD-MESO/fix_mvv_dpd.cpp index c475fa6651..18c88bd293 100644 --- a/src/DPD-MESO/fix_mvv_dpd.cpp +++ b/src/DPD-MESO/fix_mvv_dpd.cpp @@ -22,11 +22,13 @@ ------------------------------------------------------------------------- */ #include "fix_mvv_dpd.h" -#include + #include "atom.h" +#include "error.h" #include "force.h" #include "update.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -65,6 +67,9 @@ void FixMvvDPD::init() dtv = update->dt; dtf = 0.5 * update->dt * force->ftm2v; + + if (!force->pair_match("^edpd",0) && !force->pair_match("^dpd",0)) + error->all(FLERR, "Must use a dpd or edpd pair style with fix mvv/edpd"); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-MESO/fix_mvv_edpd.cpp b/src/DPD-MESO/fix_mvv_edpd.cpp index ac8ee858e3..03dd048119 100644 --- a/src/DPD-MESO/fix_mvv_edpd.cpp +++ b/src/DPD-MESO/fix_mvv_edpd.cpp @@ -31,11 +31,13 @@ ------------------------------------------------------------------------- */ #include "fix_mvv_edpd.h" -#include + #include "atom.h" +#include "error.h" #include "force.h" #include "update.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -71,6 +73,9 @@ void FixMvvEDPD::init() { dtv = update->dt; dtf = 0.5 * update->dt * force->ftm2v; + + if (!force->pair_match("^edpd",0)) + error->all(FLERR, "Must use pair style edpd with fix mvv/edpd"); } /* ---------------------------------------------------------------------- diff --git a/src/DPD-MESO/fix_mvv_tdpd.cpp b/src/DPD-MESO/fix_mvv_tdpd.cpp index d579dc778a..f3894da214 100644 --- a/src/DPD-MESO/fix_mvv_tdpd.cpp +++ b/src/DPD-MESO/fix_mvv_tdpd.cpp @@ -27,11 +27,13 @@ ------------------------------------------------------------------------- */ #include "fix_mvv_tdpd.h" -#include + #include "atom.h" +#include "error.h" #include "force.h" #include "update.h" -#include "error.h" + +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -69,6 +71,8 @@ void FixMvvTDPD::init() { dtv = update->dt; dtf = 0.5 * update->dt * force->ftm2v; + if (!force->pair_match("^tdpd",0)) + error->all(FLERR, "Must use pair style tdpd with fix mvv/tdpd"); } /* ---------------------------------------------------------------------- From e4e994f1b1bf9d57912dd26833eeed2280574635 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Mar 2023 20:59:48 -0500 Subject: [PATCH 046/109] add missing versionadded tags --- doc/src/fix_wall.rst | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/doc/src/fix_wall.rst b/doc/src/fix_wall.rst index 2ca215bf71..cdf3c16cef 100644 --- a/doc/src/fix_wall.rst +++ b/doc/src/fix_wall.rst @@ -194,6 +194,8 @@ For style *wall/morse*, the energy E is given by a Morse potential: E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c +.. versionadded:: TBD + For style *wall/lepton*, the energy E is provided as an Lepton expression string using "r" as the distance variable. The `Lepton library `_, that the *wall/lepton* @@ -213,6 +215,8 @@ spring as in fix *wall/harmonic* with a force constant *K* (same as :math:`\epsilon` above) of 100 energy units. More details on the Lepton expression strings are given below. +.. versionadded:: TBD + For style *wall/table*, the energy E and forces are determined from interpolation tables listed in one or more files as a function of distance. The interpolation tables are used to evaluate energy and From 63a391a649511a28aad1d3b3041a6dc3fe06403a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 1 Mar 2023 21:05:22 -0500 Subject: [PATCH 047/109] replace leftover -DCUDA_PROXY --- doc/src/Build_extras.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index c4f9bf6aff..ac6a27464b 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -274,7 +274,7 @@ To enable GPU binning via CUDA performance primitives set the Makefile variable most modern GPUs. To support the CUDA multiprocessor server you can set the define -``-DCUDA_PROXY``. Please note that in this case you must **not** use +``-DCUDA_MPS_SUPPORT``. Please note that in this case you must **not** use the CUDA performance primitives and thus set the variable ``CUDPP_OPT`` to empty. From de466cf998d20c8689d4c6773c4011b6379f4c3d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 2 Mar 2023 07:31:33 -0500 Subject: [PATCH 048/109] improve documentation of the use of verlet/split run style. reformat. --- doc/src/run_style.rst | 154 +++++++++++++++++++++++------------------- 1 file changed, 86 insertions(+), 68 deletions(-) diff --git a/doc/src/run_style.rst b/doc/src/run_style.rst index 423ab762b3..0804ce5c82 100644 --- a/doc/src/run_style.rst +++ b/doc/src/run_style.rst @@ -78,27 +78,41 @@ processors. See the :doc:`-partition command-line switch ` for info on how to run LAMMPS with multiple partitions. Specifically, this style performs all computation except the -:doc:`kspace_style ` portion of the force field on the first -partition. This include the :doc:`pair style `, :doc:`bond style `, :doc:`neighbor list building `, -:doc:`fixes ` including time integration, and output. The -:doc:`kspace_style ` portion of the calculation is +:doc:`kspace_style ` portion of the force field on the +first partition. This include the :doc:`pair style `, +:doc:`bond style `, :doc:`neighbor list building +`, :doc:`fixes ` including time integration, and output. +The :doc:`kspace_style ` portion of the calculation is performed on the second partition. -This is most useful for the PPPM kspace_style when its performance on -a large number of processors degrades due to the cost of communication -in its 3d FFTs. In this scenario, splitting your P total processors -into 2 subsets of processors, P1 in the first partition and P2 in the -second partition, can enable your simulation to run faster. This is -because the long-range forces in PPPM can be calculated at the same -time as pairwise and bonded forces are being calculated, and the FFTs -can actually speed up when running on fewer processors. +This can lead to a significant speedup, if the number of processors can +be easily increased and the fraction of time is spent in computing +Kspace interactions is significant, too. The two partitions may have a +different number of processors. This is most useful for the PPPM +kspace_style when its performance on a large number of processors +degrades due to the cost of communication in its 3d FFTs. In this +scenario, splitting your P total processors into 2 subsets of +processors, P1 in the first partition and P2 in the second partition, +can enable your simulation to run faster. This is because the +long-range forces in PPPM can be calculated at the same time as pairwise +and bonded forces are being calculated *and* the parallel 3d FFTs can be +faster to compute when running on fewer processors. Please note that +the scenario of using fewer MPI processes to reduce communication +overhead can also be implemented through using MPI with OpenMP threads +via the INTEL, KOKKOS, or OPENMP package. This alternative option is +typically more effective in case of a fixed number of available +processors and less complex to execute. -To use this style, you must define 2 partitions where P1 is a multiple -of P2. Typically having P1 be 3x larger than P2 is a good choice. -The 3d processor layouts in each partition must overlay in the -following sense. If P1 is a Px1 by Py1 by Pz1 grid, and P2 = Px2 by -Py2 by Pz2, then Px1 must be an integer multiple of Px2, and similarly -for Py1 a multiple of Py2, and Pz1 a multiple of Pz2. +To use the *verlet/split* style, you must define 2 partitions with the +:doc:`-partition command-line switch `, where partition P1 +is either the same size or an integer multiple of the size of the +partition P2. Typically having P1 be 3x larger than P2 is a good +choice, since the (serial) performance of LAMMPS is often best if the +time spent in the ``Pair`` computation versus ``Kspace`` is a 3:1 split. +The 3d processor layouts in each partition must overlay in the following +sense. If P1 is a Px1 by Py1 by Pz1 grid, and P2 = Px2 by Py2 by Pz2, +then Px1 must be an integer multiple of Px2, and similarly for Py1 a +multiple of Py2, and Pz1 a multiple of Pz2. Typically the best way to do this is to let the first partition choose its own optimal layout, then require the second partition's layout to @@ -122,9 +136,10 @@ of 60 and 15 processors each: When you run in 2-partition mode with the *verlet/split* style, the thermodynamic data for the entire simulation will be output to the log and screen file of the first partition, which are log.lammps.0 and -screen.0 by default; see the :doc:`-plog and -pscreen command-line switches ` to change this. The log and screen file -for the second partition will not contain thermodynamic output beyond the -first timestep of the run. +screen.0 by default; see the :doc:`-plog and -pscreen command-line +switches ` to change this. The log and screen file for the +second partition will not contain thermodynamic output beyond the first +timestep of the run. See the :doc:`Accelerator packages ` page for performance details of the speed-up offered by the *verlet/split* @@ -137,70 +152,73 @@ options to support this, and strategies are discussed in :doc:`Section ---------- The *respa* style implements the rRESPA multi-timescale integrator -:ref:`(Tuckerman) ` with N hierarchical levels, where level 1 is -the innermost loop (shortest timestep) and level N is the outermost +:ref:`(Tuckerman) ` with N hierarchical levels, where level +1 is the innermost loop (shortest timestep) and level N is the outermost loop (largest timestep). The loop factor arguments specify what the -looping factor is between levels. N1 specifies the number of -iterations of level 1 for a single iteration of level 2, N2 is the -iterations of level 2 per iteration of level 3, etc. N-1 looping -parameters must be specified. +looping factor is between levels. N1 specifies the number of iterations +of level 1 for a single iteration of level 2, N2 is the iterations of +level 2 per iteration of level 3, etc. N-1 looping parameters must be +specified. -Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors, -you could choose to have bond interactions computed 8x per large -timestep, angle interactions computed 4x, pair interactions computed -2x, and long-range interactions once per large timestep. +Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors, you +could choose to have bond interactions computed 8x per large timestep, +angle interactions computed 4x, pair interactions computed 2x, and +long-range interactions once per large timestep. The :doc:`timestep ` command sets the large timestep for the outermost rRESPA level. Thus if the 3 loop factors are "2 2 2" for -4-level rRESPA, and the outer timestep is set to 4.0 fs, then the -inner timestep would be 8x smaller or 0.5 fs. All other LAMMPS -commands that specify number of timesteps (e.g. :doc:`thermo ` -for thermo output every N steps, :doc:`neigh_modify delay/every ` parameters, :doc:`dump ` every N -steps, etc) refer to the outermost timesteps. +4-level rRESPA, and the outer timestep is set to 4.0 fs, then the inner +timestep would be 8x smaller or 0.5 fs. All other LAMMPS commands that +specify number of timesteps (e.g. :doc:`thermo ` for thermo +output every N steps, :doc:`neigh_modify delay/every ` +parameters, :doc:`dump ` every N steps, etc) refer to the +outermost timesteps. -The rRESPA keywords enable you to specify at what level of the -hierarchy various forces will be computed. If not specified, the -defaults are that bond forces are computed at level 1 (innermost -loop), angle forces are computed where bond forces are, dihedral -forces are computed where angle forces are, improper forces are -computed where dihedral forces are, pair forces are computed at the -outermost level, and kspace forces are computed where pair forces are. -The inner, middle, outer forces have no defaults. +The rRESPA keywords enable you to specify at what level of the hierarchy +various forces will be computed. If not specified, the defaults are +that bond forces are computed at level 1 (innermost loop), angle forces +are computed where bond forces are, dihedral forces are computed where +angle forces are, improper forces are computed where dihedral forces +are, pair forces are computed at the outermost level, and kspace forces +are computed where pair forces are. The inner, middle, outer forces +have no defaults. For fixes that support it, the rRESPA level at which a given fix is -active, can be selected through the :doc:`fix_modify ` command. +active, can be selected through the :doc:`fix_modify ` +command. -The *inner* and *middle* keywords take additional arguments for -cutoffs that are used by the pairwise force computations. If the 2 -cutoffs for *inner* are 5.0 and 6.0, this means that all pairs up to -6.0 apart are computed by the inner force. Those between 5.0 and 6.0 -have their force go ramped to 0.0 so the overlap with the next regime -(middle or outer) is smooth. The next regime (middle or outer) will -compute forces for all pairs from 5.0 outward, with those from 5.0 to -6.0 having their value ramped in an inverse manner. +The *inner* and *middle* keywords take additional arguments for cutoffs +that are used by the pairwise force computations. If the 2 cutoffs for +*inner* are 5.0 and 6.0, this means that all pairs up to 6.0 apart are +computed by the inner force. Those between 5.0 and 6.0 have their force +go ramped to 0.0 so the overlap with the next regime (middle or outer) +is smooth. The next regime (middle or outer) will compute forces for +all pairs from 5.0 outward, with those from 5.0 to 6.0 having their +value ramped in an inverse manner. Note that you can use *inner* and *outer* without using *middle* to split the pairwise computations into two portions instead of three. -Unless you are using a very long pairwise cutoff, a 2-way split is -often faster than a 3-way split, since it avoids too much duplicate +Unless you are using a very long pairwise cutoff, a 2-way split is often +faster than a 3-way split, since it avoids too much duplicate computation of pairwise interactions near the intermediate cutoffs. -Also note that only a few pair potentials support the use of the -*inner* and *middle* and *outer* keywords. If not, only the *pair* -keyword can be used with that pair style, meaning all pairwise forces -are computed at the same rRESPA level. See the doc pages for -individual pair styles for details. +Also note that only a few pair potentials support the use of the *inner* +and *middle* and *outer* keywords. If not, only the *pair* keyword can +be used with that pair style, meaning all pairwise forces are computed +at the same rRESPA level. See the doc pages for individual pair styles +for details. Another option for using pair potentials with rRESPA is with the -*hybrid* keyword, which requires the use of the :doc:`pair_style hybrid or hybrid/overlay ` command. In this scenario, different +*hybrid* keyword, which requires the use of the :doc:`pair_style hybrid +or hybrid/overlay ` command. In this scenario, different sub-styles of the hybrid pair style are evaluated at different rRESPA -levels. This can be useful, for example, to set different timesteps -for hybrid coarse-grained/all-atom models. The *hybrid* keyword -requires as many level assignments as there are hybrid sub-styles, -which assigns each sub-style to a rRESPA level, following their order -of definition in the pair_style command. Since the *hybrid* keyword -operates on pair style computations, it is mutually exclusive with -either the *pair* or the *inner*\ /\ *middle*\ /\ *outer* keywords. +levels. This can be useful, for example, to set different timesteps for +hybrid coarse-grained/all-atom models. The *hybrid* keyword requires as +many level assignments as there are hybrid sub-styles, which assigns +each sub-style to a rRESPA level, following their order of definition in +the pair_style command. Since the *hybrid* keyword operates on pair +style computations, it is mutually exclusive with either the *pair* or +the *inner*\ /\ *middle*\ /\ *outer* keywords. When using rRESPA (or for any MD simulation) care must be taken to choose a timestep size(s) that ensures the Hamiltonian for the chosen From da79aadc8d9f3f16facd2a31e7ab9d4498f739b6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 2 Mar 2023 07:31:38 -0500 Subject: [PATCH 049/109] spelling --- doc/utils/sphinx-config/false_positives.txt | 3 +++ 1 file changed, 3 insertions(+) diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 0a5e58e86b..e46b5dd28b 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -438,6 +438,7 @@ cfile CFL cgdna CGDNA +cgmap cgs cgsdk CGSDK @@ -1792,6 +1793,7 @@ lammps Lammps LAMMPS lammpsbin +lammpsdata lammpsplot lammpsplugin Lamoureux @@ -2072,6 +2074,7 @@ mdi MDI mdpd mDPD +mdtraj meam MEAM meamf From 4a8aaf9f46dd31bd54b468fdb445cb0b9d38ceed Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Thu, 2 Mar 2023 14:52:01 -0600 Subject: [PATCH 050/109] Added the missing factor 4\pi in epsilon0e2q to other units --- src/DIELECTRIC/fix_polarize_bem_gmres.cpp | 8 ++++---- src/DIELECTRIC/fix_polarize_bem_icc.cpp | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/src/DIELECTRIC/fix_polarize_bem_gmres.cpp b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp index e31337d0fd..14a645bb30 100644 --- a/src/DIELECTRIC/fix_polarize_bem_gmres.cpp +++ b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp @@ -311,13 +311,13 @@ void FixPolarizeBEMGMRES::setup(int /*vflag*/) epsilon0e2q = 1.0; if (strcmp(update->unit_style, "real") == 0) - epsilon0e2q = 0.000240263377163643; + epsilon0e2q = 0.000240263377163643 * (4 * MY_PI); else if (strcmp(update->unit_style, "metal") == 0) - epsilon0e2q = 0.00553386738300813; + epsilon0e2q = 0.00553386738300813 * (4 * MY_PI); else if (strcmp(update->unit_style, "si") == 0) - epsilon0e2q = 8.854187812813e-12; + epsilon0e2q = 8.854187812813e-12 * (4 * MY_PI); else if (strcmp(update->unit_style, "nano") == 0) - epsilon0e2q = 0.000345866711328125; + epsilon0e2q = 0.000345866711328125 * (4 * MY_PI); else if (strcmp(update->unit_style, "lj") != 0) error->all(FLERR, "Only unit styles 'lj', 'real', 'metal', 'si' and 'nano' are supported"); diff --git a/src/DIELECTRIC/fix_polarize_bem_icc.cpp b/src/DIELECTRIC/fix_polarize_bem_icc.cpp index 0d503d87a7..177332546a 100644 --- a/src/DIELECTRIC/fix_polarize_bem_icc.cpp +++ b/src/DIELECTRIC/fix_polarize_bem_icc.cpp @@ -214,13 +214,13 @@ void FixPolarizeBEMICC::setup(int /*vflag*/) epsilon0e2q = 1.0; if (strcmp(update->unit_style, "real") == 0) - epsilon0e2q = 0.000240263377163643; + epsilon0e2q = 0.000240263377163643 * (4 * MY_PI); else if (strcmp(update->unit_style, "metal") == 0) - epsilon0e2q = 0.00553386738300813; + epsilon0e2q = 0.00553386738300813 * (4 * MY_PI); else if (strcmp(update->unit_style, "si") == 0) - epsilon0e2q = 8.854187812813e-12; + epsilon0e2q = 8.854187812813e-12 * (4 * MY_PI); else if (strcmp(update->unit_style, "nano") == 0) - epsilon0e2q = 0.000345866711328125; + epsilon0e2q = 0.000345866711328125 * (4 * MY_PI); else if (strcmp(update->unit_style, "lj") != 0) error->all(FLERR, "Only unit styles 'lj', 'real', 'metal', 'si' and 'nano' are supported"); From b08fe855a1820ff4bf7de78076169c0df890ccff Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Thu, 2 Mar 2023 15:12:59 -0600 Subject: [PATCH 051/109] Increased the default max iterations to 50, put a note on setting the local epsilon for charged interface particles to be the mean dielectric value --- doc/src/fix_polarize.rst | 9 +++++---- examples/PACKAGES/dielectric/in.confined | 4 ++-- src/DIELECTRIC/fix_polarize_bem_gmres.cpp | 2 +- src/DIELECTRIC/fix_polarize_bem_icc.cpp | 2 +- 4 files changed, 9 insertions(+), 8 deletions(-) diff --git a/doc/src/fix_polarize.rst b/doc/src/fix_polarize.rst index 6a997aa7ea..1101fb65ae 100644 --- a/doc/src/fix_polarize.rst +++ b/doc/src/fix_polarize.rst @@ -31,7 +31,7 @@ Examples fix 2 interface polarize/bem/gmres 5 0.0001 fix 1 interface polarize/bem/icc 1 0.0001 - fix 3 interface polarize/functional 1 0.001 + fix 3 interface polarize/functional 1 0.0001 Used in input scripts: @@ -69,8 +69,9 @@ along the normal vector is then 78 - 4 = 74, the mean dielectric value is (78 + 4) / 2 = 41. Each boundary element also has its area and the local mean curvature, which is used by these fixes for computing a correction term in the local electric field. To model charged -interfaces, the interface particle will have a non-zero charge value, -coming from its area and surface charge density. +interfaces, an interface particle will have a non-zero charge value, +coming from its area and surface charge density, and its local dielectric +constant set to the mean dielectric value. For non-interface particles such as atoms and charged particles, the interface normal vectors, element area, and dielectric mismatch are @@ -223,7 +224,7 @@ Related commands Default """"""" -*iter_max* = 20 +*iter_max* = 50 *kspace* = yes diff --git a/examples/PACKAGES/dielectric/in.confined b/examples/PACKAGES/dielectric/in.confined index 0f9dab7bba..314409fc17 100644 --- a/examples/PACKAGES/dielectric/in.confined +++ b/examples/PACKAGES/dielectric/in.confined @@ -67,10 +67,10 @@ if "${method} == gmres" then & "fix 3 interface polarize/bem/gmres 1 1.0e-4" & "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" & elif "${method} == icc"& - "fix 3 interface polarize/bem/icc 1 1.0e-4 itr_max 50" & + "fix 3 interface polarize/bem/icc 1 1.0e-4" & "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" & elif "${method} == dof" & - "fix 3 interface polarize/functional 1 0.001" & + "fix 3 interface polarize/functional 1 0.0001" & "fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" & else & "print 'Unsupported polarization solver' " diff --git a/src/DIELECTRIC/fix_polarize_bem_gmres.cpp b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp index 14a645bb30..dafe4dc8e0 100644 --- a/src/DIELECTRIC/fix_polarize_bem_gmres.cpp +++ b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp @@ -81,7 +81,7 @@ FixPolarizeBEMGMRES::FixPolarizeBEMGMRES(LAMMPS *_lmp, int narg, char **arg) : double tol = utils::numeric(FLERR, arg[4], false, lmp); tol_abs = tol_rel = tol; - itr_max = 20; + itr_max = 50; mr = 0; randomized = 0; ave_charge = 0; diff --git a/src/DIELECTRIC/fix_polarize_bem_icc.cpp b/src/DIELECTRIC/fix_polarize_bem_icc.cpp index 177332546a..034ada48ab 100644 --- a/src/DIELECTRIC/fix_polarize_bem_icc.cpp +++ b/src/DIELECTRIC/fix_polarize_bem_icc.cpp @@ -67,7 +67,7 @@ FixPolarizeBEMICC::FixPolarizeBEMICC(LAMMPS *_lmp, int narg, char **arg) : Fix(_ double tol = utils::numeric(FLERR, arg[4], false, lmp); tol_abs = tol_rel = tol; - itr_max = 20; + itr_max = 50; omega = 0.7; randomized = 0; ave_charge = 0; From c4f095f9df18cd784f40319463e438b495a5dca3 Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Thu, 2 Mar 2023 15:17:32 -0600 Subject: [PATCH 052/109] Updated the doc page of fix polarize to note that polarize/functional not supporting charged interfaces yet --- doc/src/fix_polarize.rst | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/src/fix_polarize.rst b/doc/src/fix_polarize.rst index 1101fb65ae..dd8a0c7d75 100644 --- a/doc/src/fix_polarize.rst +++ b/doc/src/fix_polarize.rst @@ -212,6 +212,8 @@ Note that the *polarize/bem/gmres* and *polarize/bem/icc* fixes only support :doc:`units ` *lj*, *real*, *metal*, *si* and *nano* at the moment. +Note that *polarize/functional* does not yet support charged interfaces. + Related commands """""""""""""""" From fa38047749bcb349e0a97a97efea8ec10f9013f1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 2 Mar 2023 18:29:05 -0500 Subject: [PATCH 053/109] use sin(x+pi/2) instead of cos(x) on Intel OpenCL with double precision --- lib/gpu/lal_soft.cu | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/lib/gpu/lal_soft.cu b/lib/gpu/lal_soft.cu index 74ac0e0c97..bc96a861df 100644 --- a/lib/gpu/lal_soft.cu +++ b/lib/gpu/lal_soft.cu @@ -22,6 +22,15 @@ _texture_2d( pos_tex,int4); #endif #else #define pos_tex x_ +// hack for Intel GPU with double precision +#if defined(_DOUBLE_DOUBLE) && (CONFIG_ID == 500) +#define MY_PI_HALF (acctyp)1.57079632679489661923 +#define my_cos(x) sin(x+MY_PI_HALF) +#endif +#endif + +#if !defined(my_cos) +#define my_cos(x) cos(x) #endif #define MY_PI (acctyp)3.14159265358979323846 @@ -95,7 +104,7 @@ __kernel void k_soft(const __global numtyp4 *restrict x_, f.z+=delz*force; if (EVFLAG && eflag) { - numtyp e=coeff[mtype].x * ((numtyp)1.0+cos(arg)); + numtyp e=coeff[mtype].x * ((numtyp)1.0+my_cos(arg)); energy+=factor_lj*e; } if (EVFLAG && vflag) { @@ -186,7 +195,7 @@ __kernel void k_soft_fast(const __global numtyp4 *restrict x_, f.z+=delz*force; if (EVFLAG && eflag) { - numtyp e=coeff[mtype].x * ((numtyp)1.0+cos(arg)); + numtyp e=coeff[mtype].x * ((numtyp)1.0+my_cos(arg)); energy+=factor_lj*e; } if (EVFLAG && vflag) { From cfb967d309165587af11f3847f82313ff566f975 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 3 Mar 2023 02:01:25 -0500 Subject: [PATCH 054/109] silence static code analysis warnings --- src/REPLICA/compute_pressure_alchemy.cpp | 2 +- src/REPLICA/fix_alchemy.cpp | 2 +- src/REPLICA/fix_alchemy.h | 1 - 3 files changed, 2 insertions(+), 3 deletions(-) diff --git a/src/REPLICA/compute_pressure_alchemy.cpp b/src/REPLICA/compute_pressure_alchemy.cpp index d19ea1b893..bad2785fb8 100644 --- a/src/REPLICA/compute_pressure_alchemy.cpp +++ b/src/REPLICA/compute_pressure_alchemy.cpp @@ -24,7 +24,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ ComputePressureAlchemy::ComputePressureAlchemy(LAMMPS *lmp, int narg, char **arg) : - Compute(lmp, narg, arg) + Compute(lmp, narg, arg), fix(nullptr) { if (narg != 4) error->all(FLERR, "Illegal compute pressure/alchemy command"); if (igroup) error->all(FLERR, "Compute pressure/alchemy must use group all"); diff --git a/src/REPLICA/fix_alchemy.cpp b/src/REPLICA/fix_alchemy.cpp index c6617c4600..29801d5c8d 100644 --- a/src/REPLICA/fix_alchemy.cpp +++ b/src/REPLICA/fix_alchemy.cpp @@ -53,8 +53,8 @@ FixAlchemy::FixAlchemy(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), vector_flag = 1; size_vector = 3; extvector = 1; - ilevel_respa = 0; nmax = 6; + ivar = -1; sync_box = 0; // set up rank-to-rank communicator for inter-partition communication diff --git a/src/REPLICA/fix_alchemy.h b/src/REPLICA/fix_alchemy.h index 677a29b643..53c369d551 100644 --- a/src/REPLICA/fix_alchemy.h +++ b/src/REPLICA/fix_alchemy.h @@ -48,7 +48,6 @@ class FixAlchemy : public Fix { double pressure[6]; // joined pressure int progress; // for progress indicator int sync_box; // 1 of box dimensions need to be synchronized - int ilevel_respa; int nmax; int ivar; }; From 9cdb9283cab29f782411f803f5c697f2c22a2c9a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 3 Mar 2023 03:00:35 -0500 Subject: [PATCH 055/109] another workaround for Intel GPU with OpenCL and double precision --- lib/gpu/lal_device.cpp | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/lib/gpu/lal_device.cpp b/lib/gpu/lal_device.cpp index 891d67913e..c98253ba4c 100644 --- a/lib/gpu/lal_device.cpp +++ b/lib/gpu/lal_device.cpp @@ -389,7 +389,12 @@ int DeviceT::set_ocl_params(std::string s_config, const std::string &extra_args) #ifdef CL_VERSION_2_0 _ocl_compile_string+="-cl-std=CL2.0 "; #endif - if (params[4]!="0") _ocl_compile_string+="-cl-fast-relaxed-math "; + // workaround for double precision with Intel OpenCL + #ifdef _DOUBLE_DOUBLE + if ((params[4] != "0") && (params[0] != "500")) _ocl_compile_string+="-cl-fast-relaxed-math "; + #else + if (params[4] != "0") _ocl_compile_string+="-cl-fast-relaxed-math "; + #endif _ocl_compile_string+=std::string(OCL_INT_TYPE)+" "+ std::string(OCL_PRECISION_COMPILE); if (gpu->has_subgroup_support()) From 13f82be0353c66d1ecfed2cba66dfd5a6d6e6201 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 3 Mar 2023 09:12:57 -0500 Subject: [PATCH 056/109] fix typo --- src/fix_store_force.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp index 09406bb4f1..b6e2f4d8a1 100644 --- a/src/fix_store_force.cpp +++ b/src/fix_store_force.cpp @@ -29,7 +29,7 @@ FixStoreForce::FixStoreForce(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), foriginal(nullptr) { - if (narg < 3) error->all(FLERR,"Illegal fix store/coord command"); + if (narg < 3) error->all(FLERR,"Illegal fix store/force command"); peratom_flag = 1; size_peratom_cols = 3; From a136283312d6231ddd515804ec346feb1651986e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 3 Mar 2023 17:17:07 -0500 Subject: [PATCH 057/109] update/correct section header (this is not a fix) --- doc/src/bond_table.rst | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/doc/src/bond_table.rst b/doc/src/bond_table.rst index 51e677d74a..1924774693 100644 --- a/doc/src/bond_table.rst +++ b/doc/src/bond_table.rst @@ -112,8 +112,9 @@ are estimated (less accurately) by the first two and last two force values in the table. The "EQ" parameter is also optional. If used, it is followed by a the -equilibrium bond length, which is used, for example, by the :doc:`fix shake ` command. If not used, the equilibrium bond -length is to the distance in the table with the lowest potential energy. +equilibrium bond length, which is used, for example, by the :doc:`fix +shake ` command. If not used, the equilibrium bond length is +to the distance in the table with the lowest potential energy. Following a blank line, the next N lines list the tabulated values. On each line, the first value is the index from 1 to N, the second value is @@ -135,16 +136,15 @@ one that matches the specified keyword. ---------- -Restart, fix_modify, output, run start/stop, minimize info -""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" +Restart info +"""""""""""" -This bond style writes the settings for the "bond_style table" -command to :doc:`binary restart files `, so a bond_style -command does not need to specified in an input script that reads a -restart file. However, the coefficient information is not stored in -the restart file, since it is tabulated in the potential files. Thus, -bond_coeff commands do need to be specified in the restart input -script. +This bond style writes the settings for the "bond_style table" command +to :doc:`binary restart files `, so a bond_style command does +not need to specified in an input script that reads a restart file. +However, the coefficient information is not stored in the restart file, +since it is tabulated in the potential files. Thus, bond_coeff commands +do need to be specified in the restart input script. Restrictions """""""""""" From de182aeeed33e3ad7cd62d6ebceb6a9ce28c4e20 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 3 Mar 2023 17:25:28 -0500 Subject: [PATCH 058/109] fix issues due to incomplete conversion form txt2html markup --- doc/src/pair_gauss.rst | 13 +++++++------ doc/src/pair_tersoff_mod.rst | 2 +- doc/src/read_data.rst | 10 ++++++---- 3 files changed, 14 insertions(+), 11 deletions(-) diff --git a/doc/src/pair_gauss.rst b/doc/src/pair_gauss.rst index f6d8134467..5ac8f2aff4 100644 --- a/doc/src/pair_gauss.rst +++ b/doc/src/pair_gauss.rst @@ -103,12 +103,13 @@ Mixing, shift, table, tail correction, restart, rRESPA info For atom type pairs I,J and I != J, the A, B, H, sigma_h, r_mh parameters, and the cutoff distance for these pair styles can be mixed: -A (energy units) -sqrt(1/B) (distance units, see below) -H (energy units) -sigma_h (distance units) -r_mh (distance units) -cutoff (distance units):ul + +* A (energy units) +* :math:`\sqrt{\frac{1}{B}}` (distance units, see below) +* H (energy units) +* :math:`r_{mh}` (distance units) +* :math:`\sigma_h` (distance units) +* cutoff (distance units) The default mix value is *geometric*\ . Only *arithmetic* and *geometric* mix values are supported. diff --git a/doc/src/pair_tersoff_mod.rst b/doc/src/pair_tersoff_mod.rst index 8c9605d62c..a667ae6605 100644 --- a/doc/src/pair_tersoff_mod.rst +++ b/doc/src/pair_tersoff_mod.rst @@ -145,7 +145,7 @@ coefficients in the formulae above: * c3 * c4 * c5 -* c0 (energy units, tersoff/mod/c only):ul +* c0 (energy units, tersoff/mod/c only) The n, :math:`\eta`, :math:`\lambda_2`, B, :math:`\lambda_1`, and A parameters are only used for two-body interactions. The :math:`\beta`, :math:`\alpha`, c1, c2, c3, c4, c5, h diff --git a/doc/src/read_data.rst b/doc/src/read_data.rst index 7c08802228..0ecd2b6fa2 100644 --- a/doc/src/read_data.rst +++ b/doc/src/read_data.rst @@ -1477,10 +1477,12 @@ The *Triangles* section must appear after the *Atoms* section. where the keywords have these meanings: -vx,vy,vz = translational velocity of atom -lx,ly,lz = angular momentum of aspherical atom -wx,wy,wz = angular velocity of spherical atom -ervel = electron radial velocity (0 for fixed-core):ul + .. parsed-literal:: + + vx,vy,vz = translational velocity of atom + lx,ly,lz = angular momentum of aspherical atom + wx,wy,wz = angular velocity of spherical atom + ervel = electron radial velocity (0 for fixed-core) The velocity lines can appear in any order. This section can only be used after an *Atoms* section. This is because the *Atoms* section From e373aa39e7f7e225d62cdd7bf570d346ec682989 Mon Sep 17 00:00:00 2001 From: Christoph Junghans Date: Fri, 3 Mar 2023 16:44:34 -0700 Subject: [PATCH 059/109] Update CODEOWNERS --- .github/CODEOWNERS | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index 038f290f64..2686011281 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -150,12 +150,12 @@ tools/vim/* @hammondkd unittest/* @akohlmey # cmake -cmake/* @junghans @rbberger +cmake/* @rbberger cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey cmake/Modules/MPI4WIN.cmake @akohlmey cmake/Modules/OpenCLLoader.cmake @akohlmey -cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin -cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167 +cmake/Modules/Packages/COLVARS.cmake @rbberger @giacomofiorin +cmake/Modules/Packages/KIM.cmake @rbberger @ellio167 cmake/presets/*.cmake @akohlmey # python From 76387d003bc9236fecd244b93234ac5e645c220f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 3 Mar 2023 23:12:17 -0500 Subject: [PATCH 060/109] fine tune package check directory matching to not match bogus entries --- doc/utils/check-packages.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/doc/utils/check-packages.py b/doc/utils/check-packages.py index cb64259f15..8fc17f28df 100644 --- a/doc/utils/check-packages.py +++ b/doc/utils/check-packages.py @@ -49,7 +49,9 @@ pkgs = [] # folder, and is not called 'MAKE' is a package for d in pkgdirs: - pkg = dirs.match(d).group(1) + match = dirs.match(d) + if not match: continue + pkg = match.group(1) if not os.path.isdir(os.path.join(src_dir, pkg)): continue if pkg in ['DEPEND','MAKE','STUBS']: continue pkgs.append(pkg) From 3df51305df8819244df62a42c73a18e58ee5d478 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 4 Mar 2023 00:32:18 -0500 Subject: [PATCH 061/109] integrate updates for fix alchemy documentation from @sjplimp --- doc/src/fix_alchemy.rst | 140 +++++++++++++++++++++++++--------------- 1 file changed, 89 insertions(+), 51 deletions(-) diff --git a/doc/src/fix_alchemy.rst b/doc/src/fix_alchemy.rst index 90c436139e..056cf60369 100644 --- a/doc/src/fix_alchemy.rst +++ b/doc/src/fix_alchemy.rst @@ -12,7 +12,7 @@ Syntax * ID, group-ID are documented in :doc:`fix ` command * alchemy = style name of this fix command -* v_name = variable with name that determines the :math:`\lambda_p` value +* v_name = variable with name that determines the :math:`\lambda_R` value Examples """""""" @@ -26,80 +26,121 @@ Description .. versionadded:: TBD -This fix command enables running an "alchemical transformation" MD -simulation between two topologies (i.e. the same number and positions of -atoms, but differences in atom parameters like type, charge, bonds, -angles and so on). For this a :ref:`multi-partition run ` is -required with exactly two partitions. During the MD run, the fix will -will determine a factor, :math:`\lambda_p`, for each partition *p* that -will be taken from an equal style or equivalent :doc:`variable -`. Typically, this variable would be chose to linearly ramp -*down* from 1.0 to 0.0 for the *first* partition (*p=0*) and linearly -ramp *up* from 0.0 to 1.0 for the *second* partition (*p=1*). The -forces used for the propagation of the atoms will be the sum of the -forces of the two systems combined and scaled with their respective -:math:`\lambda_p` factor. This allows to perform transformations that -are not easily possible with :doc:`pair style hybrid/scaled -`, :doc:`fix adapt ` or :doc:`fix adapt/fep -`. +This fix command enables an "alchemical transformation" to be performed +between two systems, whereby one system slowly transforms into the other +over the course of a molecular dynamics run. This is useful for +measuring thermodynamic differences between two different systems. It +also allows transformations that are not easily possible with the +:doc:`pair style hybrid/scaled `, :doc:`fix adapt +` or :doc:`fix adapt/fep ` commmands. -.. note:: +Example inputs are included in the ``examples/PACKAGES/alchemy`` +directory for (a) transforming a pure copper system into a +copper/aluminum bronze alloy and (b) transforming two water molecules +into a hydronium plus hydroxyl ion. - Since the definition of the variable to provide the :math:`\lambda_p` is - independent in the two partitions, no check is made that the two values - remain between 0.0 and 1.0 and that they add up to 1.0. So care needs to - be taken when defining those variables that this is the case. +The two systems must be defined in :doc:`separate replicas +` and run in separate partitions of processors using the +:doc:`-partition ` command-line switch. Exacty two +partitions must be specified and each partition must use the same number +of processors and the same domain decomposition. -Due to the specifics of the implementation, the initial geometry and -dimensions of the system must be exactly the same and the fix will -synchronize them during the run. It is thus not possible to initialize -the two partitions by reading different data files or creating different -systems from scratch, but rather they have to be started from the same -system and then the desired modifications need to be applied to the -system of the second partition. The commands :doc:`pair style -hybrid/scaled `, :doc:`fix adapt ` or :doc:`fix -adapt/fep ` could be used for simulations where the -requirements for fix alchemy are not given. +Because the forces applied to the atoms are the same mix of the forces +from each partition and the simulation starts with the same atom +positions across both partitions, they will generate the same trajectory +of coordinates for each atom, and the same simulation box size and +shape. The latter two conditions are *enforced* by this fix; it +exchanges coordinates and box information between the replicas. This is +not strictly required, but since MD simulations are an example of a +chaotic system, even the tiniest random difference will eventually grow +exponentially into an unwanted divergence. -The commands below demonstrate how the setup for the second partition -can be done for the example of transforming a pure copper system into a -copper/aluminum bronze. +Otherwise the properties of each atom (type, charge, bond and angle +partners, etc), as well as energy and forces between interacting atoms +(pair, bond, angle styles, etc) can be different in the two systems. -.. code-block:: LAMMPS +This can be initialized in the same input script by using commands which +only apply to one or the other replica. The example scripts use a +world-style :doc:`variable ` command along with +:doc:`if/then/else ` commmands for this purpose. The +:doc:`partition ` command can also be used. variable name world pure alloy +.. code-block:: LAMMPS + create_box 2 box create_atoms 1 box pair_style eam/alloy pair_coeff * * AlCu.eam.alloy Cu Al # replace 5% of copper with aluminum on the second partition only + variable name world pure alloy if "${name} == alloy" then & "set type 1 type/fraction 2 0.05 6745234" - # define ramp variable to combine the two different partitions - if "${name} == pure" then & - "variable ramp equal ramp(1.0,0.0)" & - else & - "variable ramp equal ramp(0.0,1.0)" +Both replicas must define an instance of this fix, but with a different +*v_name* variable. The named variable must be an equal-style or +equivalent :doc:`variable `. The two variables should be +defined so that one ramps *down* from 1.0 to 0.0 for the *first* replica +(*R=0*) and the other ramps *up* from 0.0 to 1.0 for the *second* +replica (*R=1*). A simple way is to do this is lineraly, which can be +done using the ramp() function of the :doc:`variable ` +command. You could also define a variable which returns a value between +0.0 and 1.0 as a non-linear function of the timestep. Here is a linear +example: +.. code-block:: LAMMPS + + partition yes 1 variable ramp equal ramp(1.0,0.0) + partition yes 2 variable ramp equal ramp(0.0,1.0) fix 2 all alchemy v_ramp +.. note:: -The ``examples/PACKAGES/alchemy`` folder contains complete example -inputs for this command. + For an alchemical transformation, the two variables should sum to + exactly 1.0 at any timestep. LAMMPS does *NOT* check that this is + the case. + +If you use the ``ramp()`` function to define the two variables, this fix +can easily be used across successive runs in the same input script by +ensuring each instance of the :doc:`run ` command specifies the +appropriate *start* or *stop* options. + +At each timestep of an MD run, the two instances of this fix evaluate +their respective variables as a :math:`\lambda_R` factor, where *R* = 0 +or 1 for each replica. The forces used by each system for the +propagation of theire atoms is set to the sum of the forces for the two +systems, each scaled by their respective :math:`\lambda_R` factor. Thus +during the MD run, the system will transform incrementally from from the +first system to the second system. + +.. note:: + + As mentioned above, the coordinates of the atoms and box size/shape + must be exactly the same in the two replicas. Thus it is generally + not a good idea to initialize the two replicas by reading different + data files or creating them from scratch. Rather, a single system + should be initialized and desired modifications applied to the system + of the second replica. If your input script somehow induces the two + systems to become different (e.g. by performing :doc:`atom_modify + sort ` differently, or by adding or depositing a + different number of atoms), then LAMMPS will detect the mismatchand + generate an error. This is done by ensuring that each step the + number and ordering of atoms is identical within each pair of + processors in the two replicas. ---------- Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about this fix is written to :doc:`binary restart files `. -None of the :doc:`fix_modify ` options are relevant to this fix. +No information about this fix is written to :doc:`binary restart files +`. None of the :doc:`fix_modify ` options are +relevant to this fix. -This fix stores a global scalar (the current value of :math:`\lambda_p`) +This fix stores a global scalar (the current value of :math:`\lambda_R`) and a global vector of length 3 which contains the potential energy of the first partition, the second partition and the combined value, respectively. The global scalar is unitless and "intensive", the vector @@ -117,12 +158,9 @@ This fix is part of the REPLICA package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. -There may be only one instance of this fix in use at any time. +There may be only one instance of this fix in use at a time within +each replica. -This fix requires to perform a :ref:`multi-partition run ` -with *exactly* two partitions. - -This fix is *not* compatible with :doc:`load balancing `. Related commands """""""""""""""" From 6640e8b647384382937ea4c0bbe78e3dee5cce61 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 4 Mar 2023 00:43:43 -0500 Subject: [PATCH 062/109] address some spelling and grammar issues flagged by languagetool.org --- doc/src/fix_alchemy.rst | 54 ++++++++++----------- doc/utils/sphinx-config/false_positives.txt | 1 + 2 files changed, 27 insertions(+), 28 deletions(-) diff --git a/doc/src/fix_alchemy.rst b/doc/src/fix_alchemy.rst index 056cf60369..37c49fed47 100644 --- a/doc/src/fix_alchemy.rst +++ b/doc/src/fix_alchemy.rst @@ -32,17 +32,17 @@ over the course of a molecular dynamics run. This is useful for measuring thermodynamic differences between two different systems. It also allows transformations that are not easily possible with the :doc:`pair style hybrid/scaled `, :doc:`fix adapt -` or :doc:`fix adapt/fep ` commmands. +` or :doc:`fix adapt/fep ` commands. Example inputs are included in the ``examples/PACKAGES/alchemy`` directory for (a) transforming a pure copper system into a copper/aluminum bronze alloy and (b) transforming two water molecules -into a hydronium plus hydroxyl ion. +in a box of water into a hydronium and a hydroxyl ion. -The two systems must be defined in :doc:`separate replicas +The two systems must be defined as :doc:`separate replica ` and run in separate partitions of processors using the -:doc:`-partition ` command-line switch. Exacty two -partitions must be specified and each partition must use the same number +:doc:`-partition ` command-line switch. Exactly two +partitions must be specified, and each partition must use the same number of processors and the same domain decomposition. Because the forces applied to the atoms are the same mix of the forces @@ -55,18 +55,16 @@ not strictly required, but since MD simulations are an example of a chaotic system, even the tiniest random difference will eventually grow exponentially into an unwanted divergence. -Otherwise the properties of each atom (type, charge, bond and angle -partners, etc), as well as energy and forces between interacting atoms -(pair, bond, angle styles, etc) can be different in the two systems. +Otherwise, the properties of each atom (type, charge, bond and angle +partners, etc.), as well as energy and forces between interacting atoms +(pair, bond, angle styles, etc.) can be different in the two systems. This can be initialized in the same input script by using commands which only apply to one or the other replica. The example scripts use a world-style :doc:`variable ` command along with -:doc:`if/then/else ` commmands for this purpose. The +:doc:`if/then/else ` commands for this purpose. The :doc:`partition ` command can also be used. - variable name world pure alloy - .. code-block:: LAMMPS create_box 2 box @@ -85,7 +83,7 @@ Both replicas must define an instance of this fix, but with a different equivalent :doc:`variable `. The two variables should be defined so that one ramps *down* from 1.0 to 0.0 for the *first* replica (*R=0*) and the other ramps *up* from 0.0 to 1.0 for the *second* -replica (*R=1*). A simple way is to do this is lineraly, which can be +replica (*R=1*). A simple way is to do this is linearly, which can be done using the ramp() function of the :doc:`variable ` command. You could also define a variable which returns a value between 0.0 and 1.0 as a non-linear function of the timestep. Here is a linear @@ -111,25 +109,25 @@ appropriate *start* or *stop* options. At each timestep of an MD run, the two instances of this fix evaluate their respective variables as a :math:`\lambda_R` factor, where *R* = 0 or 1 for each replica. The forces used by each system for the -propagation of theire atoms is set to the sum of the forces for the two -systems, each scaled by their respective :math:`\lambda_R` factor. Thus -during the MD run, the system will transform incrementally from from the +propagation of their atoms is set to the sum of the forces for the two +systems, each scaled by their respective :math:`\lambda_R` factor. Thus, +during the MD run, the system will transform incrementally from the first system to the second system. .. note:: As mentioned above, the coordinates of the atoms and box size/shape - must be exactly the same in the two replicas. Thus it is generally - not a good idea to initialize the two replicas by reading different - data files or creating them from scratch. Rather, a single system - should be initialized and desired modifications applied to the system - of the second replica. If your input script somehow induces the two - systems to become different (e.g. by performing :doc:`atom_modify - sort ` differently, or by adding or depositing a - different number of atoms), then LAMMPS will detect the mismatchand - generate an error. This is done by ensuring that each step the - number and ordering of atoms is identical within each pair of - processors in the two replicas. + must be exactly the same in the two replicas. Therefore, it is + generally not a good idea to initialize the two replicas by reading + different data files or creating them individually from scratch. + Rather, a single system should be initialized and then desired + modifications applied to the system to either replica. If your + input script somehow induces the two systems to become different + (e.g. by performing :doc:`atom_modify sort ` + differently, or by adding or depositing a different number of atoms), + then LAMMPS will detect the mismatch and generate an error. This is + done by ensuring that each step the number and ordering of atoms is + identical within each pair of processors in the two replicas. ---------- @@ -146,8 +144,8 @@ the first partition, the second partition and the combined value, respectively. The global scalar is unitless and "intensive", the vector is in :doc:`energy units ` and "extensive". These values can be used by any command that uses a global value from a fix as input. See -the :doc:`Howto output ` doc page for an overview of -LAMMPS output options. +the :doc:`output howto ` page for an overview of LAMMPS +output options. This fix is not invoked during :doc:`energy minimization `. diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index e46b5dd28b..0f18e6822f 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -1444,6 +1444,7 @@ hux hwloc hx hy +hydronium hydrophobicity hydrostatic hydrostatically From 02f36f4e72baea82c2208c4384cf0677c8f44875 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 4 Mar 2023 06:30:47 -0500 Subject: [PATCH 063/109] whitespace --- doc/src/fix_alchemy.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/fix_alchemy.rst b/doc/src/fix_alchemy.rst index 37c49fed47..367b6d1cca 100644 --- a/doc/src/fix_alchemy.rst +++ b/doc/src/fix_alchemy.rst @@ -66,7 +66,7 @@ world-style :doc:`variable ` command along with :doc:`partition ` command can also be used. .. code-block:: LAMMPS - + create_box 2 box create_atoms 1 box pair_style eam/alloy @@ -115,7 +115,7 @@ during the MD run, the system will transform incrementally from the first system to the second system. .. note:: - + As mentioned above, the coordinates of the atoms and box size/shape must be exactly the same in the two replicas. Therefore, it is generally not a good idea to initialize the two replicas by reading From fcf8fc503fc71fd204af0d3c48bc217453209e0d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 4 Mar 2023 16:24:58 -0500 Subject: [PATCH 064/109] fix broken links --- doc/src/fix_shake.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index e6fbad7fdc..32cb5a2d19 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -275,8 +275,8 @@ reducing the :doc:`timestep `. Related commands """""""""""""""" -`fix rigid `, `fix ehex `, -`fix nve/manifold/rattle ` +:doc:`fix rigid `, :doc:`fix ehex `, +:doc:`fix nve/manifold/rattle ` Default From 8aad97ca4ab4cebdaf94e1c4912a27cdbb9e16d6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 4 Mar 2023 17:03:07 -0500 Subject: [PATCH 065/109] fix broken doc links --- doc/src/Build_extras.rst | 4 ++-- doc/src/Howto_mdi.rst | 22 +++++++++++----------- doc/src/Intro_features.rst | 2 +- doc/src/bond_write.rst | 2 +- doc/src/dump.rst | 2 +- doc/src/fix_nh_uef.rst | 9 +++++---- doc/src/fix_shake.rst | 16 ++++++++-------- doc/src/minimize.rst | 14 +++++++------- doc/src/pair_ylz.rst | 9 +++++---- 9 files changed, 41 insertions(+), 39 deletions(-) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index ac6a27464b..4dd8c10b3f 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -1964,10 +1964,10 @@ OPENMP package Apple offers the `Xcode package and IDE `_ for compiling software on macOS, so you have likely installed it to compile LAMMPS. Their - compiler is based on `Clang `, but while it + compiler is based on `Clang `_, but while it is capable of processing OpenMP directives, the necessary header files and OpenMP runtime library are missing. The `R developers - ` have figured out a way to build those + `_ have figured out a way to build those in a compatible fashion. One can download them from `https://mac.r-project.org/openmp/ `_. Simply adding those files as diff --git a/doc/src/Howto_mdi.rst b/doc/src/Howto_mdi.rst index 0e09ff2841..7567462397 100644 --- a/doc/src/Howto_mdi.rst +++ b/doc/src/Howto_mdi.rst @@ -63,18 +63,18 @@ The package also provides a :doc:`mdi plugin ` command, which enables LAMMPS to operate as an MDI driver and load an MDI engine as a plugin library. -The package furthermore includes a `fix mdi/qm ` command, in -which LAMMPS operates as an MDI driver in conjunction with a quantum -mechanics code as an MDI engine. The post_force() method of the -``fix_mdi_qm.cpp`` file shows how a driver issues MDI commands to another -code. This command can be used to couple to an MDI engine, which is -either a stand-alone code or a plugin library. +The package furthermore includes a :doc:`fix mdi/qm ` +command, in which LAMMPS operates as an MDI driver in conjunction with a +quantum mechanics code as an MDI engine. The post_force() method of the +``fix_mdi_qm.cpp`` file shows how a driver issues MDI commands to +another code. This command can be used to couple to an MDI engine, +which is either a stand-alone code or a plugin library. -As explained in the `fix mdi/qm ` command documentation, it -can be used to perform *ab initio* MD simulations or energy -minimizations, or to evaluate the quantum energy and forces for a series -of independent systems. The ``examples/mdi`` directory has example -input scripts for all of these use cases. +As explained in the :doc:`fix mdi/qm ` command +documentation, it can be used to perform *ab initio* MD simulations or +energy minimizations, or to evaluate the quantum energy and forces for a +series of independent systems. The ``examples/mdi`` directory has +example input scripts for all of these use cases. ---------- diff --git a/doc/src/Intro_features.rst b/doc/src/Intro_features.rst index 76b989ad69..d8fb2269e5 100644 --- a/doc/src/Intro_features.rst +++ b/doc/src/Intro_features.rst @@ -195,7 +195,7 @@ Multi-replica models * :doc:`parallel replica dynamics ` * :doc:`temperature accelerated dynamics ` * :doc:`parallel tempering ` -* path-integral MD: `first variant `, `second variant ` +* path-integral MD: :doc:`first variant `, :doc:`second variant ` * multi-walker collective variables with :doc:`Colvars ` and :doc:`Plumed ` .. _prepost: diff --git a/doc/src/bond_write.rst b/doc/src/bond_write.rst index 43015e25e7..bd63ebea29 100644 --- a/doc/src/bond_write.rst +++ b/doc/src/bond_write.rst @@ -70,7 +70,7 @@ be specified even if the potential has a finite value at r = 0.0. Related commands """""""""""""""" -:doc:`bond_style table `, `angle_write `, +:doc:`bond_style table `, :doc:`angle_write `, :doc:`bond_style `, :doc:`bond_coeff ` Default diff --git a/doc/src/dump.rst b/doc/src/dump.rst index 01fcc2e7e1..7993ae985f 100644 --- a/doc/src/dump.rst +++ b/doc/src/dump.rst @@ -375,7 +375,7 @@ output with each snapshot: nx ny nz The value dim will be 2 or 3 for 2d or 3d simulations. It is included -so that post-processing tools like `OVITO `, +so that post-processing tools like `OVITO `_, which can visualize grid-based quantities know how to draw each grid cell. The grid size will match the input script parameters for grid(s) created by the computes or fixes which are referenced by the diff --git a/doc/src/fix_nh_uef.rst b/doc/src/fix_nh_uef.rst index cf20d56ce7..922c2d515a 100644 --- a/doc/src/fix_nh_uef.rst +++ b/doc/src/fix_nh_uef.rst @@ -218,10 +218,11 @@ use :doc:`change_box ` before invoking the fix. Related commands """""""""""""""" -:doc:`fix nvt `, :doc:`fix npt `, `fix nvt/sllod -:doc:`, `compute temp/uef `, -:doc::doc:`compute pressure/uef `, `dump cfg/uef -:doc:` +:doc:`fix nvt `, :doc:`fix npt `, +:doc:`fix nvt/sllod `, +:doc:`compute temp/uef `, +:doc:`compute pressure/uef `, +:doc:`dump cfg/uef ` Default """"""" diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index 32cb5a2d19..4688fcbf2a 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -133,9 +133,9 @@ constraint lists atom types. All bonds connected to an atom of the specified type will be constrained. The *m* constraint lists atom masses. All bonds connected to atoms of the specified masses will be constrained (within a fudge factor of MASSDELTA specified in -fix_shake.cpp). The *a* constraint lists angle types. If both bonds -in the angle are constrained then the angle will also be constrained -if its type is in the list. +``src/RIGID/fix_shake.cpp``). The *a* constraint lists angle types. If +both bonds in the angle are constrained then the angle will also be +constrained if its type is in the list. For all constraints, a particular bond is only constrained if both atoms in the bond are in the group specified with the SHAKE fix. @@ -205,11 +205,11 @@ LAMMPS closely follows (:ref:`Andersen (1983) `). The *fix rattle* command modifies forces and velocities and thus should be defined after all other integration fixes in your input script. If you define other fixes that modify velocities or forces - after *fix rattle* operates, then *fix rattle* will not take them into - account and the overall time integration will typically not satisfy - the RATTLE constraints. You can check whether the constraints work - correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp - to 1 and recompiling LAMMPS. + after *fix rattle* operates, then *fix rattle* will not take them + into account and the overall time integration will typically not + satisfy the RATTLE constraints. You can check whether the + constraints work correctly by setting the value of RATTLE_DEBUG in + ``src/RIGID/fix_rattle.cpp`` to 1 and recompiling LAMMPS. ---------- diff --git a/doc/src/minimize.rst b/doc/src/minimize.rst index 5143cab5d5..6221d33aad 100644 --- a/doc/src/minimize.rst +++ b/doc/src/minimize.rst @@ -49,19 +49,19 @@ and forces) by pushing the atoms off of each other. The distance that atoms can move during individual minimization steps can be quite large, especially at the beginning of a minimization. - Thus `neighbor list settings ` of *every = 1* and + Thus :doc:`neighbor list settings ` of *every = 1* and *delay = 0* are **required**. This may be combined with either *check = no* (always update the neighbor list) or *check = yes* (only update the neighbor list if at least one atom has moved more than - half the `neighbor list skin ` distance since the last + half the :doc:`neighbor list skin ` distance since the last reneighboring). Using *check = yes* is recommended since it avoids unneeded reneighboring steps when the system is closer to the minimum - and thus atoms move only small distances. Using *check = no* may - be required for debugging or when coupling LAMMPS with external - codes that require a predictable sequence of neighbor list updates. + and thus atoms move only small distances. Using *check = no* may be + required for debugging or when coupling LAMMPS with external codes + that require a predictable sequence of neighbor list updates. - If the settings are **not** *every = 1* and *delay = 0*, LAMMPS - will temporarily apply a `neigh_modify every 1 delay 0 check yes + If the settings are **not** *every = 1* and *delay = 0*, LAMMPS will + temporarily apply a :doc:`neigh_modify every 1 delay 0 check yes ` setting during the minimization and restore the original setting at the end of the minimization. A corresponding message will be printed to the screen and log file, if this happens. diff --git a/doc/src/pair_ylz.rst b/doc/src/pair_ylz.rst index 17cf0ca639..22a707e9cb 100644 --- a/doc/src/pair_ylz.rst +++ b/doc/src/pair_ylz.rst @@ -142,10 +142,11 @@ the :doc:`atom_style ellipsoid ` command. Related commands """""""""""""""" -:doc:`pair_coeff `, :doc:`fix nve/asphere -:doc:`, `compute temp/asphere `, -:doc::doc:`pair_style resquared `, :doc:`pair_style -:doc:gayberne ` +:doc:`pair_coeff `, +:doc:`fix nve/asphere `, +:doc:`compute temp/asphere `, +:doc:`pair_style resquared `, +:doc:`pair_style gayberne ` Default """"""" From 7f934e3b2515ffa05579a19dc9697e66dd3600d9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sat, 4 Mar 2023 17:09:17 -0500 Subject: [PATCH 066/109] add check for broken doc links to doc makefile --- doc/Makefile | 15 +++++++++------ doc/src/Install_linux.rst | 2 +- 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/doc/Makefile b/doc/Makefile index ad80017b7e..2a4edc70f3 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -94,10 +94,11 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\ echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \ rst_anchor_check src/*.rst ;\ - python $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\ + $(PYTHON) $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\ env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\ env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\ - python $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\ + env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\ + $(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\ echo "############################################" ;\ deactivate ;\ ) @@ -174,10 +175,11 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\ echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \ rst_anchor_check src/*.rst ;\ - python utils/check-packages.py -s ../src -d src ;\ + $(PYTHON) utils/check-packages.py -s ../src -d src ;\ env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\ env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\ - python utils/check-styles.py -s ../src -d src ;\ + env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\ + $(PYTHON) utils/check-styles.py -s ../src -d src ;\ echo "############################################" ;\ deactivate ;\ ) @@ -208,14 +210,14 @@ anchor_check : $(ANCHORCHECK) style_check : $(VENV) @(\ . $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \ - python utils/check-styles.py -s ../src -d src ;\ + $(PYTHON) utils/check-styles.py -s ../src -d src ;\ deactivate ;\ ) package_check : $(VENV) @(\ . $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \ - python utils/check-packages.py -s ../src -d src ;\ + $(PYTHON) utils/check-packages.py -s ../src -d src ;\ deactivate ;\ ) @@ -224,6 +226,7 @@ char_check : role_check : @( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : ) + @( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : ) link_check : $(VENV) html @(\ diff --git a/doc/src/Install_linux.rst b/doc/src/Install_linux.rst index f902b1b987..91e7529879 100644 --- a/doc/src/Install_linux.rst +++ b/doc/src/Install_linux.rst @@ -42,7 +42,7 @@ static linkage, there is no ``liblammps.so`` library file and thus also the LAMMPS python module, which depends on it, is not included. The compressed tar archives available for download have names following -the pattern `lammps-linux-x86_64-.tar.gz` and will all unpack +the pattern ``lammps-linux-x86_64-.tar.gz`` and will all unpack into a ``lammps-static`` folder. The executables are then in the ``lammps-static/bin/`` folder. Since they do not depend on any other software, they may be freely moved or copied around. From 2aff3211877ce17f4c4d9e0a22885602f7adb69d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 5 Mar 2023 07:04:20 -0500 Subject: [PATCH 067/109] Revert "use sin(x+pi/2) instead of cos(x) on Intel OpenCL with double precision" This reverts commit fa38047749bcb349e0a97a97efea8ec10f9013f1 It is no longer needed since we disable fast math with Intel OpenCL and double precision setting. --- lib/gpu/lal_soft.cu | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/lib/gpu/lal_soft.cu b/lib/gpu/lal_soft.cu index bc96a861df..74ac0e0c97 100644 --- a/lib/gpu/lal_soft.cu +++ b/lib/gpu/lal_soft.cu @@ -22,15 +22,6 @@ _texture_2d( pos_tex,int4); #endif #else #define pos_tex x_ -// hack for Intel GPU with double precision -#if defined(_DOUBLE_DOUBLE) && (CONFIG_ID == 500) -#define MY_PI_HALF (acctyp)1.57079632679489661923 -#define my_cos(x) sin(x+MY_PI_HALF) -#endif -#endif - -#if !defined(my_cos) -#define my_cos(x) cos(x) #endif #define MY_PI (acctyp)3.14159265358979323846 @@ -104,7 +95,7 @@ __kernel void k_soft(const __global numtyp4 *restrict x_, f.z+=delz*force; if (EVFLAG && eflag) { - numtyp e=coeff[mtype].x * ((numtyp)1.0+my_cos(arg)); + numtyp e=coeff[mtype].x * ((numtyp)1.0+cos(arg)); energy+=factor_lj*e; } if (EVFLAG && vflag) { @@ -195,7 +186,7 @@ __kernel void k_soft_fast(const __global numtyp4 *restrict x_, f.z+=delz*force; if (EVFLAG && eflag) { - numtyp e=coeff[mtype].x * ((numtyp)1.0+my_cos(arg)); + numtyp e=coeff[mtype].x * ((numtyp)1.0+cos(arg)); energy+=factor_lj*e; } if (EVFLAG && vflag) { From 646ef15d8345a5d75002276dc23179afdee80fad Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 5 Mar 2023 07:18:12 -0500 Subject: [PATCH 068/109] more consistent way to disable fast math for Intel OpenCL with double precision --- lib/gpu/lal_device.cpp | 5 ++--- lib/gpu/lal_preprocessor.h | 2 +- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/lib/gpu/lal_device.cpp b/lib/gpu/lal_device.cpp index c98253ba4c..8d2211481d 100644 --- a/lib/gpu/lal_device.cpp +++ b/lib/gpu/lal_device.cpp @@ -391,10 +391,9 @@ int DeviceT::set_ocl_params(std::string s_config, const std::string &extra_args) #endif // workaround for double precision with Intel OpenCL #ifdef _DOUBLE_DOUBLE - if ((params[4] != "0") && (params[0] != "500")) _ocl_compile_string+="-cl-fast-relaxed-math "; - #else - if (params[4] != "0") _ocl_compile_string+="-cl-fast-relaxed-math "; + if (params[0] == "500") params[4] = "0"; #endif + if (params[4] != "0") _ocl_compile_string+="-cl-fast-relaxed-math "; _ocl_compile_string+=std::string(OCL_INT_TYPE)+" "+ std::string(OCL_PRECISION_COMPILE); if (gpu->has_subgroup_support()) diff --git a/lib/gpu/lal_preprocessor.h b/lib/gpu/lal_preprocessor.h index b3243c3b2e..30dec214e8 100644 --- a/lib/gpu/lal_preprocessor.h +++ b/lib/gpu/lal_preprocessor.h @@ -169,7 +169,7 @@ #define ucl_abs fabs #define ucl_erfc erfc -#if defined(FAST_MATH) && !defined(_DOUBLE_DOUBLE) +#if defined(FAST_MATH) && (FAST_MATH > 0) && !defined(_DOUBLE_DOUBLE) #define ucl_exp native_exp #define ucl_pow pow From b11049ba1a5fa22ff575f4d4afa6579973425962 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sun, 5 Mar 2023 19:03:38 -0700 Subject: [PATCH 069/109] CMake: Use hip::host and hip::hipcub targets --- cmake/Modules/Packages/GPU.cmake | 13 +++---------- 1 file changed, 3 insertions(+), 10 deletions(-) diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index 8ac1decc86..21d046606f 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -412,7 +412,8 @@ elseif(GPU_API STREQUAL "HIP") set_property(TARGET gpu PROPERTY CXX_STANDARD 14) endif() # add hipCUB - target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include) + find_package(hipcub REQUIRED) + target_link_libraries(gpu PRIVATE hip::hipcub) target_compile_definitions(gpu PRIVATE -DUSE_HIP_DEVICE_SORT) if(HIP_PLATFORM STREQUAL "nvcc") @@ -461,30 +462,22 @@ elseif(GPU_API STREQUAL "HIP") add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp) target_compile_definitions(hip_get_devices PRIVATE -DUCL_HIP) - target_link_libraries(hip_get_devices hip::host) + target_link_libraries(hip_get_devices PRIVATE hip::host) if(HIP_PLATFORM STREQUAL "nvcc") target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__) - target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include) target_include_directories(gpu PRIVATE ${CUDA_INCLUDE_DIRS}) target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY}) target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_NVCC__) - target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/include) target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS}) target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY}) elseif(HIP_PLATFORM STREQUAL "hcc") target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_HCC__) - target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include) - target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__) - target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include) elseif(HIP_PLATFORM STREQUAL "amd") target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__) - target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include) - target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__) - target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include) endif() target_link_libraries(lammps PRIVATE gpu) From f658a947c608c343a78ece270184864d5f3799b7 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Sun, 5 Mar 2023 19:07:13 -0700 Subject: [PATCH 070/109] gpu: fix broken HIP code path --- lib/gpu/lal_atom.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/gpu/lal_atom.cpp b/lib/gpu/lal_atom.cpp index 3d1a1cc963..17ebcca413 100644 --- a/lib/gpu/lal_atom.cpp +++ b/lib/gpu/lal_atom.cpp @@ -403,7 +403,7 @@ double AtomT::host_memory_usage() const { return _max_atoms*atom_bytes*sizeof(numtyp)+sizeof(Atom); } -#ifdef USE_CUDPP +#if defined(USE_CUDPP) || defined(USE_HIP_DEVICE_SORT) #define USE_CUDPP_ARG(arg) arg #else #define USE_CUDPP_ARG(arg) From 4089b7bd375da8af78cc16ac26df8030b7aab1f4 Mon Sep 17 00:00:00 2001 From: gtow-MD <127125244+gtow-MD@users.noreply.github.com> Date: Mon, 6 Mar 2023 11:11:49 -0500 Subject: [PATCH 071/109] Updated fix_deposit documentation --- doc/src/fix_deposit.rst | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index aa58aaee58..0199ae98ce 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -220,11 +220,11 @@ ignored if the *global* or *local* keywords are used, since those options choose a z-coordinate for insertion independently. The vx, vy, and vz components of velocity for the inserted particle -are set using the values specified for the *vx*, *vy*, and *vz* -keywords. Note that normally, new particles should be a assigned a -negative vertical velocity so that they move towards the surface. For -molecules, the same velocity is given to every particle (no rotation -or bond vibration). +are set by sampling a uniform distribution between the bounds set by +the values specified for the *vx*, *vy*, and *vz* keywords. Note that +normally, new particles should be a assigned a negative vertical +velocity so that they move towards the surface. For molecules, the +same velocity is given to every particle (no rotation or bond vibration). If the *target* option is used, the velocity vector of the inserted particle is changed so that it points from the insertion position From 376c7899abf6160db4710ee9ea05396e7d2b04bc Mon Sep 17 00:00:00 2001 From: Steve Plimpton Date: Mon, 6 Mar 2023 09:48:33 -0700 Subject: [PATCH 072/109] add user option for performing message sorting during load balancing --- doc/src/balance.rst | 12 +++++++++++- doc/src/fix_balance.rst | 11 ++++++++++- src/balance.cpp | 32 ++++++++++++++++++++------------ src/balance.h | 5 +++-- src/fix_balance.cpp | 15 +++++++++------ src/fix_balance.h | 1 + 6 files changed, 54 insertions(+), 22 deletions(-) diff --git a/doc/src/balance.rst b/doc/src/balance.rst index a18d25c7ce..c30c133a8b 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -53,6 +53,7 @@ Syntax name = name of the atom-style variable *store* name = store weight in custom atom property defined by :doc:`fix property/atom ` command name = atom property name (without d\_ prefix) + *sort* arg = *no* or *yes* *out* arg = filename filename = write each processor's subdomain to a file @@ -492,6 +493,14 @@ different kinds of custom atom vectors or arrays as arguments. ---------- +The *sort* keyword determines whether the communication of per-atom +data to other processors during load-balancing will be random or +deterministic. Random is generally faster; deterministic will ensure +the new ordering of atoms on each processor is the same each time the +same simulation is run. This can be useful for debugging purposes. +Since the balance commmand is a one-time operation, the default is +*yes* to perform sorting. + The *out* keyword writes a text file to the specified *filename* with the results of the balancing operation. The file contains the bounds of the subdomain for each processor after the balancing operation @@ -569,4 +578,5 @@ Related commands Default """"""" -none +The default setting is sort = yes. + diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index d3f4c48248..8c65e8341d 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -43,6 +43,7 @@ Syntax name = name of the atom-style variable *store* name = store weight in custom atom property defined by :doc:`fix property/atom ` command name = atom property name (without d\_ prefix) + *sort* arg = *no* or *yes* *out* arg = filename filename = write each processor's subdomain to a file, at each re-balancing @@ -308,6 +309,14 @@ in that sub-box. ---------- +The *sort* keyword determines whether the communication of per-atom +data to other processors during load-balancing will be random or +deterministic. Random is generally faster; deterministic will ensure +the new ordering of atoms on each processor is the same each time the +same simulation is run. This can be useful for debugging purposes. +Since the fix balance commmand is performed during timestepping, the +default is *no* so that sorting is not performed. + The *out* keyword writes text to the specified *filename* with the results of each re-balancing operation. The file contains the bounds of the subdomain for each processor after the balancing operation @@ -415,4 +424,4 @@ Related commands Default """"""" -none +The default setting is sort = no. diff --git a/src/balance.cpp b/src/balance.cpp index 10a3c320c5..c64f3f4c25 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -252,7 +252,7 @@ void Balance::command(int narg, char **arg) // process remaining optional args - options(iarg,narg,arg); + options(iarg,narg,arg,1); if (wtflag) weight_storage(nullptr); // ensure particles are in current box & update box via shrink-wrap @@ -344,7 +344,7 @@ void Balance::command(int narg, char **arg) if (style == BISECTION) { comm->layout = Comm::LAYOUT_TILED; - bisection(1); + bisection(); } // reset proc sub-domains @@ -359,8 +359,8 @@ void Balance::command(int narg, char **arg) if (domain->triclinic) domain->x2lamda(atom->nlocal); auto irregular = new Irregular(lmp); if (wtflag) fixstore->disable = 0; - if (style == BISECTION) irregular->migrate_atoms(1,1,rcb->sendproc); - else irregular->migrate_atoms(1); + if (style == BISECTION) irregular->migrate_atoms(sortflag,1,rcb->sendproc); + else irregular->migrate_atoms(sortflag); delete irregular; if (domain->triclinic) domain->lamda2x(atom->nlocal); @@ -421,9 +421,10 @@ void Balance::command(int narg, char **arg) /* ---------------------------------------------------------------------- process optional command args for Balance and FixBalance + sortflag_default is different for the 2 classes ------------------------------------------------------------------------- */ -void Balance::options(int iarg, int narg, char **arg) +void Balance::options(int iarg, int narg, char **arg, int sortflag_default) { // count max number of weight settings @@ -435,10 +436,11 @@ void Balance::options(int iarg, int narg, char **arg) wtflag = 0; varflag = 0; - oldrcb = 0; + sortflag = sortflag_default; outflag = 0; int outarg = 0; fp = nullptr; + oldrcb = 0; while (iarg < narg) { if (strcmp(arg[iarg],"weight") == 0) { @@ -471,14 +473,20 @@ void Balance::options(int iarg, int narg, char **arg) } iarg += 2+nopt; - } else if (strcmp(arg[iarg],"old") == 0) { - oldrcb = 1; - iarg++; + } else if (strcmp(arg[iarg+1],"sort") == 0) { + if (iarg+2 > narg) utils::missing_cmd_args(FLERR, "balance sort", error); + sortflag = utils::logical(FLERR,arg[iarg+1],false,lmp); + iarg += 2; } else if (strcmp(arg[iarg],"out") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal (fix) balance command"); outflag = 1; outarg = iarg+1; iarg += 2; + + } else if (strcmp(arg[iarg],"old") == 0) { + oldrcb = 1; + iarg++; + } else error->all(FLERR,"Illegal (fix) balance command"); } @@ -569,11 +577,10 @@ double Balance::imbalance_factor(double &maxcost) /* ---------------------------------------------------------------------- perform balancing via RCB class - sortflag = flag for sorting order of received messages by proc ID return list of procs to send my atoms to ------------------------------------------------------------------------- */ -int *Balance::bisection(int sortflag) +int *Balance::bisection() { if (!rcb) rcb = new RCB(lmp); @@ -641,6 +648,7 @@ int *Balance::bisection(int sortflag) // invoke RCB // then invert() to create list of proc assignments for my atoms + // sortflag = flag for sorting order of received messages by proc ID // if triclinic, RCB operates on lamda coords // NOTE: (3/2017) can remove undocumented "old" option at some point // ditto in rcb.cpp, or make it an option @@ -658,7 +666,7 @@ int *Balance::bisection(int sortflag) } if (triclinic) domain->lamda2x(nlocal); - + rcb->invert(sortflag); // reset RCB lo/hi bounding box to full simulation box as needed diff --git a/src/balance.h b/src/balance.h index a21f8992f2..3a6e8bf457 100644 --- a/src/balance.h +++ b/src/balance.h @@ -30,19 +30,20 @@ class Balance : public Command { class FixStorePeratom *fixstore; // per-atom weights stored in FixStorePeratom int wtflag; // 1 if particle weighting is used int varflag; // 1 if weight style var(iable) is used + int sortflag; // 1 if sorting of comm messages is done int outflag; // 1 for output of balance results to file Balance(class LAMMPS *); ~Balance() override; void command(int, char **) override; - void options(int, int, char **); + void options(int, int, char **, int); void weight_storage(char *); void init_imbalance(int); void set_weights(); double imbalance_factor(double &); void shift_setup(char *, int, double); int shift(); - int *bisection(int sortflag = 0); + int *bisection(); void dumpout(bigint); static constexpr int BSTR_SIZE = 3; diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp index 82c38d8650..0ada3d3b1f 100644 --- a/src/fix_balance.cpp +++ b/src/fix_balance.cpp @@ -104,9 +104,10 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) : balance = new Balance(lmp); if (lbstyle == SHIFT) balance->shift_setup(bstr,nitermax,thresh); - balance->options(iarg,narg,arg); + balance->options(iarg,narg,arg,0); wtflag = balance->wtflag; - + sortflag = balance->sortflag; + if (balance->varflag && nevery == 0) error->all(FLERR,"Fix balance nevery = 0 cannot be used with weight var"); @@ -295,12 +296,14 @@ void FixBalance::rebalance() // set disable = 0, so weights migrate with atoms // important to delay disable = 1 until after pre_neighbor imbfinal calc // b/c atoms may migrate again in comm->exchange() - // NOTE: for reproducible debug runs, set 1st arg of migrate_atoms() to 1 - + // sortflag determines whether irregular sorts its + // comm messages for reproducibility + // if not, message order is random, atom order is non-deterministic + if (domain->triclinic) domain->x2lamda(atom->nlocal); if (wtflag) balance->fixstore->disable = 0; - if (lbstyle == BISECTION) irregular->migrate_atoms(0,1,sendproc); - else if (irregular->migrate_check()) irregular->migrate_atoms(); + if (lbstyle == BISECTION) irregular->migrate_atoms(sortflag,1,sendproc); + else if (irregular->migrate_check()) irregular->migrate_atoms(sortflag); if (domain->triclinic) domain->lamda2x(atom->nlocal); // notify all classes that store distributed grids diff --git a/src/fix_balance.h b/src/fix_balance.h index f1a8db57ae..074548ac0c 100644 --- a/src/fix_balance.h +++ b/src/fix_balance.h @@ -44,6 +44,7 @@ class FixBalance : public Fix { double thresh, stopthresh; char bstr[4]; int wtflag; // 1 for weighted balancing + int sortflag; // 1 for sorting comm messages double imbnow; // current imbalance factor double imbprev; // imbalance factor before last rebalancing From f63eec695395f2e649ddfe95d053d91c80ceb76e Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 6 Mar 2023 09:48:54 -0700 Subject: [PATCH 073/109] gpu: drop hcc as platform and inherit compile defs hip::host already adds the __HIP_PLATFORM_AMD__ definition See https://github.com/ROCm-Developer-Tools/hipamd/blob/develop/hip-config.cmake.in#L180 --- cmake/Modules/Packages/GPU.cmake | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index 21d046606f..7317ae1c20 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -285,7 +285,7 @@ elseif(GPU_API STREQUAL "HIP") set(ENV{HIP_PLATFORM} ${HIP_PLATFORM}) - if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd") + if(HIP_PLATFORM STREQUAL "amd") set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture") elseif(HIP_PLATFORM STREQUAL "spirv") set(HIP_ARCH "spirv" CACHE STRING "HIP target architecture") @@ -358,7 +358,7 @@ elseif(GPU_API STREQUAL "HIP") set(CUBIN_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin") set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h") - if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd") + if(HIP_PLATFORM STREQUAL "amd") configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY) if(HIP_COMPILER STREQUAL "clang") @@ -472,12 +472,6 @@ elseif(GPU_API STREQUAL "HIP") target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_NVCC__) target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS}) target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY}) - elseif(HIP_PLATFORM STREQUAL "hcc") - target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_HCC__) - target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__) - elseif(HIP_PLATFORM STREQUAL "amd") - target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__) - target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__) endif() target_link_libraries(lammps PRIVATE gpu) From 4f420f8454a2780efa4f8d87fb0bcb85080a3b56 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 6 Mar 2023 12:14:57 -0500 Subject: [PATCH 074/109] incorporate changes to fix alchemy from @sjplimp --- src/REPLICA/fix_alchemy.cpp | 93 ++++++++++++++++++++++++------------- src/REPLICA/fix_alchemy.h | 2 + 2 files changed, 62 insertions(+), 33 deletions(-) diff --git a/src/REPLICA/fix_alchemy.cpp b/src/REPLICA/fix_alchemy.cpp index 29801d5c8d..4b29da5250 100644 --- a/src/REPLICA/fix_alchemy.cpp +++ b/src/REPLICA/fix_alchemy.cpp @@ -109,7 +109,51 @@ int FixAlchemy::setmask() return mask; } -/* ---------------------------------------------------------------------- */ +/* ---------------------------------------------------------------------- + check consistency of owned atom count and ordering + compare each pair of replica procs + checked before each exchange of atom coords or forces + to ensure the replicas have not become out of sync +---------------------------------------------------------------------- */ + +void FixAlchemy::check_consistency_atoms() +{ + // check that owned atom count is same for each pair of replica procs + + const int nlocal = atom->nlocal; + int my_nlocal[2] = {0, 0}; + int all_nlocal[2] = {0, 0}; + my_nlocal[universe->iworld] = nlocal; + MPI_Allreduce(my_nlocal, all_nlocal, 2, MPI_INT, MPI_SUM, samerank); + + int fail = (all_nlocal[0] == all_nlocal[1]) ? 0 : 1; + int allfail = 0; + MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld); + if (allfail) error->universe_all(FLERR, "Fix alchemy local atom count is inconsistent"); + + // check that owned atom ordering is same for each pair of replica procs + // re-use communication buffer for positions and forces + + tagint *tagbuf = (tagint *) commbuf; + tagint *tag = atom->tag; + if (universe->iworld == 0) { + for (int i = 0; i < nlocal; ++i) tagbuf[i] = tag[i]; + } + MPI_Bcast(tagbuf, nlocal, MPI_LMP_TAGINT, 0, samerank); + + fail = allfail = 0; + if (universe->iworld > 0) { + for (int i = 0; i < nlocal; ++i) + if (tag[i] != tagbuf[i]) fail = 1; + } + MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld); + if (allfail) error->universe_all(FLERR, "Fix alchemy local atom ordering is inconsistent"); +} + +/* ---------------------------------------------------------------------- + force simulation box size and shape to be identical for 2 replicas + invoked by post_integrate() after integration may have changed box +---------------------------------------------------------------------- */ static void synchronize_box(Domain *domain, MPI_Comm samerank) { @@ -180,36 +224,9 @@ void FixAlchemy::setup(int vflag) void FixAlchemy::post_integrate() { - // re-check that we have the same domain decomposition on all ranks - const int nlocal = atom->nlocal; - int my_nlocal[2] = {0, 0}; - int all_nlocal[2] = {0, 0}; - my_nlocal[universe->iworld] = nlocal; - MPI_Allreduce(my_nlocal, all_nlocal, 2, MPI_INT, MPI_SUM, samerank); - int fail = (all_nlocal[0] == all_nlocal[1]) ? 0 : 1; - int allfail = 0; - MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld); - if (allfail) - error->universe_all(FLERR, - "Number of atoms and domain decomposition must be the same on " - "all partitions"); + // check owned atom count and ordering between replicas - // check that we have the same atom order on all ranks - // re-use communication buffer for positions and forces - - tagint *tagbuf = (tagint *) commbuf; - tagint *tag = atom->tag; - if (universe->iworld == 0) { - for (int i = 0; i < nlocal; ++i) tagbuf[i] = tag[i]; - } - MPI_Bcast(tagbuf, nlocal, MPI_LMP_TAGINT, 0, samerank); - fail = allfail = 0; - if (universe->iworld > 0) { - for (int i = 0; i < nlocal; ++i) - if (tag[i] != tagbuf[i]) fail = 1; - } - MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld); - if (allfail) error->universe_all(FLERR, "Atoms must have the same order on all partitions"); + check_consistency_atoms(); // synchronize atom positions @@ -225,15 +242,25 @@ void FixAlchemy::post_integrate() void FixAlchemy::post_force(int /*vflag*/) { + // grow commbuf if necessary + if (3 * atom->nmax > nmax) { nmax = 3 * atom->nmax; memory->grow(commbuf, sizeof(double) * atom->nmax, "alchemy:commbuf"); } - const int nall = 3 * atom->nlocal; - double *f = &atom->f[0][0]; + // check owned atom count and ordering between replicas + + check_consistency_atoms(); + + // evaluate lambda variable + lambda = input->variable->compute_equal(ivar); + // sum forces multiplied by lambda across 2 replicas + + const int nall = 3 * atom->nlocal; + double *f = &atom->f[0][0]; for (int i = 0; i < nall; ++i) commbuf[i] = f[i] * lambda; MPI_Allreduce(commbuf, f, nall, MPI_DOUBLE, MPI_SUM, samerank); @@ -253,7 +280,7 @@ void FixAlchemy::post_force(int /*vflag*/) MPI_Allreduce(commbuf, pressure, 6, MPI_DOUBLE, MPI_SUM, universe->uworld); press->addstep(update->ntimestep + 1); - // print progress info + // print progress info to universe screen/logfile if (universe->me == 0) { double delta = update->ntimestep - update->beginstep; diff --git a/src/REPLICA/fix_alchemy.h b/src/REPLICA/fix_alchemy.h index 53c369d551..f14d1b05ca 100644 --- a/src/REPLICA/fix_alchemy.h +++ b/src/REPLICA/fix_alchemy.h @@ -50,6 +50,8 @@ class FixAlchemy : public Fix { int sync_box; // 1 of box dimensions need to be synchronized int nmax; int ivar; + + void check_consistency_atoms(); }; } // namespace LAMMPS_NS From 5909a0527bce12b1c81e73bea064d19149ced445 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 6 Mar 2023 13:39:50 -0500 Subject: [PATCH 075/109] update list of packages included into the Windows builds. --- doc/src/Install_windows.rst | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/doc/src/Install_windows.rst b/doc/src/Install_windows.rst index da9441fc49..f23092941a 100644 --- a/doc/src/Install_windows.rst +++ b/doc/src/Install_windows.rst @@ -17,11 +17,12 @@ install the Windows MPI package (MPICH2 from Argonne National Labs), needed to run in parallel with MPI. The LAMMPS binaries contain *all* :doc:`optional packages ` -included in the source distribution except: KIM, KOKKOS, MSCG, PYTHON, -ADIOS, H5MD, NETCDF, QMMM, ML-QUIP, and VTK. -The serial version also does not include the MPIIO and -LATBOLTZ packages. The GPU package is compiled for OpenCL with -mixed precision kernels. +included in the source distribution except: ADIOS, H5MD, KIM, ML-PACE, +ML-QUIP, MSCG, NETCDF, PLUMED, QMMM, SCAFACOS, and VTK. The serial +version also does not include the MPIIO and LATBOLTZ packages. The +PYTHON package is only available in the Python installaers that bundle a +Python runtime. The GPU package is compiled for OpenCL with mixed +precision kernels. The LAMMPS library is compiled as a shared library and the :doc:`LAMMPS Python module ` is installed, so that From 2af1949a9267dc40b375e75e713f0266435a8a01 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 6 Mar 2023 13:42:45 -0500 Subject: [PATCH 076/109] whitespace --- src/balance.cpp | 6 +++--- src/fix_balance.cpp | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/balance.cpp b/src/balance.cpp index c64f3f4c25..91b9d70378 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -482,11 +482,11 @@ void Balance::options(int iarg, int narg, char **arg, int sortflag_default) outflag = 1; outarg = iarg+1; iarg += 2; - + } else if (strcmp(arg[iarg],"old") == 0) { oldrcb = 1; iarg++; - + } else error->all(FLERR,"Illegal (fix) balance command"); } @@ -666,7 +666,7 @@ int *Balance::bisection() } if (triclinic) domain->lamda2x(nlocal); - + rcb->invert(sortflag); // reset RCB lo/hi bounding box to full simulation box as needed diff --git a/src/fix_balance.cpp b/src/fix_balance.cpp index 0ada3d3b1f..06274eea03 100644 --- a/src/fix_balance.cpp +++ b/src/fix_balance.cpp @@ -107,7 +107,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) : balance->options(iarg,narg,arg,0); wtflag = balance->wtflag; sortflag = balance->sortflag; - + if (balance->varflag && nevery == 0) error->all(FLERR,"Fix balance nevery = 0 cannot be used with weight var"); @@ -299,7 +299,7 @@ void FixBalance::rebalance() // sortflag determines whether irregular sorts its // comm messages for reproducibility // if not, message order is random, atom order is non-deterministic - + if (domain->triclinic) domain->x2lamda(atom->nlocal); if (wtflag) balance->fixstore->disable = 0; if (lbstyle == BISECTION) irregular->migrate_atoms(sortflag,1,sendproc); From 21b2bf0253c359c9024ac6e33c0ff50a8ddeebda Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 6 Mar 2023 22:17:12 -0500 Subject: [PATCH 077/109] avoid including accelerator_kokkos.h in main.cpp --- cmake/Modules/Packages/KOKKOS.cmake | 3 --- src/KOKKOS/kokkos.cpp | 9 +++++++++ src/accelerator_kokkos.h | 5 +++++ src/main.cpp | 15 +++++++++------ 4 files changed, 23 insertions(+), 9 deletions(-) diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index b4eb227d61..00486e73db 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -72,13 +72,11 @@ if(DOWNLOAD_KOKKOS) set_target_properties(LAMMPS::KOKKOSCONTAINERS PROPERTIES IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscontainers.a") target_link_libraries(lammps PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS) - target_link_libraries(lmp PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS) add_dependencies(LAMMPS::KOKKOSCORE kokkos_build) add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build) elseif(EXTERNAL_KOKKOS) find_package(Kokkos 3.7.01 REQUIRED CONFIG) target_link_libraries(lammps PRIVATE Kokkos::kokkos) - target_link_libraries(lmp PRIVATE Kokkos::kokkos) else() set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos) set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos) @@ -98,7 +96,6 @@ else() ${LAMMPS_LIB_KOKKOS_BIN_DIR}) target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS}) target_link_libraries(lammps PRIVATE kokkos) - target_link_libraries(lmp PRIVATE kokkos) if(BUILD_SHARED_LIBS_WAS_ON) set(BUILD_SHARED_LIBS ON) endif() diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 8b45c786e5..4e96e3218c 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -33,6 +33,10 @@ #include // for getpid() #endif +namespace LAMMPS_NS { + void kokkos_lmp_finalize(); +} + #ifdef LMP_KOKKOS_GPU // for detecting GPU-aware MPI support: @@ -80,6 +84,11 @@ using namespace LAMMPS_NS; int KokkosLMP::is_finalized = 0; int KokkosLMP::init_ngpus = 0; +void LAMMPS_NS::kokkos_lmp_finalize() +{ + KokkosLMP::finalize(); +} + /* ---------------------------------------------------------------------- */ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h index 36a376bff8..37d86a89e3 100644 --- a/src/accelerator_kokkos.h +++ b/src/accelerator_kokkos.h @@ -61,6 +61,11 @@ class KokkosLMP { int neigh_count(int) { return 0; } }; +void kokkos_lmp_finalize() +{ + KokkosLMP::finalize(); +} + class AtomKokkos : public Atom { public: tagint **k_special; diff --git a/src/main.cpp b/src/main.cpp index e263938e57..606f31274d 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -13,7 +13,6 @@ #include "lammps.h" -#include "accelerator_kokkos.h" #include "input.h" #include "lmppython.h" @@ -33,6 +32,10 @@ #include #endif +namespace LAMMPS_NS { +extern void kokkos_lmp_finalize(); +} + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- @@ -76,18 +79,18 @@ int main(int argc, char **argv) lammps->input->file(); delete lammps; } catch (LAMMPSAbortException &ae) { - KokkosLMP::finalize(); + kokkos_lmp_finalize(); Python::finalize(); MPI_Abort(ae.universe, 1); } catch (LAMMPSException &) { - KokkosLMP::finalize(); + kokkos_lmp_finalize(); Python::finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); exit(1); } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); - KokkosLMP::finalize(); + kokkos_lmp_finalize(); Python::finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); @@ -99,13 +102,13 @@ int main(int argc, char **argv) delete lammps; } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); - KokkosLMP::finalize(); + kokkos_lmp_finalize(); Python::finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); } #endif - KokkosLMP::finalize(); + kokkos_lmp_finalize(); Python::finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); From 76cbc6f48dcacfe294c48624f02b276c41185fe7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 6 Mar 2023 22:40:27 -0500 Subject: [PATCH 078/109] whitespace --- doc/src/fix_deposit.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst index 0199ae98ce..7d19e93148 100644 --- a/doc/src/fix_deposit.rst +++ b/doc/src/fix_deposit.rst @@ -221,9 +221,9 @@ options choose a z-coordinate for insertion independently. The vx, vy, and vz components of velocity for the inserted particle are set by sampling a uniform distribution between the bounds set by -the values specified for the *vx*, *vy*, and *vz* keywords. Note that -normally, new particles should be a assigned a negative vertical -velocity so that they move towards the surface. For molecules, the +the values specified for the *vx*, *vy*, and *vz* keywords. Note that +normally, new particles should be a assigned a negative vertical +velocity so that they move towards the surface. For molecules, the same velocity is given to every particle (no rotation or bond vibration). If the *target* option is used, the velocity vector of the inserted From 0b204c8cb3d1aac4eb7d43b7824b9a1391ceea16 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 6 Mar 2023 22:17:12 -0500 Subject: [PATCH 079/109] avoid including accelerator_kokkos.h in main.cpp --- cmake/Modules/Packages/KOKKOS.cmake | 3 --- src/KOKKOS/kokkos.cpp | 9 +++++++++ src/accelerator_kokkos.h | 5 +++++ src/main.cpp | 15 +++++++++------ 4 files changed, 23 insertions(+), 9 deletions(-) diff --git a/cmake/Modules/Packages/KOKKOS.cmake b/cmake/Modules/Packages/KOKKOS.cmake index b4eb227d61..00486e73db 100644 --- a/cmake/Modules/Packages/KOKKOS.cmake +++ b/cmake/Modules/Packages/KOKKOS.cmake @@ -72,13 +72,11 @@ if(DOWNLOAD_KOKKOS) set_target_properties(LAMMPS::KOKKOSCONTAINERS PROPERTIES IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscontainers.a") target_link_libraries(lammps PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS) - target_link_libraries(lmp PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS) add_dependencies(LAMMPS::KOKKOSCORE kokkos_build) add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build) elseif(EXTERNAL_KOKKOS) find_package(Kokkos 3.7.01 REQUIRED CONFIG) target_link_libraries(lammps PRIVATE Kokkos::kokkos) - target_link_libraries(lmp PRIVATE Kokkos::kokkos) else() set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos) set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos) @@ -98,7 +96,6 @@ else() ${LAMMPS_LIB_KOKKOS_BIN_DIR}) target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS}) target_link_libraries(lammps PRIVATE kokkos) - target_link_libraries(lmp PRIVATE kokkos) if(BUILD_SHARED_LIBS_WAS_ON) set(BUILD_SHARED_LIBS ON) endif() diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 8b45c786e5..4e96e3218c 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -33,6 +33,10 @@ #include // for getpid() #endif +namespace LAMMPS_NS { + void kokkos_lmp_finalize(); +} + #ifdef LMP_KOKKOS_GPU // for detecting GPU-aware MPI support: @@ -80,6 +84,11 @@ using namespace LAMMPS_NS; int KokkosLMP::is_finalized = 0; int KokkosLMP::init_ngpus = 0; +void LAMMPS_NS::kokkos_lmp_finalize() +{ + KokkosLMP::finalize(); +} + /* ---------------------------------------------------------------------- */ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h index 36a376bff8..37d86a89e3 100644 --- a/src/accelerator_kokkos.h +++ b/src/accelerator_kokkos.h @@ -61,6 +61,11 @@ class KokkosLMP { int neigh_count(int) { return 0; } }; +void kokkos_lmp_finalize() +{ + KokkosLMP::finalize(); +} + class AtomKokkos : public Atom { public: tagint **k_special; diff --git a/src/main.cpp b/src/main.cpp index e263938e57..606f31274d 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -13,7 +13,6 @@ #include "lammps.h" -#include "accelerator_kokkos.h" #include "input.h" #include "lmppython.h" @@ -33,6 +32,10 @@ #include #endif +namespace LAMMPS_NS { +extern void kokkos_lmp_finalize(); +} + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- @@ -76,18 +79,18 @@ int main(int argc, char **argv) lammps->input->file(); delete lammps; } catch (LAMMPSAbortException &ae) { - KokkosLMP::finalize(); + kokkos_lmp_finalize(); Python::finalize(); MPI_Abort(ae.universe, 1); } catch (LAMMPSException &) { - KokkosLMP::finalize(); + kokkos_lmp_finalize(); Python::finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); exit(1); } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); - KokkosLMP::finalize(); + kokkos_lmp_finalize(); Python::finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); @@ -99,13 +102,13 @@ int main(int argc, char **argv) delete lammps; } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); - KokkosLMP::finalize(); + kokkos_lmp_finalize(); Python::finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); } #endif - KokkosLMP::finalize(); + kokkos_lmp_finalize(); Python::finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); From 642dccceb530afc99ca6481709386be7e840e0e6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 6 Mar 2023 22:49:20 -0500 Subject: [PATCH 080/109] fix up non-KOKKOS case --- src/accelerator_kokkos.h | 5 ----- src/main.cpp | 10 ++++++++++ 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h index 37d86a89e3..36a376bff8 100644 --- a/src/accelerator_kokkos.h +++ b/src/accelerator_kokkos.h @@ -61,11 +61,6 @@ class KokkosLMP { int neigh_count(int) { return 0; } }; -void kokkos_lmp_finalize() -{ - KokkosLMP::finalize(); -} - class AtomKokkos : public Atom { public: tagint **k_special; diff --git a/src/main.cpp b/src/main.cpp index 606f31274d..543833498b 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -32,9 +32,19 @@ #include #endif +#if defined(LMP_KOKKOS) namespace LAMMPS_NS { extern void kokkos_lmp_finalize(); } +#else +#include "accelerator_kokkos.h" +namespace LAMMPS_NS { +void kokkos_lmp_finalize() +{ + KokkosLMP::finalize(); +} +} +#endif using namespace LAMMPS_NS; From 40790f6c4593e9dbdf8d785dea7ec7930825caeb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 6 Mar 2023 22:49:20 -0500 Subject: [PATCH 081/109] fix up non-KOKKOS case --- src/accelerator_kokkos.h | 5 ----- src/main.cpp | 10 ++++++++++ 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/src/accelerator_kokkos.h b/src/accelerator_kokkos.h index 37d86a89e3..36a376bff8 100644 --- a/src/accelerator_kokkos.h +++ b/src/accelerator_kokkos.h @@ -61,11 +61,6 @@ class KokkosLMP { int neigh_count(int) { return 0; } }; -void kokkos_lmp_finalize() -{ - KokkosLMP::finalize(); -} - class AtomKokkos : public Atom { public: tagint **k_special; diff --git a/src/main.cpp b/src/main.cpp index 606f31274d..543833498b 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -32,9 +32,19 @@ #include #endif +#if defined(LMP_KOKKOS) namespace LAMMPS_NS { extern void kokkos_lmp_finalize(); } +#else +#include "accelerator_kokkos.h" +namespace LAMMPS_NS { +void kokkos_lmp_finalize() +{ + KokkosLMP::finalize(); +} +} +#endif using namespace LAMMPS_NS; From 6c1ed6a9b52ffb36fc4159306aa8c8cdee8b929b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Mar 2023 08:23:36 -0500 Subject: [PATCH 082/109] use finalize wrappers from the LAMMPS library interface --- src/KOKKOS/kokkos.cpp | 9 --------- src/main.cpp | 36 +++++++++++------------------------- 2 files changed, 11 insertions(+), 34 deletions(-) diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 4e96e3218c..8b45c786e5 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -33,10 +33,6 @@ #include // for getpid() #endif -namespace LAMMPS_NS { - void kokkos_lmp_finalize(); -} - #ifdef LMP_KOKKOS_GPU // for detecting GPU-aware MPI support: @@ -84,11 +80,6 @@ using namespace LAMMPS_NS; int KokkosLMP::is_finalized = 0; int KokkosLMP::init_ngpus = 0; -void LAMMPS_NS::kokkos_lmp_finalize() -{ - KokkosLMP::finalize(); -} - /* ---------------------------------------------------------------------- */ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) diff --git a/src/main.cpp b/src/main.cpp index 543833498b..746ccc41e9 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -14,7 +14,7 @@ #include "lammps.h" #include "input.h" -#include "lmppython.h" +#include "library.h" #if defined(LAMMPS_EXCEPTIONS) #include "exceptions.h" @@ -32,20 +32,6 @@ #include #endif -#if defined(LMP_KOKKOS) -namespace LAMMPS_NS { -extern void kokkos_lmp_finalize(); -} -#else -#include "accelerator_kokkos.h" -namespace LAMMPS_NS { -void kokkos_lmp_finalize() -{ - KokkosLMP::finalize(); -} -} -#endif - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- @@ -89,19 +75,19 @@ int main(int argc, char **argv) lammps->input->file(); delete lammps; } catch (LAMMPSAbortException &ae) { - kokkos_lmp_finalize(); - Python::finalize(); + lammps_kokkos_finalize(); + lammps_python_finalize(); MPI_Abort(ae.universe, 1); } catch (LAMMPSException &) { - kokkos_lmp_finalize(); - Python::finalize(); + lammps_kokkos_finalize(); + lammps_python_finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); exit(1); } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); - kokkos_lmp_finalize(); - Python::finalize(); + lammps_kokkos_finalize(); + lammps_python_finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); } @@ -112,14 +98,14 @@ int main(int argc, char **argv) delete lammps; } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); - kokkos_lmp_finalize(); - Python::finalize(); + lammps_kokkos_finalize(); + lammps_python_finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); } #endif - kokkos_lmp_finalize(); - Python::finalize(); + lammps_kokkos_finalize(); + lammps_python_finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); } From 710baff14df381d51805ac87d00c2b0d6cdbd040 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Mar 2023 08:23:36 -0500 Subject: [PATCH 083/109] use finalize wrappers from the LAMMPS library interface --- src/KOKKOS/kokkos.cpp | 9 --------- src/main.cpp | 36 +++++++++++------------------------- 2 files changed, 11 insertions(+), 34 deletions(-) diff --git a/src/KOKKOS/kokkos.cpp b/src/KOKKOS/kokkos.cpp index 4e96e3218c..8b45c786e5 100644 --- a/src/KOKKOS/kokkos.cpp +++ b/src/KOKKOS/kokkos.cpp @@ -33,10 +33,6 @@ #include // for getpid() #endif -namespace LAMMPS_NS { - void kokkos_lmp_finalize(); -} - #ifdef LMP_KOKKOS_GPU // for detecting GPU-aware MPI support: @@ -84,11 +80,6 @@ using namespace LAMMPS_NS; int KokkosLMP::is_finalized = 0; int KokkosLMP::init_ngpus = 0; -void LAMMPS_NS::kokkos_lmp_finalize() -{ - KokkosLMP::finalize(); -} - /* ---------------------------------------------------------------------- */ KokkosLMP::KokkosLMP(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp) diff --git a/src/main.cpp b/src/main.cpp index 543833498b..746ccc41e9 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -14,7 +14,7 @@ #include "lammps.h" #include "input.h" -#include "lmppython.h" +#include "library.h" #if defined(LAMMPS_EXCEPTIONS) #include "exceptions.h" @@ -32,20 +32,6 @@ #include #endif -#if defined(LMP_KOKKOS) -namespace LAMMPS_NS { -extern void kokkos_lmp_finalize(); -} -#else -#include "accelerator_kokkos.h" -namespace LAMMPS_NS { -void kokkos_lmp_finalize() -{ - KokkosLMP::finalize(); -} -} -#endif - using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- @@ -89,19 +75,19 @@ int main(int argc, char **argv) lammps->input->file(); delete lammps; } catch (LAMMPSAbortException &ae) { - kokkos_lmp_finalize(); - Python::finalize(); + lammps_kokkos_finalize(); + lammps_python_finalize(); MPI_Abort(ae.universe, 1); } catch (LAMMPSException &) { - kokkos_lmp_finalize(); - Python::finalize(); + lammps_kokkos_finalize(); + lammps_python_finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); exit(1); } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); - kokkos_lmp_finalize(); - Python::finalize(); + lammps_kokkos_finalize(); + lammps_python_finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); } @@ -112,14 +98,14 @@ int main(int argc, char **argv) delete lammps; } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); - kokkos_lmp_finalize(); - Python::finalize(); + lammps_kokkos_finalize(); + lammps_python_finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); } #endif - kokkos_lmp_finalize(); - Python::finalize(); + lammps_kokkos_finalize(); + lammps_python_finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); } From 4265b7379ea1c6718fc4deb6d1346b09b6e9571a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Mar 2023 12:07:56 -0500 Subject: [PATCH 084/109] update precomputed constants. apply clang-format --- src/DIELECTRIC/fix_polarize_bem_gmres.cpp | 22 +++++++++---------- src/DIELECTRIC/fix_polarize_bem_icc.cpp | 26 +++++++++++------------ 2 files changed, 24 insertions(+), 24 deletions(-) diff --git a/src/DIELECTRIC/fix_polarize_bem_gmres.cpp b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp index dafe4dc8e0..b11ac7e482 100644 --- a/src/DIELECTRIC/fix_polarize_bem_gmres.cpp +++ b/src/DIELECTRIC/fix_polarize_bem_gmres.cpp @@ -61,7 +61,7 @@ using namespace LAMMPS_NS; using namespace FixConst; -using MathConst::MY_PI; +using MathConst::MY_4PI; /* ---------------------------------------------------------------------- */ @@ -311,13 +311,13 @@ void FixPolarizeBEMGMRES::setup(int /*vflag*/) epsilon0e2q = 1.0; if (strcmp(update->unit_style, "real") == 0) - epsilon0e2q = 0.000240263377163643 * (4 * MY_PI); + epsilon0e2q = 0.000240263377163643 * MY_4PI; else if (strcmp(update->unit_style, "metal") == 0) - epsilon0e2q = 0.00553386738300813 * (4 * MY_PI); + epsilon0e2q = 0.00553386738300813 * MY_4PI; else if (strcmp(update->unit_style, "si") == 0) - epsilon0e2q = 8.854187812813e-12 * (4 * MY_PI); + epsilon0e2q = 8.854187812813e-12 * MY_4PI; else if (strcmp(update->unit_style, "nano") == 0) - epsilon0e2q = 0.000345866711328125 * (4 * MY_PI); + epsilon0e2q = 0.000345866711328125 * MY_4PI; else if (strcmp(update->unit_style, "lj") != 0) error->all(FLERR, "Only unit styles 'lj', 'real', 'metal', 'si' and 'nano' are supported"); @@ -403,7 +403,7 @@ void FixPolarizeBEMGMRES::compute_induced_charges() } double ndotE = epsilon0e2q * (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / epsilon[i]; double sigma_f = q[i] / area[i]; - buffer[idx] = (1 - em[i]) * sigma_f - ed[i] * ndotE / (4 * MY_PI); + buffer[idx] = (1 - em[i]) * sigma_f - ed[i] * ndotE / MY_4PI; } MPI_Allreduce(buffer, rhs, num_induced_charges, MPI_DOUBLE, MPI_SUM, world); @@ -464,11 +464,11 @@ void FixPolarizeBEMGMRES::compute_induced_charges() int ncount = group->count(igroup); double sum = 0; MPI_Allreduce(&tmp, &sum, 1, MPI_DOUBLE, MPI_SUM, world); - double qboundave = sum/(double)ncount; + double qboundave = sum / (double) ncount; for (int i = 0; i < nlocal; i++) { if (!(mask[i] & groupbit)) continue; - q[i] -= qboundave; + q[i] -= qboundave; } } @@ -693,7 +693,7 @@ void FixPolarizeBEMGMRES::apply_operator(double *w, double *Aw, int /*n*/) Ez += efield_kspace[i][2]; } double ndotE = epsilon0e2q * (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / epsilon[i]; - buffer[idx] = em[i] * w[idx] + ed[i] * ndotE / (4 * MY_PI); + buffer[idx] = em[i] * w[idx] + ed[i] * ndotE / MY_4PI; } MPI_Allreduce(buffer, Aw, num_induced_charges, MPI_DOUBLE, MPI_SUM, world); @@ -765,8 +765,8 @@ void FixPolarizeBEMGMRES::update_residual(double *w, double *r, int /*n*/) Ey += efield_kspace[i][1]; Ez += efield_kspace[i][2]; } - double ndotE = epsilon0e2q * (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / - epsilon[i] / (4 * MY_PI); + double ndotE = + epsilon0e2q * (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / epsilon[i] / MY_4PI; double sigma_f = q[i] / area[i]; buffer[idx] = (1 - em[i]) * sigma_f - em[i] * w[idx] - ed[i] * ndotE; } diff --git a/src/DIELECTRIC/fix_polarize_bem_icc.cpp b/src/DIELECTRIC/fix_polarize_bem_icc.cpp index 034ada48ab..697d45f416 100644 --- a/src/DIELECTRIC/fix_polarize_bem_icc.cpp +++ b/src/DIELECTRIC/fix_polarize_bem_icc.cpp @@ -49,7 +49,8 @@ using namespace LAMMPS_NS; using namespace FixConst; -using MathConst::MY_PI; +using MathConst::MY_2PI; +using MathConst::MY_4PI; /* ---------------------------------------------------------------------- */ @@ -214,13 +215,13 @@ void FixPolarizeBEMICC::setup(int /*vflag*/) epsilon0e2q = 1.0; if (strcmp(update->unit_style, "real") == 0) - epsilon0e2q = 0.000240263377163643 * (4 * MY_PI); + epsilon0e2q = 0.000240263377163643 * MY_4PI; else if (strcmp(update->unit_style, "metal") == 0) - epsilon0e2q = 0.00553386738300813 * (4 * MY_PI); + epsilon0e2q = 0.00553386738300813 * MY_4PI; else if (strcmp(update->unit_style, "si") == 0) - epsilon0e2q = 8.854187812813e-12 * (4 * MY_PI); + epsilon0e2q = 8.854187812813e-12 * MY_4PI; else if (strcmp(update->unit_style, "nano") == 0) - epsilon0e2q = 0.000345866711328125 * (4 * MY_PI); + epsilon0e2q = 0.000345866711328125 * MY_4PI; else if (strcmp(update->unit_style, "lj") != 0) error->all(FLERR, "Only unit styles 'lj', 'real', 'metal', 'si' and 'nano' are supported"); @@ -286,8 +287,8 @@ void FixPolarizeBEMICC::compute_induced_charges() } // divide (Ex,Ey,Ez) by epsilon[i] here - double ndotE = epsilon0e2q * (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / - epsilon[i] / (2 * MY_PI); + double ndotE = + epsilon0e2q * (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / epsilon[i] / MY_2PI; double q_free = q[i]; double q_bound = 0; q_bound = (1.0 / em[i] - 1) * q_free - (ed[i] / (2 * em[i])) * ndotE * area[i]; @@ -326,8 +327,8 @@ void FixPolarizeBEMICC::compute_induced_charges() // note the area[i] is included here to ensure correct charge unit // for direct use in force/efield compute - double ndotE = epsilon0e2q * (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / - (4 * MY_PI) / epsilon[i]; + double ndotE = + epsilon0e2q * (Ex * norm[i][0] + Ey * norm[i][1] + Ez * norm[i][2]) / MY_4PI / epsilon[i]; double q_bound = q_scaled[i] - q_free; q_bound = (1 - omega) * q_bound + omega * ((1.0 / em[i] - 1) * q_free - (ed[i] / em[i]) * ndotE * area[i]); @@ -343,7 +344,7 @@ void FixPolarizeBEMICC::compute_induced_charges() // hence there's no epsilon_1 in the factor f //double dot = (Ex*norm[i][0] + Ey*norm[i][1] + Ez*norm[i][2]); - //double f = (ed[i] / (2 * em[i])) / (2*MY_PI); + //double f = (ed[i] / (2 * em[i])) / MY_2PI; //q[i] = (1 - omega) * q[i] - omega * epsilon0 * f * dot * area[i]; double delta = fabs(qtmp - q_bound); @@ -378,11 +379,11 @@ void FixPolarizeBEMICC::compute_induced_charges() int ncount = group->count(igroup); double sum = 0; MPI_Allreduce(&tmp, &sum, 1, MPI_DOUBLE, MPI_SUM, world); - double qboundave = sum/(double)ncount; + double qboundave = sum / (double) ncount; for (int i = 0; i < nlocal; i++) { if (!(mask[i] & groupbit)) continue; - q[i] -= qboundave; + q[i] -= qboundave; } } @@ -467,7 +468,6 @@ void FixPolarizeBEMICC::unpack_forward_comm(int n, int first, double *buf) for (m = 0, i = first; m < n; m++, i++) atom->q_scaled[i] = buf[m]; } - /* ---------------------------------------------------------------------- set dielectric params for the atoms in the group ------------------------------------------------------------------------- */ From 353e0820e32e229ddaee15ef4216326542bce6df Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Mar 2023 12:26:43 -0500 Subject: [PATCH 085/109] capture log files for dielectric examples --- examples/PACKAGES/dielectric/data.sphere | 2 +- examples/PACKAGES/dielectric/in.confined | 10 +- examples/PACKAGES/dielectric/in.nopbc | 8 +- .../log.07Mar23.confined.gmres.g++.1 | 187 +++++++++++++++++ .../log.07Mar23.confined.gmres.g++.4 | 187 +++++++++++++++++ .../dielectric/log.07Mar23.confined.icc.g++.1 | 189 ++++++++++++++++++ .../dielectric/log.07Mar23.confined.icc.g++.4 | 189 ++++++++++++++++++ .../dielectric/log.07Mar23.nopbc.gmres.g++.1 | 131 ++++++++++++ .../dielectric/log.07Mar23.nopbc.gmres.g++.4 | 131 ++++++++++++ .../dielectric/log.07Mar23.nopbc.icc.g++.1 | 132 ++++++++++++ .../dielectric/log.07Mar23.nopbc.icc.g++.4 | 132 ++++++++++++ 11 files changed, 1288 insertions(+), 10 deletions(-) create mode 100644 examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.1 create mode 100644 examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.4 create mode 100644 examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.1 create mode 100644 examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.4 create mode 100644 examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.1 create mode 100644 examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.4 create mode 100644 examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.1 create mode 100644 examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.4 diff --git a/examples/PACKAGES/dielectric/data.sphere b/examples/PACKAGES/dielectric/data.sphere index 3e98e8211f..4a81df26ec 100644 --- a/examples/PACKAGES/dielectric/data.sphere +++ b/examples/PACKAGES/dielectric/data.sphere @@ -14,7 +14,7 @@ Masses 2 1 3 1 -Atoms # dielectric: id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature +Atoms # dielectric : id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature 1 1 1 0 50 55.2573 41.4935 0 0.525731 -0.850651 0.490491 45 57.5 57.5 0 2 1 1 0 50.4064 55.7206 41.8079 0.0406403 0.572055 -0.819208 0.490491 45 57.5 57.5 0 diff --git a/examples/PACKAGES/dielectric/in.confined b/examples/PACKAGES/dielectric/in.confined index 314409fc17..276dd67afc 100644 --- a/examples/PACKAGES/dielectric/in.confined +++ b/examples/PACKAGES/dielectric/in.confined @@ -7,7 +7,7 @@ # Dielectric constants can be set to be different from the input data file variable epsilon1 index 20 -variable epsilon2 index 10 +variable epsilon2 index 10 variable data index data.confined @@ -53,11 +53,11 @@ kspace_modify slab 3.0 neigh_modify every 1 delay 0 check yes one 5000 #compute ef all efield/atom -dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] -dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] -dump_modify 1 sort id +#dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id -dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1] c_ef[2] c_ef[3] +#dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1] c_ef[2] c_ef[3] fix 1 ions nve diff --git a/examples/PACKAGES/dielectric/in.nopbc b/examples/PACKAGES/dielectric/in.nopbc index ada9af2bf5..cbb0d45377 100644 --- a/examples/PACKAGES/dielectric/in.nopbc +++ b/examples/PACKAGES/dielectric/in.nopbc @@ -25,10 +25,10 @@ pair_coeff 1 1 0.0 1.0 neigh_modify one 5000 #compute ef all efield/atom -dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] -dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] - -dump_modify 1 sort id +#dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +# +#dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id fix 1 ions nve diff --git a/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.1 b/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.1 new file mode 100644 index 0000000000..ca0c22e5d3 --- /dev/null +++ b/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.1 @@ -0,0 +1,187 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +# Two ions, a cation and an anion, confined between two interfaces: epsilon1 | epsilon2 | epsilon1 +# The interface normal vectors should be consistent with ed, pointing from region with epsilon1 to that with epsilon2 +# bottom interface: n = (0, 0, 1) +# top interface: n = (0, 0, -1) +# so that ed's are the same for both interfaces + +# Dielectric constants can be set to be different from the input data file + +variable epsilon1 index 20 +variable epsilon2 index 10 + +variable data index data.confined + +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary p p f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +# compute the relevant values for the interface particles + +variable ed equal "v_epsilon2 - v_epsilon1" +variable em equal "(v_epsilon2 + v_epsilon1)/2" +variable epsilon equal 1.0 # epsilon at the patch, not used for now +variable area equal 0.866 # patch area, same as in the data file + +read_data ${data} +read_data data.confined +Reading data file ... + orthogonal box = (0 0 0) to (40.000006 43.301277 40) + 1 by 1 by 1 MPI processor grid +WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) + reading atoms ... + 4002 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.013 seconds + +group interface type 1 +4000 atoms in group interface +group ions type 2 3 +2 atoms in group ions + +group cations type 2 +1 atoms in group cations +group anions type 3 +1 atoms in group anions + +# set the dielectric constant of the medium where the ions reside + +set group cations epsilon ${epsilon2} +set group cations epsilon 10 +Setting atom values ... + 1 settings made for epsilon +set group anions epsilon ${epsilon2} +set group anions epsilon 10 +Setting atom values ... + 1 settings made for epsilon + +pair_style lj/cut/coul/long/dielectric 1.122 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +kspace_style pppm/dielectric 0.0001 +kspace_modify slab 3.0 + +neigh_modify every 1 delay 0 check yes one 5000 + +#compute ef all efield/atom +#dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id + +#dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1] c_ef[2] c_ef[3] + +fix 1 ions nve + +# fix modify is used to set the properties of the interface particle group + +if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == dof" "fix 3 interface polarize/functional 1 0.0001" "fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" else "print 'Unsupported polarization solver' " +fix 3 interface polarize/bem/gmres 1 1.0e-4 +fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 ${em} ${epsilon} ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 15 ${epsilon} ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 15 1 ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 15 1 0.866 NULL + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair #f_3 +thermo_modify flush yes + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006 + +@Article{TrungCPC19, + author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica} + title = {Incorporating Surface Polarization Effects Into Large-Scale + Coarse-Grained Molecular Dynamics Simulation}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2019, + volume = 241, + pages = {80--91} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.24260797 + grid = 12 12 36 + stencil order = 5 + estimated absolute RMS force accuracy = 2.5219574e-07 + estimated relative force accuracy = 2.5219574e-07 + using double precision KISS FFT + 3d grid and FFT values/proc = 10982 5184 +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +BEM/GMRES solver for 4000 induced charges using maximum 3999 q-vectors +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 5000, page size: 100000 + master list distance cutoff = 10.3 + ghost atom cutoff = 10.3 + binsize = 5.15, bins = 8 9 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long/dielectric, perpetual + attributes: full, newton off + pair build: full/bin + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 381.6 | 381.6 | 381.6 Mbytes + Step E_vdwl E_coul E_long E_pair + 0 0 -1.7228107e-08 -1.8534756e-05 -1.8551984e-05 +Loop time of 1.872e-06 on 1 procs for 0 steps with 4002 atoms + +160.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.872e-06 | | |100.00 + +Nlocal: 4002 ave 4002 max 4002 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 4832 ave 4832 max 4832 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: 1.51316e+06 ave 1.51316e+06 max 1.51316e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1513160 +Ave neighs/atom = 378.10095 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + + + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.4 b/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.4 new file mode 100644 index 0000000000..f4e855ad42 --- /dev/null +++ b/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.4 @@ -0,0 +1,187 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +# Two ions, a cation and an anion, confined between two interfaces: epsilon1 | epsilon2 | epsilon1 +# The interface normal vectors should be consistent with ed, pointing from region with epsilon1 to that with epsilon2 +# bottom interface: n = (0, 0, 1) +# top interface: n = (0, 0, -1) +# so that ed's are the same for both interfaces + +# Dielectric constants can be set to be different from the input data file + +variable epsilon1 index 20 +variable epsilon2 index 10 + +variable data index data.confined + +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary p p f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +# compute the relevant values for the interface particles + +variable ed equal "v_epsilon2 - v_epsilon1" +variable em equal "(v_epsilon2 + v_epsilon1)/2" +variable epsilon equal 1.0 # epsilon at the patch, not used for now +variable area equal 0.866 # patch area, same as in the data file + +read_data ${data} +read_data data.confined +Reading data file ... + orthogonal box = (0 0 0) to (40.000006 43.301277 40) + 2 by 2 by 1 MPI processor grid +WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) + reading atoms ... + 4002 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.011 seconds + +group interface type 1 +4000 atoms in group interface +group ions type 2 3 +2 atoms in group ions + +group cations type 2 +1 atoms in group cations +group anions type 3 +1 atoms in group anions + +# set the dielectric constant of the medium where the ions reside + +set group cations epsilon ${epsilon2} +set group cations epsilon 10 +Setting atom values ... + 1 settings made for epsilon +set group anions epsilon ${epsilon2} +set group anions epsilon 10 +Setting atom values ... + 1 settings made for epsilon + +pair_style lj/cut/coul/long/dielectric 1.122 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +kspace_style pppm/dielectric 0.0001 +kspace_modify slab 3.0 + +neigh_modify every 1 delay 0 check yes one 5000 + +#compute ef all efield/atom +#dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id + +#dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1] c_ef[2] c_ef[3] + +fix 1 ions nve + +# fix modify is used to set the properties of the interface particle group + +if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == dof" "fix 3 interface polarize/functional 1 0.0001" "fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" else "print 'Unsupported polarization solver' " +fix 3 interface polarize/bem/gmres 1 1.0e-4 +fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 ${em} ${epsilon} ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 15 ${epsilon} ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 15 1 ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 15 1 0.866 NULL + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair #f_3 +thermo_modify flush yes + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006 + +@Article{TrungCPC19, + author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica} + title = {Incorporating Surface Polarization Effects Into Large-Scale + Coarse-Grained Molecular Dynamics Simulation}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2019, + volume = 241, + pages = {80--91} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.24260797 + grid = 12 12 36 + stencil order = 5 + estimated absolute RMS force accuracy = 2.5219574e-07 + estimated relative force accuracy = 2.5219574e-07 + using double precision KISS FFT + 3d grid and FFT values/proc = 4598 1296 +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +BEM/GMRES solver for 4000 induced charges using maximum 3999 q-vectors +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 5000, page size: 100000 + master list distance cutoff = 10.3 + ghost atom cutoff = 10.3 + binsize = 5.15, bins = 8 9 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long/dielectric, perpetual + attributes: full, newton off + pair build: full/bin + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 376.2 | 376.2 | 376.2 Mbytes + Step E_vdwl E_coul E_long E_pair + 0 0 -1.7228107e-08 -1.8534756e-05 -1.8551984e-05 +Loop time of 1.49983e-05 on 4 procs for 0 steps with 4002 atoms + +85.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.5e-05 | | |100.00 + +Nlocal: 1000.5 ave 1001 max 1000 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2889.5 ave 2890 max 2889 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 378290 ave 378465 max 378117 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1513160 +Ave neighs/atom = 378.10095 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + + + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.1 b/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.1 new file mode 100644 index 0000000000..9c1ab22f90 --- /dev/null +++ b/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.1 @@ -0,0 +1,189 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +# Two ions, a cation and an anion, confined between two interfaces: epsilon1 | epsilon2 | epsilon1 +# The interface normal vectors should be consistent with ed, pointing from region with epsilon1 to that with epsilon2 +# bottom interface: n = (0, 0, 1) +# top interface: n = (0, 0, -1) +# so that ed's are the same for both interfaces + +# Dielectric constants can be set to be different from the input data file + +variable epsilon1 index 20 +variable epsilon2 index 10 + +variable data index data.confined + +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary p p f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +# compute the relevant values for the interface particles + +variable ed equal "v_epsilon2 - v_epsilon1" +variable em equal "(v_epsilon2 + v_epsilon1)/2" +variable epsilon equal 1.0 # epsilon at the patch, not used for now +variable area equal 0.866 # patch area, same as in the data file + +read_data ${data} +read_data data.confined +Reading data file ... + orthogonal box = (0 0 0) to (40.000006 43.301277 40) + 1 by 1 by 1 MPI processor grid +WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) + reading atoms ... + 4002 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.013 seconds + +group interface type 1 +4000 atoms in group interface +group ions type 2 3 +2 atoms in group ions + +group cations type 2 +1 atoms in group cations +group anions type 3 +1 atoms in group anions + +# set the dielectric constant of the medium where the ions reside + +set group cations epsilon ${epsilon2} +set group cations epsilon 10 +Setting atom values ... + 1 settings made for epsilon +set group anions epsilon ${epsilon2} +set group anions epsilon 10 +Setting atom values ... + 1 settings made for epsilon + +pair_style lj/cut/coul/long/dielectric 1.122 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +kspace_style pppm/dielectric 0.0001 +kspace_modify slab 3.0 + +neigh_modify every 1 delay 0 check yes one 5000 + +#compute ef all efield/atom +#dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id + +#dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1] c_ef[2] c_ef[3] + +fix 1 ions nve + +# fix modify is used to set the properties of the interface particle group + +if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == dof" "fix 3 interface polarize/functional 1 0.0001" "fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" else "print 'Unsupported polarization solver' " +fix 3 interface polarize/bem/icc 1 1.0e-4 +fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 ${em} ${epsilon} ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 15 ${epsilon} ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 15 1 ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 15 1 0.866 NULL + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair #f_3 +thermo_modify flush yes + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006 + +@Article{TrungCPC19, + author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica} + title = {Incorporating Surface Polarization Effects Into Large-Scale + Coarse-Grained Molecular Dynamics Simulation}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2019, + volume = 241, + pages = {80--91} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.24260797 + grid = 12 12 36 + stencil order = 5 + estimated absolute RMS force accuracy = 2.5219574e-07 + estimated relative force accuracy = 2.5219574e-07 + using double precision KISS FFT + 3d grid and FFT values/proc = 10982 5184 +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +BEM/ICC solver for 4000 induced charges + using pair style lj/cut/coul/long/dielectric + using kspace style pppm/dielectric +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 5000, page size: 100000 + master list distance cutoff = 10.3 + ghost atom cutoff = 10.3 + binsize = 5.15, bins = 8 9 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long/dielectric, perpetual + attributes: full, newton off + pair build: full/bin + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 14.99 | 14.99 | 14.99 Mbytes + Step E_vdwl E_coul E_long E_pair + 0 0 -1.7228514e-08 -1.8534756e-05 -1.8551985e-05 +Loop time of 1.573e-06 on 1 procs for 0 steps with 4002 atoms + +190.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.573e-06 | | |100.00 + +Nlocal: 4002 ave 4002 max 4002 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 4832 ave 4832 max 4832 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: 1.51316e+06 ave 1.51316e+06 max 1.51316e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1513160 +Ave neighs/atom = 378.10095 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + + + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.4 b/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.4 new file mode 100644 index 0000000000..c60b803cd1 --- /dev/null +++ b/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.4 @@ -0,0 +1,189 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +# Two ions, a cation and an anion, confined between two interfaces: epsilon1 | epsilon2 | epsilon1 +# The interface normal vectors should be consistent with ed, pointing from region with epsilon1 to that with epsilon2 +# bottom interface: n = (0, 0, 1) +# top interface: n = (0, 0, -1) +# so that ed's are the same for both interfaces + +# Dielectric constants can be set to be different from the input data file + +variable epsilon1 index 20 +variable epsilon2 index 10 + +variable data index data.confined + +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary p p f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +# compute the relevant values for the interface particles + +variable ed equal "v_epsilon2 - v_epsilon1" +variable em equal "(v_epsilon2 + v_epsilon1)/2" +variable epsilon equal 1.0 # epsilon at the patch, not used for now +variable area equal 0.866 # patch area, same as in the data file + +read_data ${data} +read_data data.confined +Reading data file ... + orthogonal box = (0 0 0) to (40.000006 43.301277 40) + 2 by 2 by 1 MPI processor grid +WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) + reading atoms ... + 4002 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.012 seconds + +group interface type 1 +4000 atoms in group interface +group ions type 2 3 +2 atoms in group ions + +group cations type 2 +1 atoms in group cations +group anions type 3 +1 atoms in group anions + +# set the dielectric constant of the medium where the ions reside + +set group cations epsilon ${epsilon2} +set group cations epsilon 10 +Setting atom values ... + 1 settings made for epsilon +set group anions epsilon ${epsilon2} +set group anions epsilon 10 +Setting atom values ... + 1 settings made for epsilon + +pair_style lj/cut/coul/long/dielectric 1.122 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +kspace_style pppm/dielectric 0.0001 +kspace_modify slab 3.0 + +neigh_modify every 1 delay 0 check yes one 5000 + +#compute ef all efield/atom +#dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id + +#dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1] c_ef[2] c_ef[3] + +fix 1 ions nve + +# fix modify is used to set the properties of the interface particle group + +if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == dof" "fix 3 interface polarize/functional 1 0.0001" "fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" else "print 'Unsupported polarization solver' " +fix 3 interface polarize/bem/icc 1 1.0e-4 +fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 ${em} ${epsilon} ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 15 ${epsilon} ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 15 1 ${area} NULL +fix_modify 3 itr_max 50 dielectrics -10 15 1 0.866 NULL + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair #f_3 +thermo_modify flush yes + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006 + +@Article{TrungCPC19, + author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica} + title = {Incorporating Surface Polarization Effects Into Large-Scale + Coarse-Grained Molecular Dynamics Simulation}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2019, + volume = 241, + pages = {80--91} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.24260797 + grid = 12 12 36 + stencil order = 5 + estimated absolute RMS force accuracy = 2.5219574e-07 + estimated relative force accuracy = 2.5219574e-07 + using double precision KISS FFT + 3d grid and FFT values/proc = 4598 1296 +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +BEM/ICC solver for 4000 induced charges + using pair style lj/cut/coul/long/dielectric + using kspace style pppm/dielectric +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 5000, page size: 100000 + master list distance cutoff = 10.3 + ghost atom cutoff = 10.3 + binsize = 5.15, bins = 8 9 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long/dielectric, perpetual + attributes: full, newton off + pair build: full/bin + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.647 | 9.647 | 9.647 Mbytes + Step E_vdwl E_coul E_long E_pair + 0 0 -1.7228514e-08 -1.8534756e-05 -1.8551985e-05 +Loop time of 1.23127e-05 on 4 procs for 0 steps with 4002 atoms + +103.6% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.231e-05 | | |100.00 + +Nlocal: 1000.5 ave 1001 max 1000 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2889.5 ave 2890 max 2889 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 378290 ave 378465 max 378117 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1513160 +Ave neighs/atom = 378.10095 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + + + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.1 b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.1 new file mode 100644 index 0000000000..08cbbb2b7d --- /dev/null +++ b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.1 @@ -0,0 +1,131 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +# Interface +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary f f f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +variable data index data.sphere + +read_data ${data} +read_data data.sphere +Reading data file ... + orthogonal box = (0 0 0) to (100 100 100) + 1 by 1 by 1 MPI processor grid +WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) + reading atoms ... + 2563 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.011 seconds + +group interface type 1 +2562 atoms in group interface +group ions type 2 3 +1 atoms in group ions + +pair_style lj/cut/coul/cut/dielectric 1.122 20.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +neigh_modify one 5000 + +#compute ef all efield/atom +#dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +# +#dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id + +fix 1 ions nve + +if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" elif "${method} == dof" "fix 3 interface polarize/functional 1 1.0e-4" else "print 'Unsupported method for polarization' " +fix 3 interface polarize/bem/gmres 1 1.0e-4 + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair +thermo_modify flush yes + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006 + +@Article{TrungCPC19, + author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica} + title = {Incorporating Surface Polarization Effects Into Large-Scale + Coarse-Grained Molecular Dynamics Simulation}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2019, + volume = 241, + pages = {80--91} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +BEM/GMRES solver for 2562 induced charges using maximum 2561 q-vectors +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 5000, page size: 100000 + master list distance cutoff = 20.3 + ghost atom cutoff = 20.3 + binsize = 10.15, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/cut/dielectric, perpetual + attributes: full, newton off + pair build: full/bin + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 183.5 | 183.5 | 183.5 Mbytes + Step E_vdwl E_coul E_long E_pair + 0 0 2.1870454e-07 0 2.1870454e-07 +Loop time of 1.538e-06 on 1 procs for 0 steps with 2563 atoms + +195.1% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.538e-06 | | |100.00 + +Nlocal: 2563 ave 2563 max 2563 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 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: 6.56561e+06 ave 6.56561e+06 max 6.56561e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 6565612 +Ave neighs/atom = 2561.6902 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.4 b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.4 new file mode 100644 index 0000000000..060c00a9be --- /dev/null +++ b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.4 @@ -0,0 +1,131 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +# Interface +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary f f f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +variable data index data.sphere + +read_data ${data} +read_data data.sphere +Reading data file ... + orthogonal box = (0 0 0) to (100 100 100) + 1 by 2 by 2 MPI processor grid +WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) + reading atoms ... + 2563 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.009 seconds + +group interface type 1 +2562 atoms in group interface +group ions type 2 3 +1 atoms in group ions + +pair_style lj/cut/coul/cut/dielectric 1.122 20.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +neigh_modify one 5000 + +#compute ef all efield/atom +#dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +# +#dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id + +fix 1 ions nve + +if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" elif "${method} == dof" "fix 3 interface polarize/functional 1 1.0e-4" else "print 'Unsupported method for polarization' " +fix 3 interface polarize/bem/gmres 1 1.0e-4 + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair +thermo_modify flush yes + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006 + +@Article{TrungCPC19, + author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica} + title = {Incorporating Surface Polarization Effects Into Large-Scale + Coarse-Grained Molecular Dynamics Simulation}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2019, + volume = 241, + pages = {80--91} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +BEM/GMRES solver for 2562 induced charges using maximum 2561 q-vectors +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 5000, page size: 100000 + master list distance cutoff = 20.3 + ghost atom cutoff = 20.3 + binsize = 10.15, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/cut/dielectric, perpetual + attributes: full, newton off + pair build: full/bin + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 164.6 | 164.7 | 165 Mbytes + Step E_vdwl E_coul E_long E_pair + 0 0 2.1870454e-07 0 2.1870454e-07 +Loop time of 2.4415e-06 on 4 procs for 0 steps with 2563 atoms + +133.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.442e-06 | | |100.00 + +Nlocal: 640.75 ave 674 max 609 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +Nghost: 1922.25 ave 1954 max 1889 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1.6414e+06 ave 1.72639e+06 max 1.56007e+06 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 6565612 +Ave neighs/atom = 2561.6902 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + + +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.1 b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.1 new file mode 100644 index 0000000000..cdde6a228a --- /dev/null +++ b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.1 @@ -0,0 +1,132 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +# Interface +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary f f f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +variable data index data.sphere + +read_data ${data} +read_data data.sphere +Reading data file ... + orthogonal box = (0 0 0) to (100 100 100) + 1 by 1 by 1 MPI processor grid +WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) + reading atoms ... + 2563 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.011 seconds + +group interface type 1 +2562 atoms in group interface +group ions type 2 3 +1 atoms in group ions + +pair_style lj/cut/coul/cut/dielectric 1.122 20.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +neigh_modify one 5000 + +#compute ef all efield/atom +#dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +# +#dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id + +fix 1 ions nve + +if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" elif "${method} == dof" "fix 3 interface polarize/functional 1 1.0e-4" else "print 'Unsupported method for polarization' " +fix 3 interface polarize/bem/icc 1 1.0e-4 + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair +thermo_modify flush yes + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006 + +@Article{TrungCPC19, + author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica} + title = {Incorporating Surface Polarization Effects Into Large-Scale + Coarse-Grained Molecular Dynamics Simulation}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2019, + volume = 241, + pages = {80--91} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +BEM/ICC solver for 2562 induced charges + using pair style lj/cut/coul/cut/dielectric +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 5000, page size: 100000 + master list distance cutoff = 20.3 + ghost atom cutoff = 20.3 + binsize = 10.15, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/cut/dielectric, perpetual + attributes: full, newton off + pair build: full/bin + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 32.96 | 32.96 | 32.96 Mbytes + Step E_vdwl E_coul E_long E_pair + 0 0 2.1870503e-07 0 2.1870503e-07 +Loop time of 1.536e-06 on 1 procs for 0 steps with 2563 atoms + +195.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.536e-06 | | |100.00 + +Nlocal: 2563 ave 2563 max 2563 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 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: 6.56561e+06 ave 6.56561e+06 max 6.56561e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 6565612 +Ave neighs/atom = 2561.6902 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + + +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.4 b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.4 new file mode 100644 index 0000000000..e329d5c958 --- /dev/null +++ b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.4 @@ -0,0 +1,132 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +# Interface +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary f f f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +variable data index data.sphere + +read_data ${data} +read_data data.sphere +Reading data file ... + orthogonal box = (0 0 0) to (100 100 100) + 1 by 2 by 2 MPI processor grid +WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) + reading atoms ... + 2563 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.008 seconds + +group interface type 1 +2562 atoms in group interface +group ions type 2 3 +1 atoms in group ions + +pair_style lj/cut/coul/cut/dielectric 1.122 20.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +neigh_modify one 5000 + +#compute ef all efield/atom +#dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +# +#dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id + +fix 1 ions nve + +if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" elif "${method} == dof" "fix 3 interface polarize/functional 1 1.0e-4" else "print 'Unsupported method for polarization' " +fix 3 interface polarize/bem/icc 1 1.0e-4 + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair +thermo_modify flush yes + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006 + +@Article{TrungCPC19, + author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica} + title = {Incorporating Surface Polarization Effects Into Large-Scale + Coarse-Grained Molecular Dynamics Simulation}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2019, + volume = 241, + pages = {80--91} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +BEM/ICC solver for 2562 induced charges + using pair style lj/cut/coul/cut/dielectric +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 5000, page size: 100000 + master list distance cutoff = 20.3 + ghost atom cutoff = 20.3 + binsize = 10.15, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/cut/dielectric, perpetual + attributes: full, newton off + pair build: full/bin + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 14.03 | 14.12 | 14.41 Mbytes + Step E_vdwl E_coul E_long E_pair + 0 0 2.1870503e-07 0 2.1870503e-07 +Loop time of 2.408e-06 on 4 procs for 0 steps with 2563 atoms + +135.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.408e-06 | | |100.00 + +Nlocal: 640.75 ave 674 max 609 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +Nghost: 1922.25 ave 1954 max 1889 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1.6414e+06 ave 1.72639e+06 max 1.56007e+06 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 6565612 +Ave neighs/atom = 2561.6902 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + + +Total wall time: 0:00:00 From 9e57bedea2b4747376d8a9fc7f515a749e9d6817 Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Tue, 7 Mar 2023 11:51:14 -0600 Subject: [PATCH 086/109] Fixed bugs when mistakenly replacing all "NULL" with "nullptr" with FixPolarizeFunctional, reduced the number of induced charges so that in.nopbc with dof finishes in a reasonable time --- examples/PACKAGES/dielectric/data.sphere | 3213 ++++---------------- examples/PACKAGES/dielectric/in.nopbc | 4 +- src/DIELECTRIC/fix_polarize_functional.cpp | 6 +- 3 files changed, 651 insertions(+), 2572 deletions(-) diff --git a/examples/PACKAGES/dielectric/data.sphere b/examples/PACKAGES/dielectric/data.sphere index 4a81df26ec..ede3849635 100644 --- a/examples/PACKAGES/dielectric/data.sphere +++ b/examples/PACKAGES/dielectric/data.sphere @@ -1,6 +1,6 @@ -LAMMPS data file: 2563 atoms for a single point charge near a dielectric sphere, 2564 for two opposite charges +LAMMPS data file: sphere radius = 5; ion distance to center = 7, epsilon inside = 35 outside = 80 -2563 atoms +643 atoms 3 atom types 0.000000 100.000000 xlo xhi @@ -14,2569 +14,648 @@ Masses 2 1 3 1 -Atoms # dielectric : id mol type q x y z normx normy normz area_per_patch ed em epsilon curvature +Atoms # dielectric -1 1 1 0 50 55.2573 41.4935 0 0.525731 -0.850651 0.490491 45 57.5 57.5 0 -2 1 1 0 50.4064 55.7206 41.8079 0.0406403 0.572055 -0.819208 0.490491 45 57.5 57.5 0 -3 1 1 0 49.5936 55.7206 41.8079 -0.0406403 0.572055 -0.819208 0.490491 45 57.5 57.5 0 -4 1 1 0 50.8109 56.1564 42.1616 0.081086 0.615642 -0.783843 0.490491 45 57.5 57.5 0 -5 1 1 0 50 56.1768 42.1357 0 0.617676 -0.786433 0.490491 45 57.5 57.5 0 -6 1 1 0 49.1891 56.1564 42.1616 -0.081086 0.615642 -0.783843 0.490491 45 57.5 57.5 0 -7 1 1 0 51.2114 56.5628 42.5527 0.121144 0.656282 -0.744727 0.490491 45 57.5 57.5 0 -8 1 1 0 50.4064 56.6088 42.5061 0.0406418 0.660883 -0.749387 0.490491 45 57.5 57.5 0 -9 1 1 0 51.6062 56.9378 42.9795 0.160622 0.69378 -0.702047 0.490491 45 57.5 57.5 0 -10 1 1 0 50.8057 57.0062 42.9103 0.0805729 0.700622 -0.708969 0.490491 45 57.5 57.5 0 -11 1 1 0 50 57.0291 42.8872 0 0.702907 -0.711282 0.490491 45 57.5 57.5 0 -12 1 1 0 49.5936 56.6088 42.5061 -0.0406418 0.660883 -0.749387 0.490491 45 57.5 57.5 0 -13 1 1 0 48.7886 56.5628 42.5527 -0.121144 0.656282 -0.744727 0.490491 45 57.5 57.5 0 -14 1 1 0 49.1943 57.0062 42.9103 -0.0805729 0.700622 -0.708969 0.490491 45 57.5 57.5 0 -15 1 1 0 48.3938 56.9378 42.9795 -0.160622 0.69378 -0.702047 0.490491 45 57.5 57.5 0 -16 1 1 0 51.9933 57.2796 43.4399 0.199331 0.727959 -0.656006 0.490491 45 57.5 57.5 0 -17 1 1 0 51.2119 57.3889 43.3716 0.121192 0.738887 -0.662842 0.490491 45 57.5 57.5 0 -18 1 1 0 52.3709 57.5865 43.9317 0.237086 0.758652 -0.606825 0.490491 45 57.5 57.5 0 -19 1 1 0 51.5961 57.7184 43.8454 0.159613 0.771841 -0.615456 0.490491 45 57.5 57.5 0 -20 1 1 0 50.8114 57.802 43.7976 0.0811417 0.780205 -0.620239 0.490491 45 57.5 57.5 0 -21 1 1 0 52.7371 57.8572 44.4526 0.273706 0.785715 -0.55474 0.490491 45 57.5 57.5 0 -22 1 1 0 51.9727 58.015 44.3549 0.197274 0.801504 -0.564513 0.490491 45 57.5 57.5 0 -23 1 1 0 53.0902 58.0902 45 0.309017 0.809017 -0.5 0.490491 45 57.5 57.5 0 -24 1 1 0 52.3345 58.2715 44.888 0.233445 0.827147 -0.511205 0.490491 45 57.5 57.5 0 -25 1 1 0 51.5643 58.4018 44.8074 0.156434 0.840178 -0.519259 0.490491 45 57.5 57.5 0 -26 1 1 0 51.1908 58.1217 44.2886 0.119078 0.81217 -0.57114 0.490491 45 57.5 57.5 0 -27 1 1 0 50.4067 58.1752 44.2554 0.040675 0.817523 -0.574458 0.490491 45 57.5 57.5 0 -28 1 1 0 50.7846 58.4803 44.7589 0.0784592 0.848029 -0.52411 0.490491 45 57.5 57.5 0 -29 1 1 0 50 58.5065 44.7427 0 0.850651 -0.525731 0.490491 45 57.5 57.5 0 -30 1 1 0 48.7881 57.3889 43.3716 -0.121192 0.738887 -0.662842 0.490491 45 57.5 57.5 0 -31 1 1 0 48.0067 57.2796 43.4399 -0.199331 0.727959 -0.656006 0.490491 45 57.5 57.5 0 -32 1 1 0 49.1886 57.802 43.7976 -0.0811417 0.780205 -0.620239 0.490491 45 57.5 57.5 0 -33 1 1 0 48.4039 57.7184 43.8454 -0.159613 0.771841 -0.615456 0.490491 45 57.5 57.5 0 -34 1 1 0 47.6291 57.5865 43.9317 -0.237086 0.758652 -0.606825 0.490491 45 57.5 57.5 0 -35 1 1 0 49.5933 58.1752 44.2554 -0.040675 0.817523 -0.574458 0.490491 45 57.5 57.5 0 -36 1 1 0 48.8092 58.1217 44.2886 -0.119078 0.81217 -0.57114 0.490491 45 57.5 57.5 0 -37 1 1 0 49.2154 58.4803 44.7589 -0.0784592 0.848029 -0.52411 0.490491 45 57.5 57.5 0 -38 1 1 0 48.4357 58.4018 44.8074 -0.156434 0.840178 -0.519259 0.490491 45 57.5 57.5 0 -39 1 1 0 48.0273 58.015 44.3549 -0.197274 0.801504 -0.564513 0.490491 45 57.5 57.5 0 -40 1 1 0 47.2629 57.8572 44.4526 -0.273706 0.785715 -0.55474 0.490491 45 57.5 57.5 0 -41 1 1 0 47.6655 58.2715 44.888 -0.233445 0.827147 -0.511205 0.490491 45 57.5 57.5 0 -42 1 1 0 46.9098 58.0902 45 -0.309017 0.809017 -0.5 0.490491 45 57.5 57.5 0 -43 1 1 0 50.4068 57.435 43.325 0.0406769 0.743496 -0.667502 0.490491 45 57.5 57.5 0 -44 1 1 0 50 57.8279 43.7771 0 0.782786 -0.622291 0.490491 45 57.5 57.5 0 -45 1 1 0 49.5932 57.435 43.325 -0.0406769 0.743496 -0.667502 0.490491 45 57.5 57.5 0 -46 1 1 0 53.4285 58.2845 45.5713 0.342848 0.828447 -0.442867 0.490491 45 57.5 57.5 0 -47 1 1 0 52.7469 58.5264 45.5554 0.274694 0.85264 -0.444464 0.490491 45 57.5 57.5 0 -48 1 1 0 53.7504 58.4391 46.1639 0.375038 0.843912 -0.383614 0.490491 45 57.5 57.5 0 -49 1 1 0 53.0766 58.6973 46.1409 0.307659 0.869725 -0.385906 0.490491 45 57.5 57.5 0 -50 1 1 0 52.3868 58.9101 46.1381 0.238677 0.891007 -0.386187 0.490491 45 57.5 57.5 0 -51 1 1 0 54.0543 58.5534 46.7748 0.405434 0.855337 -0.322525 0.490491 45 57.5 57.5 0 -52 1 1 0 53.3921 58.8284 46.7514 0.339209 0.882837 -0.324863 0.490491 45 57.5 57.5 0 -53 1 1 0 54.3389 58.6267 47.4011 0.433888 0.862669 -0.259892 0.490491 45 57.5 57.5 0 -54 1 1 0 53.6852 58.9174 47.3734 0.368518 0.891742 -0.262661 0.490491 45 57.5 57.5 0 -55 1 1 0 53.0126 59.1624 47.3592 0.301258 0.916244 -0.264082 0.490491 45 57.5 57.5 0 -56 1 1 0 52.7063 59.0583 46.7407 0.270627 0.905832 -0.325929 0.490491 45 57.5 57.5 0 -57 1 1 0 52.0119 59.2388 46.7447 0.201189 0.92388 -0.32553 0.490491 45 57.5 57.5 0 -58 1 1 0 52.3245 59.3605 47.3585 0.232455 0.93605 -0.264151 0.490491 45 57.5 57.5 0 -59 1 1 0 51.6246 59.5106 47.3713 0.16246 0.951057 -0.262865 0.490491 45 57.5 57.5 0 -60 1 1 0 54.6027 58.6587 48.0398 0.460266 0.865871 -0.196015 0.490491 45 57.5 57.5 0 -61 1 1 0 53.9735 58.964 48.0359 0.39735 0.896401 -0.196412 0.490491 45 57.5 57.5 0 -62 1 1 0 54.8444 58.6493 48.688 0.484441 0.864929 -0.1312 0.490491 45 57.5 57.5 0 -63 1 1 0 54.2236 58.968 48.6825 0.422363 0.896801 -0.131749 0.490491 45 57.5 57.5 0 -64 1 1 0 53.5823 59.243 48.6834 0.358229 0.924305 -0.131656 0.490491 45 57.5 57.5 0 -65 1 1 0 55.063 58.5985 49.3424 0.506298 0.859848 -0.0657577 0.490491 45 57.5 57.5 0 -66 1 1 0 54.4537 58.9293 49.3418 0.445365 0.892927 -0.0658169 0.490491 45 57.5 57.5 0 -67 1 1 0 55.2573 58.5065 50 0.525731 0.850651 0 0.490491 45 57.5 57.5 0 -68 1 1 0 54.6566 58.8497 50 0.465657 0.884965 0 0.490491 45 57.5 57.5 0 -69 1 1 0 54.0336 59.1504 50 0.403355 0.915043 0 0.490491 45 57.5 57.5 0 -70 1 1 0 53.8172 59.2192 49.3401 0.381722 0.921919 -0.0659886 0.490491 45 57.5 57.5 0 -71 1 1 0 53.1678 59.462 49.3396 0.316778 0.946198 -0.0660427 0.490491 45 57.5 57.5 0 -72 1 1 0 53.3912 59.4074 50 0.339122 0.940742 0 0.490491 45 57.5 57.5 0 -73 1 1 0 52.7327 59.6194 50 0.273267 0.961938 0 0.490491 45 57.5 57.5 0 -74 1 1 0 51.9178 59.6119 48.0166 0.19178 0.961188 -0.198337 0.490491 45 57.5 57.5 0 -75 1 1 0 51.2273 59.7237 48.0142 0.122729 0.97237 -0.198581 0.490491 45 57.5 57.5 0 -76 1 1 0 52.2012 59.6639 48.6721 0.220117 0.966393 -0.132792 0.490491 45 57.5 57.5 0 -77 1 1 0 51.5155 59.7943 48.6674 0.151549 0.979426 -0.133256 0.490491 45 57.5 57.5 0 -78 1 1 0 50.8224 59.8769 48.6693 0.0822422 0.987688 -0.133071 0.490491 45 57.5 57.5 0 -79 1 1 0 52.4733 59.6664 49.3343 0.247326 0.966643 -0.0665668 0.490491 45 57.5 57.5 0 -80 1 1 0 51.796 59.8148 49.334 0.179596 0.981483 -0.0666046 0.490491 45 57.5 57.5 0 -81 1 1 0 52.061 59.7853 50 0.206103 0.97853 0 0.490491 45 57.5 57.5 0 -82 1 1 0 51.3795 59.9044 50 0.137952 0.990439 0 0.490491 45 57.5 57.5 0 -83 1 1 0 51.1039 59.9165 49.3329 0.110385 0.991648 -0.0667095 0.490491 45 57.5 57.5 0 -84 1 1 0 50.4125 59.9692 49.3326 0.0412479 0.996917 -0.0667412 0.490491 45 57.5 57.5 0 -85 1 1 0 50.6914 59.9761 50 0.0691418 0.997607 0 0.490491 45 57.5 57.5 0 -86 1 1 0 50 60 50 0 1 0 0.490491 45 57.5 57.5 0 -87 1 1 0 53.3061 59.2268 48.0161 0.330606 0.922682 -0.198387 0.490491 45 57.5 57.5 0 -88 1 1 0 52.8993 59.4782 48.6743 0.289929 0.947822 -0.13257 0.490491 45 57.5 57.5 0 -89 1 1 0 52.6155 59.4443 48.0091 0.26155 0.944433 -0.199094 0.490491 45 57.5 57.5 0 -90 1 1 0 47.2531 58.5264 45.5554 -0.274694 0.85264 -0.444464 0.490491 45 57.5 57.5 0 -91 1 1 0 46.5715 58.2845 45.5713 -0.342848 0.828447 -0.442867 0.490491 45 57.5 57.5 0 -92 1 1 0 47.6132 58.9101 46.1381 -0.238677 0.891007 -0.386187 0.490491 45 57.5 57.5 0 -93 1 1 0 46.9234 58.6973 46.1409 -0.307659 0.869725 -0.385906 0.490491 45 57.5 57.5 0 -94 1 1 0 46.2496 58.4391 46.1639 -0.375038 0.843912 -0.383614 0.490491 45 57.5 57.5 0 -95 1 1 0 47.9881 59.2388 46.7447 -0.201189 0.92388 -0.32553 0.490491 45 57.5 57.5 0 -96 1 1 0 47.2937 59.0583 46.7407 -0.270627 0.905832 -0.325929 0.490491 45 57.5 57.5 0 -97 1 1 0 48.3754 59.5106 47.3713 -0.16246 0.951057 -0.262865 0.490491 45 57.5 57.5 0 -98 1 1 0 47.6755 59.3605 47.3585 -0.232455 0.93605 -0.264151 0.490491 45 57.5 57.5 0 -99 1 1 0 46.9874 59.1624 47.3592 -0.301258 0.916244 -0.264082 0.490491 45 57.5 57.5 0 -100 1 1 0 46.6079 58.8284 46.7514 -0.339209 0.882837 -0.324863 0.490491 45 57.5 57.5 0 -101 1 1 0 45.9457 58.5534 46.7748 -0.405434 0.855337 -0.322525 0.490491 45 57.5 57.5 0 -102 1 1 0 46.3148 58.9174 47.3734 -0.368518 0.891742 -0.262661 0.490491 45 57.5 57.5 0 -103 1 1 0 45.6611 58.6267 47.4011 -0.433888 0.862669 -0.259892 0.490491 45 57.5 57.5 0 -104 1 1 0 48.7727 59.7237 48.0142 -0.122729 0.97237 -0.198581 0.490491 45 57.5 57.5 0 -105 1 1 0 48.0822 59.6119 48.0166 -0.19178 0.961188 -0.198337 0.490491 45 57.5 57.5 0 -106 1 1 0 49.1776 59.8769 48.6693 -0.0822422 0.987688 -0.133071 0.490491 45 57.5 57.5 0 -107 1 1 0 48.4845 59.7943 48.6674 -0.151549 0.979426 -0.133256 0.490491 45 57.5 57.5 0 -108 1 1 0 47.7988 59.6639 48.6721 -0.220117 0.966393 -0.132792 0.490491 45 57.5 57.5 0 -109 1 1 0 49.5875 59.9692 49.3326 -0.0412479 0.996917 -0.0667412 0.490491 45 57.5 57.5 0 -110 1 1 0 48.8961 59.9165 49.3329 -0.110385 0.991648 -0.0667095 0.490491 45 57.5 57.5 0 -111 1 1 0 49.3086 59.9761 50 -0.0691418 0.997607 0 0.490491 45 57.5 57.5 0 -112 1 1 0 48.6205 59.9044 50 -0.137952 0.990439 0 0.490491 45 57.5 57.5 0 -113 1 1 0 48.204 59.8148 49.334 -0.179596 0.981483 -0.0666046 0.490491 45 57.5 57.5 0 -114 1 1 0 47.5267 59.6664 49.3343 -0.247326 0.966643 -0.0665668 0.490491 45 57.5 57.5 0 -115 1 1 0 47.939 59.7853 50 -0.206103 0.97853 0 0.490491 45 57.5 57.5 0 -116 1 1 0 47.2673 59.6194 50 -0.273267 0.961938 0 0.490491 45 57.5 57.5 0 -117 1 1 0 46.0265 58.964 48.0359 -0.39735 0.896401 -0.196412 0.490491 45 57.5 57.5 0 -118 1 1 0 45.3973 58.6587 48.0398 -0.460266 0.865871 -0.196015 0.490491 45 57.5 57.5 0 -119 1 1 0 46.4177 59.243 48.6834 -0.358229 0.924305 -0.131656 0.490491 45 57.5 57.5 0 -120 1 1 0 45.7764 58.968 48.6825 -0.422363 0.896801 -0.131749 0.490491 45 57.5 57.5 0 -121 1 1 0 45.1556 58.6493 48.688 -0.484441 0.864929 -0.1312 0.490491 45 57.5 57.5 0 -122 1 1 0 46.8322 59.462 49.3396 -0.316778 0.946198 -0.0660427 0.490491 45 57.5 57.5 0 -123 1 1 0 46.1828 59.2192 49.3401 -0.381722 0.921919 -0.0659886 0.490491 45 57.5 57.5 0 -124 1 1 0 46.6088 59.4074 50 -0.339122 0.940742 0 0.490491 45 57.5 57.5 0 -125 1 1 0 45.9664 59.1504 50 -0.403355 0.915043 0 0.490491 45 57.5 57.5 0 -126 1 1 0 45.5463 58.9293 49.3418 -0.445365 0.892927 -0.0658169 0.490491 45 57.5 57.5 0 -127 1 1 0 44.937 58.5985 49.3424 -0.506298 0.859848 -0.0657577 0.490491 45 57.5 57.5 0 -128 1 1 0 45.3434 58.8497 50 -0.465657 0.884965 0 0.490491 45 57.5 57.5 0 -129 1 1 0 44.7427 58.5065 50 -0.525731 0.850651 0 0.490491 45 57.5 57.5 0 -130 1 1 0 47.3845 59.4443 48.0091 -0.26155 0.944433 -0.199094 0.490491 45 57.5 57.5 0 -131 1 1 0 47.1007 59.4782 48.6743 -0.289929 0.947822 -0.13257 0.490491 45 57.5 57.5 0 -132 1 1 0 46.6939 59.2268 48.0161 -0.330606 0.922682 -0.198387 0.490491 45 57.5 57.5 0 -133 1 1 0 51.9823 58.6853 45.4574 0.198227 0.868535 -0.454262 0.490491 45 57.5 57.5 0 -134 1 1 0 51.6101 59.0484 46.0586 0.161007 0.904839 -0.394136 0.490491 45 57.5 57.5 0 -135 1 1 0 51.228 59.3513 46.6766 0.1228 0.93513 -0.332342 0.490491 45 57.5 57.5 0 -136 1 1 0 50.8232 59.1298 46.0039 0.0823235 0.912983 -0.399607 0.490491 45 57.5 57.5 0 -137 1 1 0 51.1976 58.7934 45.3912 0.119755 0.879344 -0.460882 0.490491 45 57.5 57.5 0 -138 1 1 0 50.413 58.8476 45.3579 0.0412991 0.88476 -0.464213 0.490491 45 57.5 57.5 0 -139 1 1 0 50.815 59.6065 47.3448 0.081501 0.960655 -0.265519 0.490491 45 57.5 57.5 0 -140 1 1 0 50.4125 59.7885 47.9963 0.0412506 0.978852 -0.200368 0.490491 45 57.5 57.5 0 -141 1 1 0 50 59.6386 47.336 0 0.963861 -0.266405 0.490491 45 57.5 57.5 0 -142 1 1 0 50 59.9105 48.6648 0 0.991046 -0.133524 0.490491 45 57.5 57.5 0 -143 1 1 0 49.5875 59.7885 47.9963 -0.0412506 0.978852 -0.200368 0.490491 45 57.5 57.5 0 -144 1 1 0 49.185 59.6065 47.3448 -0.081501 0.960655 -0.265519 0.490491 45 57.5 57.5 0 -145 1 1 0 49.587 58.8476 45.3579 -0.0412991 0.88476 -0.464213 0.490491 45 57.5 57.5 0 -146 1 1 0 49.1768 59.1298 46.0039 -0.0823235 0.912983 -0.399607 0.490491 45 57.5 57.5 0 -147 1 1 0 48.8024 58.7934 45.3912 -0.119755 0.879344 -0.460882 0.490491 45 57.5 57.5 0 -148 1 1 0 48.772 59.3513 46.6766 -0.1228 0.93513 -0.332342 0.490491 45 57.5 57.5 0 -149 1 1 0 48.3899 59.0484 46.0586 -0.161007 0.904839 -0.394136 0.490491 45 57.5 57.5 0 -150 1 1 0 48.0177 58.6853 45.4574 -0.198227 0.868535 -0.454262 0.490491 45 57.5 57.5 0 -151 1 1 0 50.413 59.4162 46.6586 0.0413021 0.941618 -0.33414 0.490491 45 57.5 57.5 0 -152 1 1 0 49.587 59.4162 46.6586 -0.0413021 0.941618 -0.33414 0.490491 45 57.5 57.5 0 -153 1 1 0 50 59.1609 45.9903 0 0.916092 -0.400968 0.490491 45 57.5 57.5 0 -154 1 1 0 50 55.2573 58.5065 0 0.525731 0.850651 0.490491 45 57.5 57.5 0 -155 1 1 0 49.5936 55.7206 58.1921 -0.0406403 0.572055 0.819208 0.490491 45 57.5 57.5 0 -156 1 1 0 50.4064 55.7206 58.1921 0.0406403 0.572055 0.819208 0.490491 45 57.5 57.5 0 -157 1 1 0 49.1891 56.1564 57.8384 -0.081086 0.615642 0.783843 0.490491 45 57.5 57.5 0 -158 1 1 0 50 56.1768 57.8643 0 0.617676 0.786433 0.490491 45 57.5 57.5 0 -159 1 1 0 50.8109 56.1564 57.8384 0.081086 0.615642 0.783843 0.490491 45 57.5 57.5 0 -160 1 1 0 48.7886 56.5628 57.4473 -0.121144 0.656282 0.744727 0.490491 45 57.5 57.5 0 -161 1 1 0 49.5936 56.6088 57.4939 -0.0406418 0.660883 0.749387 0.490491 45 57.5 57.5 0 -162 1 1 0 48.3938 56.9378 57.0205 -0.160622 0.69378 0.702047 0.490491 45 57.5 57.5 0 -163 1 1 0 49.1943 57.0062 57.0897 -0.0805729 0.700622 0.708969 0.490491 45 57.5 57.5 0 -164 1 1 0 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0.606825 0.490491 45 57.5 57.5 0 -188 1 1 0 50.4067 58.1752 55.7446 0.040675 0.817523 0.574458 0.490491 45 57.5 57.5 0 -189 1 1 0 51.1908 58.1217 55.7114 0.119078 0.81217 0.57114 0.490491 45 57.5 57.5 0 -190 1 1 0 50.7846 58.4803 55.2411 0.0784592 0.848029 0.52411 0.490491 45 57.5 57.5 0 -191 1 1 0 51.5643 58.4018 55.1926 0.156434 0.840178 0.519259 0.490491 45 57.5 57.5 0 -192 1 1 0 51.9727 58.015 55.6451 0.197274 0.801504 0.564513 0.490491 45 57.5 57.5 0 -193 1 1 0 52.7371 57.8572 55.5474 0.273706 0.785715 0.55474 0.490491 45 57.5 57.5 0 -194 1 1 0 52.3345 58.2715 55.112 0.233445 0.827147 0.511205 0.490491 45 57.5 57.5 0 -195 1 1 0 53.0902 58.0902 55 0.309017 0.809017 0.5 0.490491 45 57.5 57.5 0 -196 1 1 0 49.5932 57.435 56.675 -0.0406769 0.743496 0.667502 0.490491 45 57.5 57.5 0 -197 1 1 0 50 57.8279 56.2229 0 0.782786 0.622291 0.490491 45 57.5 57.5 0 -198 1 1 0 50.4068 57.435 56.675 0.0406769 0.743496 0.667502 0.490491 45 57.5 57.5 0 -199 1 1 0 46.5715 58.2845 54.4287 -0.342848 0.828447 0.442867 0.490491 45 57.5 57.5 0 -200 1 1 0 47.2531 58.5264 54.4446 -0.274694 0.85264 0.444464 0.490491 45 57.5 57.5 0 -201 1 1 0 46.2496 58.4391 53.8361 -0.375038 0.843912 0.383614 0.490491 45 57.5 57.5 0 -202 1 1 0 46.9234 58.6973 53.8591 -0.307659 0.869725 0.385906 0.490491 45 57.5 57.5 0 -203 1 1 0 47.6132 58.9101 53.8619 -0.238677 0.891007 0.386187 0.490491 45 57.5 57.5 0 -204 1 1 0 45.9457 58.5534 53.2252 -0.405434 0.855337 0.322525 0.490491 45 57.5 57.5 0 -205 1 1 0 46.6079 58.8284 53.2486 -0.339209 0.882837 0.324863 0.490491 45 57.5 57.5 0 -206 1 1 0 45.6611 58.6267 52.5989 -0.433888 0.862669 0.259892 0.490491 45 57.5 57.5 0 -207 1 1 0 46.3148 58.9174 52.6266 -0.368518 0.891742 0.262661 0.490491 45 57.5 57.5 0 -208 1 1 0 46.9874 59.1624 52.6408 -0.301258 0.916244 0.264082 0.490491 45 57.5 57.5 0 -209 1 1 0 47.2937 59.0583 53.2593 -0.270627 0.905832 0.325929 0.490491 45 57.5 57.5 0 -210 1 1 0 47.9881 59.2388 53.2553 -0.201189 0.92388 0.32553 0.490491 45 57.5 57.5 0 -211 1 1 0 47.6755 59.3605 52.6415 -0.232455 0.93605 0.264151 0.490491 45 57.5 57.5 0 -212 1 1 0 48.3754 59.5106 52.6287 -0.16246 0.951057 0.262865 0.490491 45 57.5 57.5 0 -213 1 1 0 45.3973 58.6587 51.9602 -0.460266 0.865871 0.196015 0.490491 45 57.5 57.5 0 -214 1 1 0 46.0265 58.964 51.9641 -0.39735 0.896401 0.196412 0.490491 45 57.5 57.5 0 -215 1 1 0 45.1556 58.6493 51.312 -0.484441 0.864929 0.1312 0.490491 45 57.5 57.5 0 -216 1 1 0 45.7764 58.968 51.3175 -0.422363 0.896801 0.131749 0.490491 45 57.5 57.5 0 -217 1 1 0 46.4177 59.243 51.3166 -0.358229 0.924305 0.131656 0.490491 45 57.5 57.5 0 -218 1 1 0 44.937 58.5985 50.6576 -0.506298 0.859848 0.0657577 0.490491 45 57.5 57.5 0 -219 1 1 0 45.5463 58.9293 50.6582 -0.445365 0.892927 0.0658169 0.490491 45 57.5 57.5 0 -220 1 1 0 46.1828 59.2192 50.6599 -0.381722 0.921919 0.0659886 0.490491 45 57.5 57.5 0 -221 1 1 0 46.8322 59.462 50.6604 -0.316778 0.946198 0.0660427 0.490491 45 57.5 57.5 0 -222 1 1 0 48.0822 59.6119 51.9834 -0.19178 0.961188 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0 52.7469 58.5264 54.4446 0.274694 0.85264 0.444464 0.490491 45 57.5 57.5 0 -235 1 1 0 53.4285 58.2845 54.4287 0.342848 0.828447 0.442867 0.490491 45 57.5 57.5 0 -236 1 1 0 52.3868 58.9101 53.8619 0.238677 0.891007 0.386187 0.490491 45 57.5 57.5 0 -237 1 1 0 53.0766 58.6973 53.8591 0.307659 0.869725 0.385906 0.490491 45 57.5 57.5 0 -238 1 1 0 53.7504 58.4391 53.8361 0.375038 0.843912 0.383614 0.490491 45 57.5 57.5 0 -239 1 1 0 52.0119 59.2388 53.2553 0.201189 0.92388 0.32553 0.490491 45 57.5 57.5 0 -240 1 1 0 52.7063 59.0583 53.2593 0.270627 0.905832 0.325929 0.490491 45 57.5 57.5 0 -241 1 1 0 51.6246 59.5106 52.6287 0.16246 0.951057 0.262865 0.490491 45 57.5 57.5 0 -242 1 1 0 52.3245 59.3605 52.6415 0.232455 0.93605 0.264151 0.490491 45 57.5 57.5 0 -243 1 1 0 53.0126 59.1624 52.6408 0.301258 0.916244 0.264082 0.490491 45 57.5 57.5 0 -244 1 1 0 53.3921 58.8284 53.2486 0.339209 0.882837 0.324863 0.490491 45 57.5 57.5 0 -245 1 1 0 54.0543 58.5534 53.2252 0.405434 0.855337 0.322525 0.490491 45 57.5 57.5 0 -246 1 1 0 53.6852 58.9174 52.6266 0.368518 0.891742 0.262661 0.490491 45 57.5 57.5 0 -247 1 1 0 54.3389 58.6267 52.5989 0.433888 0.862669 0.259892 0.490491 45 57.5 57.5 0 -248 1 1 0 51.2273 59.7237 51.9858 0.122729 0.97237 0.198581 0.490491 45 57.5 57.5 0 -249 1 1 0 51.9178 59.6119 51.9834 0.19178 0.961188 0.198337 0.490491 45 57.5 57.5 0 -250 1 1 0 50.8224 59.8769 51.3307 0.0822422 0.987688 0.133071 0.490491 45 57.5 57.5 0 -251 1 1 0 51.5155 59.7943 51.3326 0.151549 0.979426 0.133256 0.490491 45 57.5 57.5 0 -252 1 1 0 52.2012 59.6639 51.3279 0.220117 0.966393 0.132792 0.490491 45 57.5 57.5 0 -253 1 1 0 50.4125 59.9692 50.6674 0.0412479 0.996917 0.0667412 0.490491 45 57.5 57.5 0 -254 1 1 0 51.1039 59.9165 50.6671 0.110385 0.991648 0.0667095 0.490491 45 57.5 57.5 0 -255 1 1 0 51.796 59.8148 50.666 0.179596 0.981483 0.0666046 0.490491 45 57.5 57.5 0 -256 1 1 0 52.4733 59.6664 50.6657 0.247326 0.966643 0.0665668 0.490491 45 57.5 57.5 0 -257 1 1 0 53.9735 58.964 51.9641 0.39735 0.896401 0.196412 0.490491 45 57.5 57.5 0 -258 1 1 0 54.6027 58.6587 51.9602 0.460266 0.865871 0.196015 0.490491 45 57.5 57.5 0 -259 1 1 0 53.5823 59.243 51.3166 0.358229 0.924305 0.131656 0.490491 45 57.5 57.5 0 -260 1 1 0 54.2236 58.968 51.3175 0.422363 0.896801 0.131749 0.490491 45 57.5 57.5 0 -261 1 1 0 54.8444 58.6493 51.312 0.484441 0.864929 0.1312 0.490491 45 57.5 57.5 0 -262 1 1 0 53.1678 59.462 50.6604 0.316778 0.946198 0.0660427 0.490491 45 57.5 57.5 0 -263 1 1 0 53.8172 59.2192 50.6599 0.381722 0.921919 0.0659886 0.490491 45 57.5 57.5 0 -264 1 1 0 54.4537 58.9293 50.6582 0.445365 0.892927 0.0658169 0.490491 45 57.5 57.5 0 -265 1 1 0 55.063 58.5985 50.6576 0.506298 0.859848 0.0657577 0.490491 45 57.5 57.5 0 -266 1 1 0 52.6155 59.4443 51.9909 0.26155 0.944433 0.199094 0.490491 45 57.5 57.5 0 -267 1 1 0 52.8993 59.4782 51.3257 0.289929 0.947822 0.13257 0.490491 45 57.5 57.5 0 -268 1 1 0 53.3061 59.2268 51.9839 0.330606 0.922682 0.198387 0.490491 45 57.5 57.5 0 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57.5 57.5 0 -281 1 1 0 50.413 58.8476 54.6421 0.0412991 0.88476 0.464213 0.490491 45 57.5 57.5 0 -282 1 1 0 50.8232 59.1298 53.9961 0.0823235 0.912983 0.399607 0.490491 45 57.5 57.5 0 -283 1 1 0 51.1976 58.7934 54.6088 0.119755 0.879344 0.460882 0.490491 45 57.5 57.5 0 -284 1 1 0 51.228 59.3513 53.3234 0.1228 0.93513 0.332342 0.490491 45 57.5 57.5 0 -285 1 1 0 51.6101 59.0484 53.9414 0.161007 0.904839 0.394136 0.490491 45 57.5 57.5 0 -286 1 1 0 51.9823 58.6853 54.5426 0.198227 0.868535 0.454262 0.490491 45 57.5 57.5 0 -287 1 1 0 49.587 59.4162 53.3414 -0.0413021 0.941618 0.33414 0.490491 45 57.5 57.5 0 -288 1 1 0 50.413 59.4162 53.3414 0.0413021 0.941618 0.33414 0.490491 45 57.5 57.5 0 -289 1 1 0 50 59.1609 54.0097 0 0.916092 0.400968 0.490491 45 57.5 57.5 0 -290 1 1 0 50 54.6566 58.8497 0 0.465657 0.884965 0.490491 45 57.5 57.5 0 -291 1 1 0 49.3424 55.063 58.5985 -0.0657577 0.506298 0.859848 0.490491 45 57.5 57.5 0 -292 1 1 0 50 54.0336 59.1504 0 0.403355 0.915043 0.490491 45 57.5 57.5 0 -293 1 1 0 49.3418 54.4537 58.9293 -0.0658169 0.445365 0.892927 0.490491 45 57.5 57.5 0 -294 1 1 0 48.688 54.8444 58.6493 -0.1312 0.484441 0.864929 0.490491 45 57.5 57.5 0 -295 1 1 0 50 53.3912 59.4074 0 0.339122 0.940742 0.490491 45 57.5 57.5 0 -296 1 1 0 49.3401 53.8172 59.2192 -0.0659885 0.381722 0.921919 0.490491 45 57.5 57.5 0 -297 1 1 0 50 52.7327 59.6194 0 0.273267 0.961938 0.490491 45 57.5 57.5 0 -298 1 1 0 49.3396 53.1678 59.462 -0.0660427 0.316778 0.946198 0.490491 45 57.5 57.5 0 -299 1 1 0 48.6834 53.5823 59.243 -0.131656 0.358229 0.924305 0.490491 45 57.5 57.5 0 -300 1 1 0 48.6825 54.2236 58.968 -0.131749 0.422363 0.896801 0.490491 45 57.5 57.5 0 -301 1 1 0 48.0398 54.6027 58.6587 -0.196015 0.460266 0.865871 0.490491 45 57.5 57.5 0 -302 1 1 0 48.0359 53.9735 58.964 -0.196412 0.39735 0.896401 0.490491 45 57.5 57.5 0 -303 1 1 0 47.4011 54.3389 58.6267 -0.259892 0.433888 0.862669 0.490491 45 57.5 57.5 0 -304 1 1 0 50 52.061 59.7853 0 0.206103 0.97853 0.490491 45 57.5 57.5 0 -305 1 1 0 49.3343 52.4733 59.6664 -0.0665668 0.247326 0.966643 0.490491 45 57.5 57.5 0 -306 1 1 0 50 51.3795 59.9044 0 0.137952 0.990439 0.490491 45 57.5 57.5 0 -307 1 1 0 49.334 51.796 59.8148 -0.0666046 0.179596 0.981483 0.490491 45 57.5 57.5 0 -308 1 1 0 48.6721 52.2012 59.6639 -0.132792 0.220117 0.966393 0.490491 45 57.5 57.5 0 -309 1 1 0 50 50.6914 59.9761 0 0.0691418 0.997607 0.490491 45 57.5 57.5 0 -310 1 1 0 49.3329 51.1039 59.9165 -0.0667095 0.110385 0.991648 0.490491 45 57.5 57.5 0 -311 1 1 0 50 50 60 0 0 1 0.490491 45 57.5 57.5 0 -312 1 1 0 49.3326 50.4125 59.9692 -0.0667412 0.0412479 0.996917 0.490491 45 57.5 57.5 0 -313 1 1 0 48.6693 50.8224 59.8769 -0.133071 0.0822422 0.987688 0.490491 45 57.5 57.5 0 -314 1 1 0 48.6674 51.5155 59.7943 -0.133256 0.151549 0.979426 0.490491 45 57.5 57.5 0 -315 1 1 0 48.0166 51.9178 59.6119 -0.198337 0.19178 0.961188 0.490491 45 57.5 57.5 0 -316 1 1 0 48.0142 51.2273 59.7237 -0.198581 0.122729 0.97237 0.490491 45 57.5 57.5 0 -317 1 1 0 47.3713 51.6246 59.5106 -0.262865 0.16246 0.951057 0.490491 45 57.5 57.5 0 -318 1 1 0 47.3734 53.6852 58.9174 -0.262661 0.368518 0.891742 0.490491 45 57.5 57.5 0 -319 1 1 0 46.7748 54.0543 58.5534 -0.322525 0.405434 0.855337 0.490491 45 57.5 57.5 0 -320 1 1 0 47.3592 53.0126 59.1624 -0.264082 0.301258 0.916244 0.490491 45 57.5 57.5 0 -321 1 1 0 46.7514 53.3921 58.8284 -0.324863 0.339209 0.882837 0.490491 45 57.5 57.5 0 -322 1 1 0 46.1639 53.7504 58.4391 -0.383614 0.375038 0.843912 0.490491 45 57.5 57.5 0 -323 1 1 0 47.3585 52.3245 59.3605 -0.264151 0.232455 0.93605 0.490491 45 57.5 57.5 0 -324 1 1 0 46.7407 52.7063 59.0583 -0.325929 0.270627 0.905832 0.490491 45 57.5 57.5 0 -325 1 1 0 46.7447 52.0119 59.2388 -0.32553 0.201189 0.92388 0.490491 45 57.5 57.5 0 -326 1 1 0 46.1381 52.3868 58.9101 -0.386187 0.238677 0.891007 0.490491 45 57.5 57.5 0 -327 1 1 0 46.1409 53.0766 58.6973 -0.385906 0.307659 0.869725 0.490491 45 57.5 57.5 0 -328 1 1 0 45.5713 53.4285 58.2845 -0.442867 0.342848 0.828447 0.490491 45 57.5 57.5 0 -329 1 1 0 45.5554 52.7469 58.5264 -0.444464 0.274694 0.85264 0.490491 45 57.5 57.5 0 -330 1 1 0 45 53.0902 58.0902 -0.5 0.309017 0.809017 0.490491 45 57.5 57.5 0 -331 1 1 0 48.6743 52.8993 59.4782 -0.13257 0.289929 0.947822 0.490491 45 57.5 57.5 0 -332 1 1 0 48.0091 52.6155 59.4443 -0.199094 0.26155 0.944433 0.490491 45 57.5 57.5 0 -333 1 1 0 48.0161 53.3061 59.2268 -0.198387 0.330606 0.922682 0.490491 45 57.5 57.5 0 -334 1 1 0 50 49.3086 59.9761 0 -0.0691418 0.997607 0.490491 45 57.5 57.5 0 -335 1 1 0 49.3326 49.5875 59.9692 -0.0667412 -0.0412479 0.996917 0.490491 45 57.5 57.5 0 -336 1 1 0 50 48.6205 59.9044 0 -0.137952 0.990439 0.490491 45 57.5 57.5 0 -337 1 1 0 49.3329 48.8961 59.9165 -0.0667095 -0.110385 0.991648 0.490491 45 57.5 57.5 0 -338 1 1 0 48.6693 49.1776 59.8769 -0.133071 -0.0822422 0.987688 0.490491 45 57.5 57.5 0 -339 1 1 0 50 47.939 59.7853 0 -0.206103 0.97853 0.490491 45 57.5 57.5 0 -340 1 1 0 49.334 48.204 59.8148 -0.0666046 -0.179596 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47.3592 46.9874 59.1624 -0.264082 -0.301258 0.916244 0.490491 45 57.5 57.5 0 -365 1 1 0 46.7407 47.2937 59.0583 -0.325929 -0.270627 0.905832 0.490491 45 57.5 57.5 0 -366 1 1 0 46.1381 47.6132 58.9101 -0.386187 -0.238677 0.891007 0.490491 45 57.5 57.5 0 -367 1 1 0 47.3734 46.3148 58.9174 -0.262661 -0.368518 0.891742 0.490491 45 57.5 57.5 0 -368 1 1 0 46.7514 46.6079 58.8284 -0.324863 -0.339209 0.882837 0.490491 45 57.5 57.5 0 -369 1 1 0 46.7748 45.9457 58.5534 -0.322525 -0.405434 0.855337 0.490491 45 57.5 57.5 0 -370 1 1 0 46.1639 46.2496 58.4391 -0.383614 -0.375038 0.843912 0.490491 45 57.5 57.5 0 -371 1 1 0 46.1409 46.9234 58.6973 -0.385906 -0.307659 0.869725 0.490491 45 57.5 57.5 0 -372 1 1 0 45.5554 47.2531 58.5264 -0.444464 -0.274694 0.85264 0.490491 45 57.5 57.5 0 -373 1 1 0 45.5713 46.5715 58.2845 -0.442867 -0.342848 0.828447 0.490491 45 57.5 57.5 0 -374 1 1 0 45 46.9098 58.0902 -0.5 -0.309017 0.809017 0.490491 45 57.5 57.5 0 -375 1 1 0 48.6743 47.1007 59.4782 -0.13257 -0.289929 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57.802 -0.620239 0.0811417 0.780205 0.490491 45 57.5 57.5 0 -388 1 1 0 43.8454 51.5961 57.7184 -0.615456 0.159613 0.771841 0.490491 45 57.5 57.5 0 -389 1 1 0 43.4399 51.9933 57.2796 -0.656006 0.199331 0.727959 0.490491 45 57.5 57.5 0 -390 1 1 0 43.3716 51.2119 57.3889 -0.662842 0.121192 0.738887 0.490491 45 57.5 57.5 0 -391 1 1 0 42.9795 51.6062 56.9378 -0.702047 0.160622 0.69378 0.490491 45 57.5 57.5 0 -392 1 1 0 44.7589 49.2154 58.4803 -0.52411 -0.0784592 0.848029 0.490491 45 57.5 57.5 0 -393 1 1 0 44.2554 49.5933 58.1752 -0.574458 -0.040675 0.817523 0.490491 45 57.5 57.5 0 -394 1 1 0 44.8074 48.4357 58.4018 -0.519259 -0.156434 0.840178 0.490491 45 57.5 57.5 0 -395 1 1 0 44.2886 48.8092 58.1217 -0.57114 -0.119078 0.81217 0.490491 45 57.5 57.5 0 -396 1 1 0 43.7976 49.1886 57.802 -0.620239 -0.0811417 0.780205 0.490491 45 57.5 57.5 0 -397 1 1 0 44.888 47.6655 58.2715 -0.511205 -0.233445 0.827147 0.490491 45 57.5 57.5 0 -398 1 1 0 44.3549 48.0273 58.015 -0.564513 -0.197274 0.801504 0.490491 45 57.5 57.5 0 -399 1 1 0 44.4526 47.2629 57.8572 -0.55474 -0.273706 0.785715 0.490491 45 57.5 57.5 0 -400 1 1 0 43.9317 47.6291 57.5865 -0.606825 -0.237086 0.758652 0.490491 45 57.5 57.5 0 -401 1 1 0 43.8454 48.4039 57.7184 -0.615456 -0.159613 0.771841 0.490491 45 57.5 57.5 0 -402 1 1 0 43.3716 48.7881 57.3889 -0.662842 -0.121192 0.738887 0.490491 45 57.5 57.5 0 -403 1 1 0 43.4399 48.0067 57.2796 -0.656006 -0.199331 0.727959 0.490491 45 57.5 57.5 0 -404 1 1 0 42.9795 48.3938 56.9378 -0.702047 -0.160622 0.69378 0.490491 45 57.5 57.5 0 -405 1 1 0 42.9103 50.8057 57.0062 -0.708969 0.0805729 0.700622 0.490491 45 57.5 57.5 0 -406 1 1 0 42.5527 51.2114 56.5628 -0.744727 0.121144 0.656282 0.490491 45 57.5 57.5 0 -407 1 1 0 42.8872 50 57.0291 -0.711282 0 0.702907 0.490491 45 57.5 57.5 0 -408 1 1 0 42.5061 50.4064 56.6088 -0.749387 0.0406418 0.660883 0.490491 45 57.5 57.5 0 -409 1 1 0 42.1616 50.8109 56.1564 -0.783843 0.081086 0.615642 0.490491 45 57.5 57.5 0 -410 1 1 0 42.9103 49.1943 57.0062 -0.708969 -0.0805729 0.700622 0.490491 45 57.5 57.5 0 -411 1 1 0 42.5061 49.5936 56.6088 -0.749387 -0.0406418 0.660883 0.490491 45 57.5 57.5 0 -412 1 1 0 42.5527 48.7886 56.5628 -0.744727 -0.121144 0.656282 0.490491 45 57.5 57.5 0 -413 1 1 0 42.1616 49.1891 56.1564 -0.783843 -0.081086 0.615642 0.490491 45 57.5 57.5 0 -414 1 1 0 42.1357 50 56.1768 -0.786433 0 0.617676 0.490491 45 57.5 57.5 0 -415 1 1 0 41.8079 50.4064 55.7206 -0.819207 0.0406403 0.572055 0.490491 45 57.5 57.5 0 -416 1 1 0 41.8079 49.5936 55.7206 -0.819207 -0.0406403 0.572055 0.490491 45 57.5 57.5 0 -417 1 1 0 41.4935 50 55.2573 -0.850651 0 0.525731 0.490491 45 57.5 57.5 0 -418 1 1 0 43.7771 50 57.8279 -0.622291 0 0.782786 0.490491 45 57.5 57.5 0 -419 1 1 0 43.325 49.5932 57.435 -0.667502 -0.0406769 0.743496 0.490491 45 57.5 57.5 0 -420 1 1 0 43.325 50.4068 57.435 -0.667502 0.0406769 0.743496 0.490491 45 57.5 57.5 0 -421 1 1 0 48.6648 50 59.9105 -0.133524 0 0.991046 0.490491 45 57.5 57.5 0 -422 1 1 0 47.9963 49.5875 59.7885 -0.200368 -0.0412506 0.978852 0.490491 45 57.5 57.5 0 -423 1 1 0 47.3448 49.185 59.6065 -0.265519 -0.081501 0.960655 0.490491 45 57.5 57.5 0 -424 1 1 0 47.336 50 59.6386 -0.266405 0 0.963861 0.490491 45 57.5 57.5 0 -425 1 1 0 47.9963 50.4125 59.7885 -0.200368 0.0412506 0.978852 0.490491 45 57.5 57.5 0 -426 1 1 0 47.3448 50.815 59.6065 -0.265519 0.081501 0.960655 0.490491 45 57.5 57.5 0 -427 1 1 0 46.6766 48.772 59.3513 -0.332342 -0.1228 0.93513 0.490491 45 57.5 57.5 0 -428 1 1 0 46.0586 48.3899 59.0484 -0.394136 -0.161007 0.904839 0.490491 45 57.5 57.5 0 -429 1 1 0 46.0039 49.1768 59.1298 -0.399607 -0.0823235 0.912983 0.490491 45 57.5 57.5 0 -430 1 1 0 45.4574 48.0177 58.6853 -0.454262 -0.198227 0.868535 0.490491 45 57.5 57.5 0 -431 1 1 0 45.3912 48.8024 58.7934 -0.460882 -0.119755 0.879344 0.490491 45 57.5 57.5 0 -432 1 1 0 45.3579 49.587 58.8476 -0.464213 -0.0412991 0.88476 0.490491 45 57.5 57.5 0 -433 1 1 0 46.6766 51.228 59.3513 -0.332342 0.1228 0.93513 0.490491 45 57.5 57.5 0 -434 1 1 0 46.0039 50.8232 59.1298 -0.399607 0.0823235 0.912983 0.490491 45 57.5 57.5 0 -435 1 1 0 46.0586 51.6101 59.0484 -0.394136 0.161007 0.904839 0.490491 45 57.5 57.5 0 -436 1 1 0 45.3579 50.413 58.8476 -0.464213 0.0412991 0.88476 0.490491 45 57.5 57.5 0 -437 1 1 0 45.3912 51.1976 58.7934 -0.460882 0.119755 0.879344 0.490491 45 57.5 57.5 0 -438 1 1 0 45.4574 51.9823 58.6853 -0.454262 0.198227 0.868535 0.490491 45 57.5 57.5 0 -439 1 1 0 46.6586 49.587 59.4162 -0.33414 -0.0413021 0.941618 0.490491 45 57.5 57.5 0 -440 1 1 0 45.9903 50 59.1609 -0.400968 0 0.916092 0.490491 45 57.5 57.5 0 -441 1 1 0 46.6586 50.413 59.4162 -0.33414 0.0413021 0.941618 0.490491 45 57.5 57.5 0 -442 1 1 0 50.6576 55.063 58.5985 0.0657577 0.506298 0.859848 0.490491 45 57.5 57.5 0 -443 1 1 0 51.312 54.8444 58.6493 0.1312 0.484441 0.864929 0.490491 45 57.5 57.5 0 -444 1 1 0 50.6582 54.4537 58.9293 0.0658169 0.445365 0.892927 0.490491 45 57.5 57.5 0 -445 1 1 0 51.9602 54.6027 58.6587 0.196015 0.460266 0.865871 0.490491 45 57.5 57.5 0 -446 1 1 0 51.3175 54.2236 58.968 0.131749 0.422363 0.896801 0.490491 45 57.5 57.5 0 -447 1 1 0 52.5989 54.3389 58.6267 0.259892 0.433888 0.862669 0.490491 45 57.5 57.5 0 -448 1 1 0 51.9641 53.9735 58.964 0.196412 0.39735 0.896401 0.490491 45 57.5 57.5 0 -449 1 1 0 51.3166 53.5823 59.243 0.131656 0.358229 0.924305 0.490491 45 57.5 57.5 0 -450 1 1 0 50.6599 53.8172 59.2192 0.0659885 0.381722 0.921919 0.490491 45 57.5 57.5 0 -451 1 1 0 50.6604 53.1678 59.462 0.0660427 0.316778 0.946198 0.490491 45 57.5 57.5 0 -452 1 1 0 53.2252 54.0543 58.5534 0.322525 0.405434 0.855337 0.490491 45 57.5 57.5 0 -453 1 1 0 52.6266 53.6852 58.9174 0.262661 0.368518 0.891742 0.490491 45 57.5 57.5 0 -454 1 1 0 53.8361 53.7504 58.4391 0.383614 0.375038 0.843912 0.490491 45 57.5 57.5 0 -455 1 1 0 53.2486 53.3921 58.8284 0.324863 0.339209 0.882837 0.490491 45 57.5 57.5 0 -456 1 1 0 52.6408 53.0126 59.1624 0.264082 0.301258 0.916244 0.490491 45 57.5 57.5 0 -457 1 1 0 54.4287 53.4285 58.2845 0.442867 0.342848 0.828447 0.490491 45 57.5 57.5 0 -458 1 1 0 53.8591 53.0766 58.6973 0.385906 0.307659 0.869725 0.490491 45 57.5 57.5 0 -459 1 1 0 55 53.0902 58.0902 0.5 0.309017 0.809017 0.490491 45 57.5 57.5 0 -460 1 1 0 54.4446 52.7469 58.5264 0.444464 0.274694 0.85264 0.490491 45 57.5 57.5 0 -461 1 1 0 53.8619 52.3868 58.9101 0.386187 0.238677 0.891007 0.490491 45 57.5 57.5 0 -462 1 1 0 53.2593 52.7063 59.0583 0.325929 0.270627 0.905832 0.490491 45 57.5 57.5 0 -463 1 1 0 52.6415 52.3245 59.3605 0.264151 0.232455 0.93605 0.490491 45 57.5 57.5 0 -464 1 1 0 53.2553 52.0119 59.2388 0.32553 0.201189 0.92388 0.490491 45 57.5 57.5 0 -465 1 1 0 52.6287 51.6246 59.5106 0.262865 0.16246 0.951057 0.490491 45 57.5 57.5 0 -466 1 1 0 50.6657 52.4733 59.6664 0.0665668 0.247326 0.966643 0.490491 45 57.5 57.5 0 -467 1 1 0 51.3279 52.2012 59.6639 0.132792 0.220117 0.966393 0.490491 45 57.5 57.5 0 -468 1 1 0 50.666 51.796 59.8148 0.0666046 0.179596 0.981483 0.490491 45 57.5 57.5 0 -469 1 1 0 51.9834 51.9178 59.6119 0.198337 0.19178 0.961188 0.490491 45 57.5 57.5 0 -470 1 1 0 51.3326 51.5155 59.7943 0.133256 0.151549 0.979426 0.490491 45 57.5 57.5 0 -471 1 1 0 51.9858 51.2273 59.7237 0.198581 0.122729 0.97237 0.490491 45 57.5 57.5 0 -472 1 1 0 51.3307 50.8224 59.8769 0.133071 0.0822422 0.987688 0.490491 45 57.5 57.5 0 -473 1 1 0 50.6671 51.1039 59.9165 0.0667095 0.110385 0.991648 0.490491 45 57.5 57.5 0 -474 1 1 0 50.6674 50.4125 59.9692 0.0667412 0.0412479 0.996917 0.490491 45 57.5 57.5 0 -475 1 1 0 51.9839 53.3061 59.2268 0.198387 0.330606 0.922682 0.490491 45 57.5 57.5 0 -476 1 1 0 51.9909 52.6155 59.4443 0.199094 0.26155 0.944433 0.490491 45 57.5 57.5 0 -477 1 1 0 51.3257 52.8993 59.4782 0.13257 0.289929 0.947822 0.490491 45 57.5 57.5 0 -478 1 1 0 55.5474 52.7371 57.8572 0.55474 0.273706 0.785715 0.490491 45 57.5 57.5 0 -479 1 1 0 55.112 52.3345 58.2715 0.511205 0.233445 0.827147 0.490491 45 57.5 57.5 0 -480 1 1 0 56.0683 52.3709 57.5865 0.606825 0.237086 0.758652 0.490491 45 57.5 57.5 0 -481 1 1 0 55.6451 51.9727 58.015 0.564513 0.197274 0.801504 0.490491 45 57.5 57.5 0 -482 1 1 0 55.1926 51.5643 58.4018 0.519259 0.156434 0.840178 0.490491 45 57.5 57.5 0 -483 1 1 0 56.5601 51.9933 57.2796 0.656006 0.199331 0.727959 0.490491 45 57.5 57.5 0 -484 1 1 0 56.1546 51.5961 57.7184 0.615456 0.159613 0.771841 0.490491 45 57.5 57.5 0 -485 1 1 0 57.0205 51.6062 56.9378 0.702047 0.160622 0.69378 0.490491 45 57.5 57.5 0 -486 1 1 0 56.6284 51.2119 57.3889 0.662842 0.121192 0.738887 0.490491 45 57.5 57.5 0 -487 1 1 0 56.2024 50.8114 57.802 0.620239 0.0811417 0.780205 0.490491 45 57.5 57.5 0 -488 1 1 0 55.7114 51.1908 58.1217 0.57114 0.119078 0.81217 0.490491 45 57.5 57.5 0 -489 1 1 0 55.2411 50.7846 58.4803 0.52411 0.0784592 0.848029 0.490491 45 57.5 57.5 0 -490 1 1 0 55.7446 50.4067 58.1752 0.574458 0.040675 0.817523 0.490491 45 57.5 57.5 0 -491 1 1 0 55.2573 50 58.5065 0.525731 0 0.850651 0.490491 45 57.5 57.5 0 -492 1 1 0 57.4473 51.2114 56.5628 0.744727 0.121144 0.656282 0.490491 45 57.5 57.5 0 -493 1 1 0 57.0897 50.8057 57.0062 0.708969 0.0805729 0.700622 0.490491 45 57.5 57.5 0 -494 1 1 0 57.8384 50.8109 56.1564 0.783843 0.081086 0.615642 0.490491 45 57.5 57.5 0 -495 1 1 0 57.4939 50.4064 56.6088 0.749387 0.0406418 0.660883 0.490491 45 57.5 57.5 0 -496 1 1 0 57.1128 50 57.0291 0.711282 0 0.702907 0.490491 45 57.5 57.5 0 -497 1 1 0 58.1921 50.4064 55.7206 0.819207 0.0406403 0.572055 0.490491 45 57.5 57.5 0 -498 1 1 0 57.8643 50 56.1768 0.786433 0 0.617676 0.490491 45 57.5 57.5 0 -499 1 1 0 58.5065 50 55.2573 0.850651 0 0.525731 0.490491 45 57.5 57.5 0 -500 1 1 0 58.1921 49.5936 55.7206 0.819207 -0.0406403 0.572055 0.490491 45 57.5 57.5 0 -501 1 1 0 57.8384 49.1891 56.1564 0.783843 -0.081086 0.615642 0.490491 45 57.5 57.5 0 -502 1 1 0 57.4939 49.5936 56.6088 0.749387 -0.0406418 0.660883 0.490491 45 57.5 57.5 0 -503 1 1 0 57.0897 49.1943 57.0062 0.708969 -0.0805729 0.700622 0.490491 45 57.5 57.5 0 -504 1 1 0 57.4473 48.7886 56.5628 0.744727 -0.121144 0.656282 0.490491 45 57.5 57.5 0 -505 1 1 0 57.0205 48.3938 56.9378 0.702047 -0.160622 0.69378 0.490491 45 57.5 57.5 0 -506 1 1 0 55.7446 49.5933 58.1752 0.574458 -0.040675 0.817523 0.490491 45 57.5 57.5 0 -507 1 1 0 55.2411 49.2154 58.4803 0.52411 -0.0784592 0.848029 0.490491 45 57.5 57.5 0 -508 1 1 0 56.2024 49.1886 57.802 0.620239 -0.0811417 0.780205 0.490491 45 57.5 57.5 0 -509 1 1 0 55.7114 48.8092 58.1217 0.57114 -0.119078 0.81217 0.490491 45 57.5 57.5 0 -510 1 1 0 55.1926 48.4357 58.4018 0.519259 -0.156434 0.840178 0.490491 45 57.5 57.5 0 -511 1 1 0 56.6284 48.7881 57.3889 0.662842 -0.121192 0.738887 0.490491 45 57.5 57.5 0 -512 1 1 0 56.1546 48.4039 57.7184 0.615456 -0.159613 0.771841 0.490491 45 57.5 57.5 0 -513 1 1 0 56.5601 48.0067 57.2796 0.656006 -0.199331 0.727959 0.490491 45 57.5 57.5 0 -514 1 1 0 56.0683 47.6291 57.5865 0.606825 -0.237086 0.758652 0.490491 45 57.5 57.5 0 -515 1 1 0 55.6451 48.0273 58.015 0.564513 -0.197274 0.801504 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1 0 54.4287 46.5715 58.2845 0.442867 -0.342848 0.828447 0.490491 45 57.5 57.5 0 -540 1 1 0 53.8361 46.2496 58.4391 0.383614 -0.375038 0.843912 0.490491 45 57.5 57.5 0 -541 1 1 0 53.2486 46.6079 58.8284 0.324863 -0.339209 0.882837 0.490491 45 57.5 57.5 0 -542 1 1 0 52.6266 46.3148 58.9174 0.262661 -0.368518 0.891742 0.490491 45 57.5 57.5 0 -543 1 1 0 53.2252 45.9457 58.5534 0.322525 -0.405434 0.855337 0.490491 45 57.5 57.5 0 -544 1 1 0 52.5989 45.6611 58.6267 0.259892 -0.433888 0.862669 0.490491 45 57.5 57.5 0 -545 1 1 0 50.6604 46.8322 59.462 0.0660427 -0.316778 0.946198 0.490491 45 57.5 57.5 0 -546 1 1 0 51.3166 46.4177 59.243 0.131656 -0.358229 0.924305 0.490491 45 57.5 57.5 0 -547 1 1 0 50.6599 46.1828 59.2192 0.0659885 -0.381722 0.921919 0.490491 45 57.5 57.5 0 -548 1 1 0 51.9641 46.0265 58.964 0.196412 -0.39735 0.896401 0.490491 45 57.5 57.5 0 -549 1 1 0 51.3175 45.7764 58.968 0.131749 -0.422363 0.896801 0.490491 45 57.5 57.5 0 -550 1 1 0 51.9602 45.3973 58.6587 0.196015 -0.460266 0.865871 0.490491 45 57.5 57.5 0 -551 1 1 0 51.312 45.1556 58.6493 0.1312 -0.484441 0.864929 0.490491 45 57.5 57.5 0 -552 1 1 0 50.6582 45.5463 58.9293 0.0658169 -0.445365 0.892927 0.490491 45 57.5 57.5 0 -553 1 1 0 50.6576 44.937 58.5985 0.0657577 -0.506298 0.859848 0.490491 45 57.5 57.5 0 -554 1 1 0 51.9909 47.3845 59.4443 0.199094 -0.26155 0.944433 0.490491 45 57.5 57.5 0 -555 1 1 0 51.9839 46.6939 59.2268 0.198387 -0.330606 0.922682 0.490491 45 57.5 57.5 0 -556 1 1 0 51.3257 47.1007 59.4782 0.13257 -0.289929 0.947822 0.490491 45 57.5 57.5 0 -557 1 1 0 54.5426 51.9823 58.6853 0.454262 0.198227 0.868535 0.490491 45 57.5 57.5 0 -558 1 1 0 54.6088 51.1976 58.7934 0.460882 0.119755 0.879344 0.490491 45 57.5 57.5 0 -559 1 1 0 54.6421 50.413 58.8476 0.464213 0.0412991 0.88476 0.490491 45 57.5 57.5 0 -560 1 1 0 53.9961 50.8232 59.1298 0.399607 0.0823235 0.912983 0.490491 45 57.5 57.5 0 -561 1 1 0 53.9414 51.6101 59.0484 0.394136 0.161007 0.904839 0.490491 45 57.5 57.5 0 -562 1 1 0 53.3234 51.228 59.3513 0.332342 0.1228 0.93513 0.490491 45 57.5 57.5 0 -563 1 1 0 54.6421 49.587 58.8476 0.464213 -0.0412991 0.88476 0.490491 45 57.5 57.5 0 -564 1 1 0 54.6088 48.8024 58.7934 0.460882 -0.119755 0.879344 0.490491 45 57.5 57.5 0 -565 1 1 0 53.9961 49.1768 59.1298 0.399607 -0.0823235 0.912983 0.490491 45 57.5 57.5 0 -566 1 1 0 54.5426 48.0177 58.6853 0.454262 -0.198227 0.868535 0.490491 45 57.5 57.5 0 -567 1 1 0 53.9414 48.3899 59.0484 0.394136 -0.161007 0.904839 0.490491 45 57.5 57.5 0 -568 1 1 0 53.3234 48.772 59.3513 0.332342 -0.1228 0.93513 0.490491 45 57.5 57.5 0 -569 1 1 0 52.6552 50.815 59.6065 0.265519 0.081501 0.960655 0.490491 45 57.5 57.5 0 -570 1 1 0 52.664 50 59.6386 0.266405 0 0.963861 0.490491 45 57.5 57.5 0 -571 1 1 0 52.0037 50.4125 59.7885 0.200368 0.0412506 0.978852 0.490491 45 57.5 57.5 0 -572 1 1 0 52.6552 49.185 59.6065 0.265519 -0.081501 0.960655 0.490491 45 57.5 57.5 0 -573 1 1 0 52.0037 49.5875 59.7885 0.200368 -0.0412506 0.978852 0.490491 45 57.5 57.5 0 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0.0660427 0.316778 -0.946198 0.490491 45 57.5 57.5 0 -587 1 1 0 51.3166 53.5823 40.757 0.131656 0.358229 -0.924305 0.490491 45 57.5 57.5 0 -588 1 1 0 51.3175 54.2236 41.032 0.131749 0.422363 -0.896801 0.490491 45 57.5 57.5 0 -589 1 1 0 51.9602 54.6027 41.3413 0.196015 0.460266 -0.865871 0.490491 45 57.5 57.5 0 -590 1 1 0 51.9641 53.9735 41.036 0.196412 0.39735 -0.896401 0.490491 45 57.5 57.5 0 -591 1 1 0 52.5989 54.3389 41.3733 0.259892 0.433888 -0.862669 0.490491 45 57.5 57.5 0 -592 1 1 0 50 52.061 40.2147 0 0.206103 -0.97853 0.490491 45 57.5 57.5 0 -593 1 1 0 50.6657 52.4733 40.3336 0.0665668 0.247326 -0.966643 0.490491 45 57.5 57.5 0 -594 1 1 0 50 51.3795 40.0956 0 0.137952 -0.990439 0.490491 45 57.5 57.5 0 -595 1 1 0 50.666 51.796 40.1852 0.0666046 0.179596 -0.981483 0.490491 45 57.5 57.5 0 -596 1 1 0 51.3279 52.2012 40.3361 0.132792 0.220117 -0.966393 0.490491 45 57.5 57.5 0 -597 1 1 0 50 50.6914 40.0239 0 0.0691418 -0.997607 0.490491 45 57.5 57.5 0 -598 1 1 0 50.6671 51.1039 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57.5 57.5 0 -899 1 1 0 49.5933 41.8248 55.7446 -0.040675 -0.817523 0.574458 0.490491 45 57.5 57.5 0 -900 1 1 0 48.8092 41.8783 55.7114 -0.119078 -0.81217 0.57114 0.490491 45 57.5 57.5 0 -901 1 1 0 49.2154 41.5197 55.2411 -0.0784592 -0.848029 0.52411 0.490491 45 57.5 57.5 0 -902 1 1 0 48.4357 41.5982 55.1926 -0.156434 -0.840178 0.519259 0.490491 45 57.5 57.5 0 -903 1 1 0 48.0273 41.985 55.6451 -0.197274 -0.801504 0.564513 0.490491 45 57.5 57.5 0 -904 1 1 0 47.2629 42.1428 55.5474 -0.273706 -0.785715 0.55474 0.490491 45 57.5 57.5 0 -905 1 1 0 47.6655 41.7285 55.112 -0.233445 -0.827147 0.511205 0.490491 45 57.5 57.5 0 -906 1 1 0 46.9098 41.9098 55 -0.309017 -0.809017 0.5 0.490491 45 57.5 57.5 0 -907 1 1 0 50.4068 42.565 56.675 0.0406769 -0.743496 0.667502 0.490491 45 57.5 57.5 0 -908 1 1 0 50 42.1721 56.2229 0 -0.782786 0.622291 0.490491 45 57.5 57.5 0 -909 1 1 0 49.5932 42.565 56.675 -0.0406769 -0.743496 0.667502 0.490491 45 57.5 57.5 0 -910 1 1 0 53.4285 41.7155 54.4287 0.342848 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-922 1 1 0 52.3245 40.6395 52.6415 0.232455 -0.93605 0.264151 0.490491 45 57.5 57.5 0 -923 1 1 0 51.6246 40.4894 52.6287 0.16246 -0.951057 0.262865 0.490491 45 57.5 57.5 0 -924 1 1 0 54.6027 41.3413 51.9602 0.460266 -0.865871 0.196015 0.490491 45 57.5 57.5 0 -925 1 1 0 53.9735 41.036 51.9641 0.39735 -0.896401 0.196412 0.490491 45 57.5 57.5 0 -926 1 1 0 54.8444 41.3507 51.312 0.484441 -0.864929 0.1312 0.490491 45 57.5 57.5 0 -927 1 1 0 54.2236 41.032 51.3175 0.422363 -0.896801 0.131749 0.490491 45 57.5 57.5 0 -928 1 1 0 53.5823 40.757 51.3166 0.358229 -0.924305 0.131656 0.490491 45 57.5 57.5 0 -929 1 1 0 55.063 41.4015 50.6576 0.506298 -0.859848 0.0657577 0.490491 45 57.5 57.5 0 -930 1 1 0 54.4537 41.0707 50.6582 0.445365 -0.892927 0.0658169 0.490491 45 57.5 57.5 0 -931 1 1 0 55.2573 41.4935 50 0.525731 -0.850651 0 0.490491 45 57.5 57.5 0 -932 1 1 0 54.6566 41.1503 50 0.465657 -0.884965 0 0.490491 45 57.5 57.5 0 -933 1 1 0 54.0336 40.8496 50 0.403355 -0.915043 0 0.490491 45 57.5 57.5 0 -934 1 1 0 53.8172 40.7808 50.6599 0.381722 -0.921919 0.0659886 0.490491 45 57.5 57.5 0 -935 1 1 0 53.1678 40.538 50.6604 0.316778 -0.946198 0.0660427 0.490491 45 57.5 57.5 0 -936 1 1 0 53.3912 40.5926 50 0.339122 -0.940742 0 0.490491 45 57.5 57.5 0 -937 1 1 0 52.7327 40.3806 50 0.273267 -0.961938 0 0.490491 45 57.5 57.5 0 -938 1 1 0 51.9178 40.3881 51.9834 0.19178 -0.961188 0.198337 0.490491 45 57.5 57.5 0 -939 1 1 0 51.2273 40.2763 51.9858 0.122729 -0.97237 0.198581 0.490491 45 57.5 57.5 0 -940 1 1 0 52.2012 40.3361 51.3279 0.220117 -0.966393 0.132792 0.490491 45 57.5 57.5 0 -941 1 1 0 51.5155 40.2057 51.3326 0.151549 -0.979426 0.133256 0.490491 45 57.5 57.5 0 -942 1 1 0 50.8224 40.1231 51.3307 0.0822422 -0.987688 0.133071 0.490491 45 57.5 57.5 0 -943 1 1 0 52.4733 40.3336 50.6657 0.247326 -0.966643 0.0665668 0.490491 45 57.5 57.5 0 -944 1 1 0 51.796 40.1852 50.666 0.179596 -0.981483 0.0666046 0.490491 45 57.5 57.5 0 -945 1 1 0 52.061 40.2147 50 0.206103 -0.97853 0 0.490491 45 57.5 57.5 0 -946 1 1 0 51.3795 40.0956 50 0.137952 -0.990439 0 0.490491 45 57.5 57.5 0 -947 1 1 0 51.1039 40.0835 50.6671 0.110385 -0.991648 0.0667095 0.490491 45 57.5 57.5 0 -948 1 1 0 50.4125 40.0308 50.6674 0.0412479 -0.996917 0.0667412 0.490491 45 57.5 57.5 0 -949 1 1 0 50.6914 40.0239 50 0.0691418 -0.997607 0 0.490491 45 57.5 57.5 0 -950 1 1 0 50 40 50 0 -1 0 0.490491 45 57.5 57.5 0 -951 1 1 0 53.3061 40.7732 51.9839 0.330606 -0.922682 0.198387 0.490491 45 57.5 57.5 0 -952 1 1 0 52.8993 40.5218 51.3257 0.289929 -0.947822 0.13257 0.490491 45 57.5 57.5 0 -953 1 1 0 52.6155 40.5557 51.9909 0.26155 -0.944433 0.199094 0.490491 45 57.5 57.5 0 -954 1 1 0 47.2531 41.4736 54.4446 -0.274694 -0.85264 0.444464 0.490491 45 57.5 57.5 0 -955 1 1 0 46.5715 41.7155 54.4287 -0.342848 -0.828447 0.442867 0.490491 45 57.5 57.5 0 -956 1 1 0 47.6132 41.0899 53.8619 -0.238677 -0.891007 0.386187 0.490491 45 57.5 57.5 0 -957 1 1 0 46.9234 41.3027 53.8591 -0.307659 -0.869725 0.385906 0.490491 45 57.5 57.5 0 -958 1 1 0 46.2496 41.5609 53.8361 -0.375038 -0.843912 0.383614 0.490491 45 57.5 57.5 0 -959 1 1 0 47.9881 40.7612 53.2553 -0.201189 -0.92388 0.32553 0.490491 45 57.5 57.5 0 -960 1 1 0 47.2937 40.9417 53.2593 -0.270627 -0.905832 0.325929 0.490491 45 57.5 57.5 0 -961 1 1 0 48.3754 40.4894 52.6287 -0.16246 -0.951057 0.262865 0.490491 45 57.5 57.5 0 -962 1 1 0 47.6755 40.6395 52.6415 -0.232455 -0.93605 0.264151 0.490491 45 57.5 57.5 0 -963 1 1 0 46.9874 40.8376 52.6408 -0.301258 -0.916244 0.264082 0.490491 45 57.5 57.5 0 -964 1 1 0 46.6079 41.1716 53.2486 -0.339209 -0.882837 0.324863 0.490491 45 57.5 57.5 0 -965 1 1 0 45.9457 41.4466 53.2252 -0.405434 -0.855337 0.322525 0.490491 45 57.5 57.5 0 -966 1 1 0 46.3148 41.0826 52.6266 -0.368518 -0.891742 0.262661 0.490491 45 57.5 57.5 0 -967 1 1 0 45.6611 41.3733 52.5989 -0.433888 -0.862669 0.259892 0.490491 45 57.5 57.5 0 -968 1 1 0 48.7727 40.2763 51.9858 -0.122729 -0.97237 0.198581 0.490491 45 57.5 57.5 0 -969 1 1 0 48.0822 40.3881 51.9834 -0.19178 -0.961188 0.198337 0.490491 45 57.5 57.5 0 -970 1 1 0 49.1776 40.1231 51.3307 -0.0822422 -0.987688 0.133071 0.490491 45 57.5 57.5 0 -971 1 1 0 48.4845 40.2057 51.3326 -0.151549 -0.979426 0.133256 0.490491 45 57.5 57.5 0 -972 1 1 0 47.7988 40.3361 51.3279 -0.220117 -0.966393 0.132792 0.490491 45 57.5 57.5 0 -973 1 1 0 49.5875 40.0308 50.6674 -0.0412479 -0.996917 0.0667412 0.490491 45 57.5 57.5 0 -974 1 1 0 48.8961 40.0835 50.6671 -0.110385 -0.991648 0.0667095 0.490491 45 57.5 57.5 0 -975 1 1 0 49.3086 40.0239 50 -0.0691418 -0.997607 0 0.490491 45 57.5 57.5 0 -976 1 1 0 48.6205 40.0956 50 -0.137952 -0.990439 0 0.490491 45 57.5 57.5 0 -977 1 1 0 48.204 40.1852 50.666 -0.179596 -0.981483 0.0666046 0.490491 45 57.5 57.5 0 -978 1 1 0 47.5267 40.3336 50.6657 -0.247326 -0.966643 0.0665668 0.490491 45 57.5 57.5 0 -979 1 1 0 47.939 40.2147 50 -0.206103 -0.97853 0 0.490491 45 57.5 57.5 0 -980 1 1 0 47.2673 40.3806 50 -0.273267 -0.961938 0 0.490491 45 57.5 57.5 0 -981 1 1 0 46.0265 41.036 51.9641 -0.39735 -0.896401 0.196412 0.490491 45 57.5 57.5 0 -982 1 1 0 45.3973 41.3413 51.9602 -0.460266 -0.865871 0.196015 0.490491 45 57.5 57.5 0 -983 1 1 0 46.4177 40.757 51.3166 -0.358229 -0.924305 0.131656 0.490491 45 57.5 57.5 0 -984 1 1 0 45.7764 41.032 51.3175 -0.422363 -0.896801 0.131749 0.490491 45 57.5 57.5 0 -985 1 1 0 45.1556 41.3507 51.312 -0.484441 -0.864929 0.1312 0.490491 45 57.5 57.5 0 -986 1 1 0 46.8322 40.538 50.6604 -0.316778 -0.946198 0.0660427 0.490491 45 57.5 57.5 0 -987 1 1 0 46.1828 40.7808 50.6599 -0.381722 -0.921919 0.0659886 0.490491 45 57.5 57.5 0 -988 1 1 0 46.6088 40.5926 50 -0.339122 -0.940742 0 0.490491 45 57.5 57.5 0 -989 1 1 0 45.9664 40.8496 50 -0.403355 -0.915043 0 0.490491 45 57.5 57.5 0 -990 1 1 0 45.5463 41.0707 50.6582 -0.445365 -0.892927 0.0658169 0.490491 45 57.5 57.5 0 -991 1 1 0 44.937 41.4015 50.6576 -0.506298 -0.859848 0.0657577 0.490491 45 57.5 57.5 0 -992 1 1 0 45.3434 41.1503 50 -0.465657 -0.884965 0 0.490491 45 57.5 57.5 0 -993 1 1 0 44.7427 41.4935 50 -0.525731 -0.850651 0 0.490491 45 57.5 57.5 0 -994 1 1 0 47.3845 40.5557 51.9909 -0.26155 -0.944433 0.199094 0.490491 45 57.5 57.5 0 -995 1 1 0 47.1007 40.5218 51.3257 -0.289929 -0.947822 0.13257 0.490491 45 57.5 57.5 0 -996 1 1 0 46.6939 40.7732 51.9839 -0.330606 -0.922682 0.198387 0.490491 45 57.5 57.5 0 -997 1 1 0 51.9823 41.3147 54.5426 0.198227 -0.868535 0.454262 0.490491 45 57.5 57.5 0 -998 1 1 0 51.6101 40.9516 53.9414 0.161007 -0.904839 0.394136 0.490491 45 57.5 57.5 0 -999 1 1 0 51.228 40.6487 53.3234 0.1228 -0.93513 0.332342 0.490491 45 57.5 57.5 0 -1000 1 1 0 50.8232 40.8702 53.9961 0.0823235 -0.912983 0.399607 0.490491 45 57.5 57.5 0 -1001 1 1 0 51.1976 41.2066 54.6088 0.119755 -0.879344 0.460882 0.490491 45 57.5 57.5 0 -1002 1 1 0 50.413 41.1524 54.6421 0.0412991 -0.88476 0.464213 0.490491 45 57.5 57.5 0 -1003 1 1 0 50.815 40.3935 52.6552 0.081501 -0.960655 0.265519 0.490491 45 57.5 57.5 0 -1004 1 1 0 50.4125 40.2115 52.0037 0.0412506 -0.978852 0.200368 0.490491 45 57.5 57.5 0 -1005 1 1 0 50 40.3614 52.664 0 -0.963861 0.266405 0.490491 45 57.5 57.5 0 -1006 1 1 0 50 40.0895 51.3352 0 -0.991046 0.133524 0.490491 45 57.5 57.5 0 -1007 1 1 0 49.5875 40.2115 52.0037 -0.0412506 -0.978852 0.200368 0.490491 45 57.5 57.5 0 -1008 1 1 0 49.185 40.3935 52.6552 -0.081501 -0.960655 0.265519 0.490491 45 57.5 57.5 0 -1009 1 1 0 49.587 41.1524 54.6421 -0.0412991 -0.88476 0.464213 0.490491 45 57.5 57.5 0 -1010 1 1 0 49.1768 40.8702 53.9961 -0.0823235 -0.912983 0.399607 0.490491 45 57.5 57.5 0 -1011 1 1 0 48.8024 41.2066 54.6088 -0.119755 -0.879344 0.460882 0.490491 45 57.5 57.5 0 -1012 1 1 0 48.772 40.6487 53.3234 -0.1228 -0.93513 0.332342 0.490491 45 57.5 57.5 0 -1013 1 1 0 48.3899 40.9516 53.9414 -0.161007 -0.904839 0.394136 0.490491 45 57.5 57.5 0 -1014 1 1 0 48.0177 41.3147 54.5426 -0.198227 -0.868535 0.454262 0.490491 45 57.5 57.5 0 -1015 1 1 0 50.413 40.5838 53.3414 0.0413021 -0.941618 0.33414 0.490491 45 57.5 57.5 0 -1016 1 1 0 49.587 40.5838 53.3414 -0.0413021 -0.941618 0.33414 0.490491 45 57.5 57.5 0 -1017 1 1 0 50 40.8391 54.0097 0 -0.916092 0.400968 0.490491 45 57.5 57.5 0 -1018 1 1 0 49.5936 44.2794 41.8079 -0.0406403 -0.572055 -0.819208 0.490491 45 57.5 57.5 0 -1019 1 1 0 50.4064 44.2794 41.8079 0.0406403 -0.572055 -0.819208 0.490491 45 57.5 57.5 0 -1020 1 1 0 49.1891 43.8436 42.1616 -0.081086 -0.615642 -0.783843 0.490491 45 57.5 57.5 0 -1021 1 1 0 50 43.8232 42.1357 0 -0.617676 -0.786433 0.490491 45 57.5 57.5 0 -1022 1 1 0 50.8109 43.8436 42.1616 0.081086 -0.615642 -0.783843 0.490491 45 57.5 57.5 0 -1023 1 1 0 48.7886 43.4372 42.5527 -0.121144 -0.656282 -0.744727 0.490491 45 57.5 57.5 0 -1024 1 1 0 49.5936 43.3912 42.5061 -0.0406418 -0.660883 -0.749387 0.490491 45 57.5 57.5 0 -1025 1 1 0 48.3938 43.0622 42.9795 -0.160622 -0.69378 -0.702047 0.490491 45 57.5 57.5 0 -1026 1 1 0 49.1943 42.9938 42.9103 -0.0805729 -0.700622 -0.708969 0.490491 45 57.5 57.5 0 -1027 1 1 0 50 42.9709 42.8872 0 -0.702907 -0.711282 0.490491 45 57.5 57.5 0 -1028 1 1 0 50.4064 43.3912 42.5061 0.0406418 -0.660883 -0.749387 0.490491 45 57.5 57.5 0 -1029 1 1 0 51.2114 43.4372 42.5527 0.121144 -0.656282 -0.744727 0.490491 45 57.5 57.5 0 -1030 1 1 0 50.8057 42.9938 42.9103 0.0805729 -0.700622 -0.708969 0.490491 45 57.5 57.5 0 -1031 1 1 0 51.6062 43.0622 42.9795 0.160622 -0.69378 -0.702047 0.490491 45 57.5 57.5 0 -1032 1 1 0 48.0067 42.7204 43.4399 -0.199331 -0.727959 -0.656006 0.490491 45 57.5 57.5 0 -1033 1 1 0 48.7881 42.6111 43.3716 -0.121192 -0.738887 -0.662842 0.490491 45 57.5 57.5 0 -1034 1 1 0 47.6291 42.4135 43.9317 -0.237086 -0.758652 -0.606825 0.490491 45 57.5 57.5 0 -1035 1 1 0 48.4039 42.2816 43.8454 -0.159613 -0.771841 -0.615456 0.490491 45 57.5 57.5 0 -1036 1 1 0 49.1886 42.198 43.7976 -0.0811417 -0.780205 -0.620239 0.490491 45 57.5 57.5 0 -1037 1 1 0 47.2629 42.1428 44.4526 -0.273706 -0.785715 -0.55474 0.490491 45 57.5 57.5 0 -1038 1 1 0 48.0273 41.985 44.3549 -0.197274 -0.801504 -0.564513 0.490491 45 57.5 57.5 0 -1039 1 1 0 46.9098 41.9098 45 -0.309017 -0.809017 -0.5 0.490491 45 57.5 57.5 0 -1040 1 1 0 47.6655 41.7285 44.888 -0.233445 -0.827147 -0.511205 0.490491 45 57.5 57.5 0 -1041 1 1 0 48.4357 41.5982 44.8074 -0.156434 -0.840178 -0.519259 0.490491 45 57.5 57.5 0 -1042 1 1 0 48.8092 41.8783 44.2886 -0.119078 -0.81217 -0.57114 0.490491 45 57.5 57.5 0 -1043 1 1 0 49.5933 41.8248 44.2554 -0.040675 -0.817523 -0.574458 0.490491 45 57.5 57.5 0 -1044 1 1 0 49.2154 41.5197 44.7589 -0.0784592 -0.848029 -0.52411 0.490491 45 57.5 57.5 0 -1045 1 1 0 50 41.4935 44.7427 0 -0.850651 -0.525731 0.490491 45 57.5 57.5 0 -1046 1 1 0 51.2119 42.6111 43.3716 0.121192 -0.738887 -0.662842 0.490491 45 57.5 57.5 0 -1047 1 1 0 51.9933 42.7204 43.4399 0.199331 -0.727959 -0.656006 0.490491 45 57.5 57.5 0 -1048 1 1 0 50.8114 42.198 43.7976 0.0811417 -0.780205 -0.620239 0.490491 45 57.5 57.5 0 -1049 1 1 0 51.5961 42.2816 43.8454 0.159613 -0.771841 -0.615456 0.490491 45 57.5 57.5 0 -1050 1 1 0 52.3709 42.4135 43.9317 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50.6604 53.1678 -0.946198 0.0660427 0.316778 0.490491 45 57.5 57.5 0 -1222 1 1 0 40.5926 50 53.3912 -0.940742 0 0.339122 0.490491 45 57.5 57.5 0 -1223 1 1 0 40.3806 50 52.7327 -0.961938 0 0.273267 0.490491 45 57.5 57.5 0 -1224 1 1 0 40.3881 51.9834 51.9178 -0.961188 0.198337 0.19178 0.490491 45 57.5 57.5 0 -1225 1 1 0 40.2763 51.9858 51.2273 -0.97237 0.198581 0.122729 0.490491 45 57.5 57.5 0 -1226 1 1 0 40.3361 51.3279 52.2012 -0.966393 0.132792 0.220117 0.490491 45 57.5 57.5 0 -1227 1 1 0 40.2057 51.3326 51.5155 -0.979426 0.133256 0.151549 0.490491 45 57.5 57.5 0 -1228 1 1 0 40.1231 51.3307 50.8224 -0.987688 0.133071 0.0822422 0.490491 45 57.5 57.5 0 -1229 1 1 0 40.3336 50.6657 52.4733 -0.966643 0.0665668 0.247326 0.490491 45 57.5 57.5 0 -1230 1 1 0 40.1852 50.666 51.796 -0.981483 0.0666046 0.179596 0.490491 45 57.5 57.5 0 -1231 1 1 0 40.2147 50 52.061 -0.97853 0 0.206103 0.490491 45 57.5 57.5 0 -1232 1 1 0 40.0956 50 51.3795 -0.990439 0 0.137952 0.490491 45 57.5 57.5 0 -1233 1 1 0 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0 -1245 1 1 0 40.7612 53.2553 47.9881 -0.92388 0.32553 -0.201189 0.490491 45 57.5 57.5 0 -1246 1 1 0 40.9417 53.2593 47.2937 -0.905832 0.325929 -0.270627 0.490491 45 57.5 57.5 0 -1247 1 1 0 40.4894 52.6287 48.3754 -0.951057 0.262865 -0.16246 0.490491 45 57.5 57.5 0 -1248 1 1 0 40.6395 52.6415 47.6755 -0.93605 0.264151 -0.232455 0.490491 45 57.5 57.5 0 -1249 1 1 0 40.8376 52.6408 46.9874 -0.916244 0.264082 -0.301258 0.490491 45 57.5 57.5 0 -1250 1 1 0 41.1716 53.2486 46.6079 -0.882837 0.324863 -0.339209 0.490491 45 57.5 57.5 0 -1251 1 1 0 41.4466 53.2252 45.9457 -0.855337 0.322525 -0.405434 0.490491 45 57.5 57.5 0 -1252 1 1 0 41.0826 52.6266 46.3148 -0.891742 0.262661 -0.368518 0.490491 45 57.5 57.5 0 -1253 1 1 0 41.3733 52.5989 45.6611 -0.862669 0.259892 -0.433888 0.490491 45 57.5 57.5 0 -1254 1 1 0 40.2763 51.9858 48.7727 -0.97237 0.198581 -0.122729 0.490491 45 57.5 57.5 0 -1255 1 1 0 40.3881 51.9834 48.0822 -0.961188 0.198337 -0.19178 0.490491 45 57.5 57.5 0 -1256 1 1 0 40.1231 51.3307 49.1776 -0.987688 0.133071 -0.0822422 0.490491 45 57.5 57.5 0 -1257 1 1 0 40.2057 51.3326 48.4845 -0.979426 0.133256 -0.151549 0.490491 45 57.5 57.5 0 -1258 1 1 0 40.3361 51.3279 47.7988 -0.966393 0.132792 -0.220117 0.490491 45 57.5 57.5 0 -1259 1 1 0 40.0308 50.6674 49.5875 -0.996917 0.0667412 -0.0412479 0.490491 45 57.5 57.5 0 -1260 1 1 0 40.0835 50.6671 48.8961 -0.991648 0.0667095 -0.110385 0.490491 45 57.5 57.5 0 -1261 1 1 0 40.0239 50 49.3086 -0.997607 0 -0.0691418 0.490491 45 57.5 57.5 0 -1262 1 1 0 40.0956 50 48.6205 -0.990439 0 -0.137952 0.490491 45 57.5 57.5 0 -1263 1 1 0 40.1852 50.666 48.204 -0.981483 0.0666046 -0.179596 0.490491 45 57.5 57.5 0 -1264 1 1 0 40.3336 50.6657 47.5267 -0.966643 0.0665668 -0.247326 0.490491 45 57.5 57.5 0 -1265 1 1 0 40.2147 50 47.939 -0.97853 0 -0.206103 0.490491 45 57.5 57.5 0 -1266 1 1 0 40.3806 50 47.2673 -0.961938 0 -0.273267 0.490491 45 57.5 57.5 0 -1267 1 1 0 41.036 51.9641 46.0265 -0.896401 0.196412 -0.39735 0.490491 45 57.5 57.5 0 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40.0895 51.3352 50 -0.991046 0.133524 0 0.490491 45 57.5 57.5 0 -1292 1 1 0 40.2115 52.0037 49.5875 -0.978852 0.200368 -0.0412506 0.490491 45 57.5 57.5 0 -1293 1 1 0 40.3935 52.6552 49.185 -0.960655 0.265519 -0.081501 0.490491 45 57.5 57.5 0 -1294 1 1 0 41.1524 54.6421 49.587 -0.88476 0.464213 -0.0412991 0.490491 45 57.5 57.5 0 -1295 1 1 0 40.8702 53.9961 49.1768 -0.912983 0.399607 -0.0823235 0.490491 45 57.5 57.5 0 -1296 1 1 0 41.2066 54.6088 48.8024 -0.879344 0.460882 -0.119755 0.490491 45 57.5 57.5 0 -1297 1 1 0 40.6487 53.3234 48.772 -0.93513 0.332342 -0.1228 0.490491 45 57.5 57.5 0 -1298 1 1 0 40.9516 53.9414 48.3899 -0.904839 0.394136 -0.161007 0.490491 45 57.5 57.5 0 -1299 1 1 0 41.3147 54.5426 48.0177 -0.868535 0.454262 -0.198227 0.490491 45 57.5 57.5 0 -1300 1 1 0 40.5838 53.3414 50.413 -0.941618 0.33414 0.0413021 0.490491 45 57.5 57.5 0 -1301 1 1 0 40.5838 53.3414 49.587 -0.941618 0.33414 -0.0413021 0.490491 45 57.5 57.5 0 -1302 1 1 0 40.8391 54.0097 50 -0.916092 0.400968 0 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43.4372 42.5527 51.2114 -0.656282 -0.744727 0.121144 0.490491 45 57.5 57.5 0 -1315 1 1 0 42.9938 42.9103 50.8057 -0.700622 -0.708969 0.0805729 0.490491 45 57.5 57.5 0 -1316 1 1 0 43.0622 42.9795 51.6062 -0.69378 -0.702047 0.160622 0.490491 45 57.5 57.5 0 -1317 1 1 0 42.7204 43.4399 48.0067 -0.727959 -0.656006 -0.199331 0.490491 45 57.5 57.5 0 -1318 1 1 0 42.6111 43.3716 48.7881 -0.738887 -0.662842 -0.121192 0.490491 45 57.5 57.5 0 -1319 1 1 0 42.4135 43.9317 47.6291 -0.758652 -0.606825 -0.237086 0.490491 45 57.5 57.5 0 -1320 1 1 0 42.2816 43.8454 48.4039 -0.771841 -0.615456 -0.159613 0.490491 45 57.5 57.5 0 -1321 1 1 0 42.198 43.7976 49.1886 -0.780205 -0.620239 -0.0811417 0.490491 45 57.5 57.5 0 -1322 1 1 0 42.1428 44.4526 47.2629 -0.785715 -0.55474 -0.273706 0.490491 45 57.5 57.5 0 -1323 1 1 0 41.985 44.3549 48.0273 -0.801504 -0.564513 -0.197274 0.490491 45 57.5 57.5 0 -1324 1 1 0 41.9098 45 46.9098 -0.809017 -0.5 -0.309017 0.490491 45 57.5 57.5 0 -1325 1 1 0 41.7285 44.888 47.6655 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0.490491 45 57.5 57.5 0 -1520 1 1 0 59.9761 50 49.3086 0.997607 0 -0.0691418 0.490491 45 57.5 57.5 0 -1521 1 1 0 60 50 50 1 0 0 0.490491 45 57.5 57.5 0 -1522 1 1 0 59.2268 51.9839 46.6939 0.922682 0.198387 -0.330606 0.490491 45 57.5 57.5 0 -1523 1 1 0 59.4782 51.3257 47.1007 0.947822 0.13257 -0.289929 0.490491 45 57.5 57.5 0 -1524 1 1 0 59.4443 51.9909 47.3845 0.944433 0.199094 -0.26155 0.490491 45 57.5 57.5 0 -1525 1 1 0 58.5264 54.4446 52.7469 0.85264 0.444464 0.274694 0.490491 45 57.5 57.5 0 -1526 1 1 0 58.2845 54.4287 53.4285 0.828447 0.442867 0.342848 0.490491 45 57.5 57.5 0 -1527 1 1 0 58.9101 53.8619 52.3868 0.891007 0.386187 0.238677 0.490491 45 57.5 57.5 0 -1528 1 1 0 58.6973 53.8591 53.0766 0.869725 0.385906 0.307659 0.490491 45 57.5 57.5 0 -1529 1 1 0 58.4391 53.8361 53.7504 0.843912 0.383614 0.375038 0.490491 45 57.5 57.5 0 -1530 1 1 0 59.2388 53.2553 52.0119 0.92388 0.32553 0.201189 0.490491 45 57.5 57.5 0 -1531 1 1 0 59.0583 53.2593 52.7063 0.905832 0.325929 0.270627 0.490491 45 57.5 57.5 0 -1532 1 1 0 59.5106 52.6287 51.6246 0.951057 0.262865 0.16246 0.490491 45 57.5 57.5 0 -1533 1 1 0 59.3605 52.6415 52.3245 0.93605 0.264151 0.232455 0.490491 45 57.5 57.5 0 -1534 1 1 0 59.1624 52.6408 53.0126 0.916244 0.264082 0.301258 0.490491 45 57.5 57.5 0 -1535 1 1 0 58.8284 53.2486 53.3921 0.882837 0.324863 0.339209 0.490491 45 57.5 57.5 0 -1536 1 1 0 58.5534 53.2252 54.0543 0.855337 0.322525 0.405434 0.490491 45 57.5 57.5 0 -1537 1 1 0 58.9174 52.6266 53.6852 0.891742 0.262661 0.368518 0.490491 45 57.5 57.5 0 -1538 1 1 0 58.6267 52.5989 54.3389 0.862669 0.259892 0.433888 0.490491 45 57.5 57.5 0 -1539 1 1 0 59.7237 51.9858 51.2273 0.97237 0.198581 0.122729 0.490491 45 57.5 57.5 0 -1540 1 1 0 59.6119 51.9834 51.9178 0.961188 0.198337 0.19178 0.490491 45 57.5 57.5 0 -1541 1 1 0 59.8769 51.3307 50.8224 0.987688 0.133071 0.0822422 0.490491 45 57.5 57.5 0 -1542 1 1 0 59.7943 51.3326 51.5155 0.979426 0.133256 0.151549 0.490491 45 57.5 57.5 0 -1543 1 1 0 59.6639 51.3279 52.2012 0.966393 0.132792 0.220117 0.490491 45 57.5 57.5 0 -1544 1 1 0 59.9692 50.6674 50.4125 0.996917 0.0667412 0.0412479 0.490491 45 57.5 57.5 0 -1545 1 1 0 59.9165 50.6671 51.1039 0.991648 0.0667095 0.110385 0.490491 45 57.5 57.5 0 -1546 1 1 0 59.9761 50 50.6914 0.997607 0 0.0691418 0.490491 45 57.5 57.5 0 -1547 1 1 0 59.9044 50 51.3795 0.990439 0 0.137952 0.490491 45 57.5 57.5 0 -1548 1 1 0 59.8148 50.666 51.796 0.981483 0.0666046 0.179596 0.490491 45 57.5 57.5 0 -1549 1 1 0 59.6664 50.6657 52.4733 0.966643 0.0665668 0.247326 0.490491 45 57.5 57.5 0 -1550 1 1 0 59.7853 50 52.061 0.97853 0 0.206103 0.490491 45 57.5 57.5 0 -1551 1 1 0 59.6194 50 52.7327 0.961938 0 0.273267 0.490491 45 57.5 57.5 0 -1552 1 1 0 58.964 51.9641 53.9735 0.896401 0.196412 0.39735 0.490491 45 57.5 57.5 0 -1553 1 1 0 58.6587 51.9602 54.6027 0.865871 0.196015 0.460266 0.490491 45 57.5 57.5 0 -1554 1 1 0 59.243 51.3166 53.5823 0.924305 0.131656 0.358229 0.490491 45 57.5 57.5 0 -1555 1 1 0 58.968 51.3175 54.2236 0.896801 0.131749 0.422363 0.490491 45 57.5 57.5 0 -1556 1 1 0 58.6493 51.312 54.8444 0.864929 0.1312 0.484441 0.490491 45 57.5 57.5 0 -1557 1 1 0 59.462 50.6604 53.1678 0.946198 0.0660427 0.316778 0.490491 45 57.5 57.5 0 -1558 1 1 0 59.2192 50.6599 53.8172 0.921919 0.0659886 0.381722 0.490491 45 57.5 57.5 0 -1559 1 1 0 59.4074 50 53.3912 0.940742 0 0.339122 0.490491 45 57.5 57.5 0 -1560 1 1 0 59.1504 50 54.0336 0.915043 0 0.403355 0.490491 45 57.5 57.5 0 -1561 1 1 0 58.9293 50.6582 54.4537 0.892927 0.0658169 0.445365 0.490491 45 57.5 57.5 0 -1562 1 1 0 58.5985 50.6576 55.063 0.859848 0.0657577 0.506298 0.490491 45 57.5 57.5 0 -1563 1 1 0 58.8497 50 54.6566 0.884965 0 0.465657 0.490491 45 57.5 57.5 0 -1564 1 1 0 59.4443 51.9909 52.6155 0.944433 0.199094 0.26155 0.490491 45 57.5 57.5 0 -1565 1 1 0 59.4782 51.3257 52.8993 0.947822 0.13257 0.289929 0.490491 45 57.5 57.5 0 -1566 1 1 0 59.2268 51.9839 53.3061 0.922682 0.198387 0.330606 0.490491 45 57.5 57.5 0 -1567 1 1 0 58.6853 54.5426 48.0177 0.868535 0.454262 -0.198227 0.490491 45 57.5 57.5 0 -1568 1 1 0 59.0484 53.9414 48.3899 0.904839 0.394136 -0.161007 0.490491 45 57.5 57.5 0 -1569 1 1 0 59.3513 53.3234 48.772 0.93513 0.332342 -0.1228 0.490491 45 57.5 57.5 0 -1570 1 1 0 59.1298 53.9961 49.1768 0.912983 0.399607 -0.0823235 0.490491 45 57.5 57.5 0 -1571 1 1 0 58.7934 54.6088 48.8024 0.879344 0.460882 -0.119755 0.490491 45 57.5 57.5 0 -1572 1 1 0 58.8476 54.6421 49.587 0.88476 0.464213 -0.0412991 0.490491 45 57.5 57.5 0 -1573 1 1 0 59.6065 52.6552 49.185 0.960655 0.265519 -0.081501 0.490491 45 57.5 57.5 0 -1574 1 1 0 59.7885 52.0037 49.5875 0.978852 0.200368 -0.0412506 0.490491 45 57.5 57.5 0 -1575 1 1 0 59.6386 52.664 50 0.963861 0.266405 0 0.490491 45 57.5 57.5 0 -1576 1 1 0 59.9105 51.3352 50 0.991046 0.133524 0 0.490491 45 57.5 57.5 0 -1577 1 1 0 59.7885 52.0037 50.4125 0.978852 0.200368 0.0412506 0.490491 45 57.5 57.5 0 -1578 1 1 0 59.6065 52.6552 50.815 0.960655 0.265519 0.081501 0.490491 45 57.5 57.5 0 -1579 1 1 0 58.8476 54.6421 50.413 0.88476 0.464213 0.0412991 0.490491 45 57.5 57.5 0 -1580 1 1 0 59.1298 53.9961 50.8232 0.912983 0.399607 0.0823235 0.490491 45 57.5 57.5 0 -1581 1 1 0 58.7934 54.6088 51.1976 0.879344 0.460882 0.119755 0.490491 45 57.5 57.5 0 -1582 1 1 0 59.3513 53.3234 51.228 0.93513 0.332342 0.1228 0.490491 45 57.5 57.5 0 -1583 1 1 0 59.0484 53.9414 51.6101 0.904839 0.394136 0.161007 0.490491 45 57.5 57.5 0 -1584 1 1 0 58.6853 54.5426 51.9823 0.868535 0.454262 0.198227 0.490491 45 57.5 57.5 0 -1585 1 1 0 59.4162 53.3414 49.587 0.941618 0.33414 -0.0413021 0.490491 45 57.5 57.5 0 -1586 1 1 0 59.4162 53.3414 50.413 0.941618 0.33414 0.0413021 0.490491 45 57.5 57.5 0 -1587 1 1 0 59.1609 54.0097 50 0.916092 0.400968 0 0.490491 45 57.5 57.5 0 -1588 1 1 0 55.7206 41.8079 50.4064 0.572055 -0.819207 0.0406403 0.490491 45 57.5 57.5 0 -1589 1 1 0 55.7206 41.8079 49.5936 0.572055 -0.819207 -0.0406403 0.490491 45 57.5 57.5 0 -1590 1 1 0 56.1564 42.1616 50.8109 0.615642 -0.783843 0.081086 0.490491 45 57.5 57.5 0 -1591 1 1 0 56.1768 42.1357 50 0.617676 -0.786433 0 0.490491 45 57.5 57.5 0 -1592 1 1 0 56.1564 42.1616 49.1891 0.615642 -0.783843 -0.081086 0.490491 45 57.5 57.5 0 -1593 1 1 0 56.5628 42.5527 51.2114 0.656282 -0.744727 0.121144 0.490491 45 57.5 57.5 0 -1594 1 1 0 56.6088 42.5061 50.4064 0.660883 -0.749387 0.0406418 0.490491 45 57.5 57.5 0 -1595 1 1 0 56.9378 42.9795 51.6062 0.69378 -0.702047 0.160622 0.490491 45 57.5 57.5 0 -1596 1 1 0 57.0062 42.9103 50.8057 0.700622 -0.708969 0.0805729 0.490491 45 57.5 57.5 0 -1597 1 1 0 57.0291 42.8872 50 0.702907 -0.711282 0 0.490491 45 57.5 57.5 0 -1598 1 1 0 56.6088 42.5061 49.5936 0.660883 -0.749387 -0.0406418 0.490491 45 57.5 57.5 0 -1599 1 1 0 56.5628 42.5527 48.7886 0.656282 -0.744727 -0.121144 0.490491 45 57.5 57.5 0 -1600 1 1 0 57.0062 42.9103 49.1943 0.700622 -0.708969 -0.0805729 0.490491 45 57.5 57.5 0 -1601 1 1 0 56.9378 42.9795 48.3938 0.69378 -0.702047 -0.160622 0.490491 45 57.5 57.5 0 -1602 1 1 0 57.2796 43.4399 51.9933 0.727959 -0.656006 0.199331 0.490491 45 57.5 57.5 0 -1603 1 1 0 57.3889 43.3716 51.2119 0.738887 -0.662842 0.121192 0.490491 45 57.5 57.5 0 -1604 1 1 0 57.5865 43.9317 52.3709 0.758652 -0.606825 0.237086 0.490491 45 57.5 57.5 0 -1605 1 1 0 57.7184 43.8454 51.5961 0.771841 -0.615456 0.159613 0.490491 45 57.5 57.5 0 -1606 1 1 0 57.802 43.7976 50.8114 0.780205 -0.620239 0.0811417 0.490491 45 57.5 57.5 0 -1607 1 1 0 57.8572 44.4526 52.7371 0.785715 -0.55474 0.273706 0.490491 45 57.5 57.5 0 -1608 1 1 0 58.015 44.3549 51.9727 0.801504 -0.564513 0.197274 0.490491 45 57.5 57.5 0 -1609 1 1 0 58.0902 45 53.0902 0.809017 -0.5 0.309017 0.490491 45 57.5 57.5 0 -1610 1 1 0 58.2715 44.888 52.3345 0.827147 -0.511205 0.233445 0.490491 45 57.5 57.5 0 -1611 1 1 0 58.4018 44.8074 51.5643 0.840178 -0.519259 0.156434 0.490491 45 57.5 57.5 0 -1612 1 1 0 58.1217 44.2886 51.1908 0.81217 -0.57114 0.119078 0.490491 45 57.5 57.5 0 -1613 1 1 0 58.1752 44.2554 50.4067 0.817523 -0.574458 0.040675 0.490491 45 57.5 57.5 0 -1614 1 1 0 58.4803 44.7589 50.7846 0.848029 -0.52411 0.0784592 0.490491 45 57.5 57.5 0 -1615 1 1 0 58.5065 44.7427 50 0.850651 -0.525731 0 0.490491 45 57.5 57.5 0 -1616 1 1 0 57.3889 43.3716 48.7881 0.738887 -0.662842 -0.121192 0.490491 45 57.5 57.5 0 -1617 1 1 0 57.2796 43.4399 48.0067 0.727959 -0.656006 -0.199331 0.490491 45 57.5 57.5 0 -1618 1 1 0 57.802 43.7976 49.1886 0.780205 -0.620239 -0.0811417 0.490491 45 57.5 57.5 0 -1619 1 1 0 57.7184 43.8454 48.4039 0.771841 -0.615456 -0.159613 0.490491 45 57.5 57.5 0 -1620 1 1 0 57.5865 43.9317 47.6291 0.758652 -0.606825 -0.237086 0.490491 45 57.5 57.5 0 -1621 1 1 0 58.1752 44.2554 49.5933 0.817523 -0.574458 -0.040675 0.490491 45 57.5 57.5 0 -1622 1 1 0 58.1217 44.2886 48.8092 0.81217 -0.57114 -0.119078 0.490491 45 57.5 57.5 0 -1623 1 1 0 58.4803 44.7589 49.2154 0.848029 -0.52411 -0.0784592 0.490491 45 57.5 57.5 0 -1624 1 1 0 58.4018 44.8074 48.4357 0.840178 -0.519259 -0.156434 0.490491 45 57.5 57.5 0 -1625 1 1 0 58.015 44.3549 48.0273 0.801504 -0.564513 -0.197274 0.490491 45 57.5 57.5 0 -1626 1 1 0 57.8572 44.4526 47.2629 0.785715 -0.55474 -0.273706 0.490491 45 57.5 57.5 0 -1627 1 1 0 58.2715 44.888 47.6655 0.827147 -0.511205 -0.233445 0.490491 45 57.5 57.5 0 -1628 1 1 0 58.0902 45 46.9098 0.809017 -0.5 -0.309017 0.490491 45 57.5 57.5 0 -1629 1 1 0 57.435 43.325 50.4068 0.743496 -0.667502 0.0406769 0.490491 45 57.5 57.5 0 -1630 1 1 0 57.8279 43.7771 50 0.782786 -0.622291 0 0.490491 45 57.5 57.5 0 -1631 1 1 0 57.435 43.325 49.5932 0.743496 -0.667502 -0.0406769 0.490491 45 57.5 57.5 0 -1632 1 1 0 58.2845 45.5713 53.4285 0.828447 -0.442867 0.342848 0.490491 45 57.5 57.5 0 -1633 1 1 0 58.5264 45.5554 52.7469 0.85264 -0.444464 0.274694 0.490491 45 57.5 57.5 0 -1634 1 1 0 58.4391 46.1639 53.7504 0.843912 -0.383614 0.375038 0.490491 45 57.5 57.5 0 -1635 1 1 0 58.6973 46.1409 53.0766 0.869725 -0.385906 0.307659 0.490491 45 57.5 57.5 0 -1636 1 1 0 58.9101 46.1381 52.3868 0.891007 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42.9476 56.5662 52.6738 -0.705236 0.65662 0.267381 0.490491 45 57.5 57.5 0 -1797 1 1 0 43.2768 57.0398 52.289 -0.672319 0.703983 0.228899 0.490491 45 57.5 57.5 0 -1798 1 1 0 44.9579 58.3036 52.3723 -0.504209 0.830359 0.237228 0.490491 45 57.5 57.5 0 -1799 1 1 0 44.2875 57.9265 52.1302 -0.571251 0.79265 0.213023 0.490491 45 57.5 57.5 0 -1800 1 1 0 44.7087 58.3081 51.7253 -0.529135 0.830812 0.172532 0.490491 45 57.5 57.5 0 -1801 1 1 0 43.6542 57.4979 51.8743 -0.634579 0.749786 0.187432 0.490491 45 57.5 57.5 0 -1802 1 1 0 44.051 57.9017 51.4741 -0.594895 0.79017 0.147413 0.490491 45 57.5 57.5 0 -1803 1 1 0 44.4814 58.2711 51.0649 -0.551859 0.82711 0.106494 0.490491 45 57.5 57.5 0 -1804 1 1 0 44.1631 57.4534 53.2214 -0.583692 0.745339 0.322141 0.490491 45 57.5 57.5 0 -1805 1 1 0 43.8907 57.4944 52.5518 -0.610926 0.749435 0.25518 0.490491 45 57.5 57.5 0 -1806 1 1 0 44.5489 57.9011 52.8032 -0.545109 0.790112 0.280319 0.490491 45 57.5 57.5 0 -1807 1 1 0 44.6322 54.1427 57.3501 -0.536784 0.414272 0.735011 0.490491 45 57.5 57.5 0 -1808 1 1 0 44.1528 54.4396 56.7898 -0.584716 0.443957 0.678977 0.490491 45 57.5 57.5 0 -1809 1 1 0 43.7169 54.7092 56.1924 -0.628313 0.470917 0.619242 0.490491 45 57.5 57.5 0 -1810 1 1 0 44.3575 55.1338 56.4658 -0.564254 0.513375 0.646578 0.490491 45 57.5 57.5 0 -1811 1 1 0 44.8203 54.8521 57.0447 -0.51797 0.485208 0.704471 0.490491 45 57.5 57.5 0 -1812 1 1 0 45.0356 55.5242 56.6961 -0.496441 0.552418 0.669612 0.490491 45 57.5 57.5 0 -1813 1 1 0 43.3039 54.9644 55.5242 -0.669612 0.496441 0.552418 0.490491 45 57.5 57.5 0 -1814 1 1 0 42.9553 55.1797 54.8521 -0.704471 0.51797 0.485208 0.490491 45 57.5 57.5 0 -1815 1 1 0 43.5342 55.6425 55.1338 -0.646578 0.564254 0.513375 0.490491 45 57.5 57.5 0 -1816 1 1 0 42.6499 55.3678 54.1427 -0.735011 0.536784 0.414272 0.490491 45 57.5 57.5 0 -1817 1 1 0 43.2102 55.8472 54.4396 -0.678977 0.584716 0.443957 0.490491 45 57.5 57.5 0 -1818 1 1 0 43.8076 56.2831 54.7092 -0.619242 0.628313 0.470917 0.490491 45 57.5 57.5 0 -1819 1 1 0 45.2908 56.1924 56.2831 -0.470917 0.619242 0.628313 0.490491 45 57.5 57.5 0 -1820 1 1 0 44.8662 56.4658 55.6425 -0.513375 0.646578 0.564254 0.490491 45 57.5 57.5 0 -1821 1 1 0 45.5604 56.7898 55.8472 -0.443957 0.678977 0.584716 0.490491 45 57.5 57.5 0 -1822 1 1 0 44.4758 56.6961 54.9644 -0.552418 0.669612 0.496441 0.490491 45 57.5 57.5 0 -1823 1 1 0 45.1479 57.0447 55.1797 -0.485208 0.704471 0.51797 0.490491 45 57.5 57.5 0 -1824 1 1 0 45.8573 57.3501 55.3678 -0.414272 0.735011 0.536784 0.490491 45 57.5 57.5 0 -1825 1 1 0 43.9252 55.4065 55.8195 -0.607478 0.54065 0.581952 0.490491 45 57.5 57.5 0 -1826 1 1 0 44.1805 56.0748 55.4065 -0.581952 0.607478 0.54065 0.490491 45 57.5 57.5 0 -1827 1 1 0 44.5935 55.8195 56.0748 -0.54065 0.581952 0.607478 0.490491 45 57.5 57.5 0 -1828 1 1 0 51.0649 55.5186 58.2711 0.106494 0.551859 0.82711 0.490491 45 57.5 57.5 0 -1829 1 1 0 51.4741 55.949 57.9017 0.147413 0.594895 0.79017 0.490491 45 57.5 57.5 0 -1830 1 1 0 51.8743 56.3458 57.4979 0.187432 0.634579 0.749786 0.490491 45 57.5 57.5 0 -1831 1 1 0 52.1302 55.7125 57.9265 0.213023 0.571251 0.79265 0.490491 45 57.5 57.5 0 -1832 1 1 0 51.7253 55.2913 58.3081 0.172532 0.529135 0.830812 0.490491 45 57.5 57.5 0 -1833 1 1 0 52.3723 55.0421 58.3036 0.237228 0.504209 0.830359 0.490491 45 57.5 57.5 0 -1834 1 1 0 52.289 56.7232 57.0398 0.228899 0.672319 0.703983 0.490491 45 57.5 57.5 0 -1835 1 1 0 52.6738 57.0524 56.5662 0.267381 0.705236 0.65662 0.490491 45 57.5 57.5 0 -1836 1 1 0 52.96 56.4741 57.0231 0.296004 0.647412 0.70231 0.490491 45 57.5 57.5 0 -1837 1 1 0 53.0521 57.3479 56.0574 0.305212 0.734794 0.605742 0.490491 45 57.5 57.5 0 -1838 1 1 0 53.4143 57.6041 55.5245 0.341435 0.760406 0.552454 0.490491 45 57.5 57.5 0 -1839 1 1 0 53.7175 57.0711 56.015 0.371748 0.707107 0.601501 0.490491 45 57.5 57.5 0 -1840 1 1 0 53.3469 56.7891 56.535 0.334691 0.678913 0.653497 0.490491 45 57.5 57.5 0 -1841 1 1 0 53.6159 56.1919 56.9704 0.361591 0.619186 0.697037 0.490491 45 57.5 57.5 0 -1842 1 1 0 53.9977 56.4945 56.4684 0.399769 0.649448 0.64684 0.490491 45 57.5 57.5 0 -1843 1 1 0 54.2533 55.8779 56.8819 0.425325 0.587785 0.688191 0.490491 45 57.5 57.5 0 -1844 1 1 0 53.038 54.7623 58.2518 0.303801 0.476225 0.825175 0.490491 45 57.5 57.5 0 -1845 1 1 0 53.4615 55.1612 57.8345 0.346153 0.516122 0.783452 0.490491 45 57.5 57.5 0 -1846 1 1 0 53.6603 54.4698 58.1623 0.366027 0.446977 0.816233 0.490491 45 57.5 57.5 0 -1847 1 1 0 53.8673 55.5337 57.3771 0.38673 0.553372 0.737712 0.490491 45 57.5 57.5 0 -1848 1 1 0 54.0829 54.8624 57.7258 0.408286 0.48624 0.772575 0.490491 45 57.5 57.5 0 -1849 1 1 0 54.4826 55.225 57.253 0.448259 0.522499 0.725299 0.490491 45 57.5 57.5 0 -1850 1 1 0 54.6843 54.5399 57.5794 0.46843 0.45399 0.757936 0.490491 45 57.5 57.5 0 -1851 1 1 0 54.2713 54.156 58.0302 0.427135 0.415597 0.803016 0.490491 45 57.5 57.5 0 -1852 1 1 0 54.8571 53.8268 57.859 0.485712 0.382683 0.785899 0.490491 45 57.5 57.5 0 -1853 1 1 0 52.5518 56.1093 57.4944 0.25518 0.610926 0.749435 0.490491 45 57.5 57.5 0 -1854 1 1 0 53.2214 55.8369 57.4534 0.322141 0.583692 0.745339 0.490491 45 57.5 57.5 0 -1855 1 1 0 52.8032 55.4511 57.9011 0.280319 0.545109 0.790112 0.490491 45 57.5 57.5 0 -1856 1 1 0 53.8268 57.859 54.8571 0.382683 0.785899 0.485712 0.490491 45 57.5 57.5 0 -1857 1 1 0 54.156 58.0302 54.2713 0.415597 0.803016 0.427135 0.490491 45 57.5 57.5 0 -1858 1 1 0 54.5399 57.5794 54.6843 0.45399 0.757936 0.46843 0.490491 45 57.5 57.5 0 -1859 1 1 0 54.4698 58.1623 53.6603 0.446977 0.816233 0.366027 0.490491 45 57.5 57.5 0 -1860 1 1 0 54.7623 58.2518 53.038 0.476225 0.825175 0.303801 0.490491 45 57.5 57.5 0 -1861 1 1 0 55.1612 57.8345 53.4615 0.516122 0.783452 0.346153 0.490491 45 57.5 57.5 0 -1862 1 1 0 54.8624 57.7258 54.0829 0.48624 0.772575 0.408286 0.490491 45 57.5 57.5 0 -1863 1 1 0 55.225 57.253 54.4826 0.522499 0.725299 0.448259 0.490491 45 57.5 57.5 0 -1864 1 1 0 55.5337 57.3771 53.8673 0.553372 0.737712 0.38673 0.490491 45 57.5 57.5 0 -1865 1 1 0 55.8779 56.8819 54.2533 0.587785 0.688191 0.425325 0.490491 45 57.5 57.5 0 -1866 1 1 0 55.0421 58.3036 52.3723 0.504209 0.830359 0.237228 0.490491 45 57.5 57.5 0 -1867 1 1 0 55.2913 58.3081 51.7253 0.529135 0.830812 0.172532 0.490491 45 57.5 57.5 0 -1868 1 1 0 55.7125 57.9265 52.1302 0.571251 0.79265 0.213023 0.490491 45 57.5 57.5 0 -1869 1 1 0 55.5186 58.2711 51.0649 0.551859 0.82711 0.106494 0.490491 45 57.5 57.5 0 -1870 1 1 0 55.949 57.9017 51.4741 0.594895 0.79017 0.147413 0.490491 45 57.5 57.5 0 -1871 1 1 0 56.3458 57.4979 51.8743 0.634579 0.749786 0.187432 0.490491 45 57.5 57.5 0 -1872 1 1 0 56.1919 56.9704 53.6159 0.619186 0.697037 0.361591 0.490491 45 57.5 57.5 0 -1873 1 1 0 56.4945 56.4684 53.9977 0.649448 0.64684 0.399769 0.490491 45 57.5 57.5 0 -1874 1 1 0 56.4741 57.0231 52.96 0.647412 0.70231 0.296004 0.490491 45 57.5 57.5 0 -1875 1 1 0 56.7891 56.535 53.3469 0.678913 0.653497 0.334691 0.490491 45 57.5 57.5 0 -1876 1 1 0 57.0711 56.015 53.7175 0.707107 0.601501 0.371748 0.490491 45 57.5 57.5 0 -1877 1 1 0 56.7232 57.0398 52.289 0.672319 0.703983 0.228899 0.490491 45 57.5 57.5 0 -1878 1 1 0 57.0524 56.5662 52.6738 0.705236 0.65662 0.267381 0.490491 45 57.5 57.5 0 -1879 1 1 0 57.3479 56.0574 53.0521 0.734794 0.605742 0.305212 0.490491 45 57.5 57.5 0 -1880 1 1 0 57.6041 55.5245 53.4143 0.760406 0.552454 0.341435 0.490491 45 57.5 57.5 0 -1881 1 1 0 55.4511 57.9011 52.8032 0.545109 0.790112 0.280319 0.490491 45 57.5 57.5 0 -1882 1 1 0 56.1093 57.4944 52.5518 0.610926 0.749435 0.25518 0.490491 45 57.5 57.5 0 -1883 1 1 0 55.8369 57.4534 53.2214 0.583692 0.745339 0.322141 0.490491 45 57.5 57.5 0 -1884 1 1 0 55.5245 53.4143 57.6041 0.552454 0.341435 0.760406 0.490491 45 57.5 57.5 0 -1885 1 1 0 56.015 53.7175 57.0711 0.601501 0.371748 0.707107 0.490491 45 57.5 57.5 0 -1886 1 1 0 56.0574 53.0521 57.3479 0.605742 0.305212 0.734794 0.490491 45 57.5 57.5 0 -1887 1 1 0 56.4684 53.9977 56.4945 0.64684 0.399769 0.649448 0.490491 45 57.5 57.5 0 -1888 1 1 0 56.535 53.3469 56.7891 0.653497 0.334691 0.678913 0.490491 45 57.5 57.5 0 -1889 1 1 0 56.8819 54.2533 55.8779 0.688191 0.425325 0.587785 0.490491 45 57.5 57.5 0 -1890 1 1 0 56.9704 53.6159 56.1919 0.697037 0.361591 0.619186 0.490491 45 57.5 57.5 0 -1891 1 1 0 57.0231 52.96 56.4741 0.70231 0.296004 0.647412 0.490491 45 57.5 57.5 0 -1892 1 1 0 56.5662 52.6738 57.0524 0.65662 0.267381 0.705236 0.490491 45 57.5 57.5 0 -1893 1 1 0 57.0398 52.289 56.7232 0.703983 0.228899 0.672319 0.490491 45 57.5 57.5 0 -1894 1 1 0 57.253 54.4826 55.225 0.725299 0.448259 0.522499 0.490491 45 57.5 57.5 0 -1895 1 1 0 57.3771 53.8673 55.5337 0.737712 0.38673 0.553372 0.490491 45 57.5 57.5 0 -1896 1 1 0 57.5794 54.6843 54.5399 0.757936 0.46843 0.45399 0.490491 45 57.5 57.5 0 -1897 1 1 0 57.7258 54.0829 54.8624 0.772575 0.408286 0.48624 0.490491 45 57.5 57.5 0 -1898 1 1 0 57.8345 53.4615 55.1612 0.783452 0.346153 0.516122 0.490491 45 57.5 57.5 0 -1899 1 1 0 57.859 54.8571 53.8268 0.785899 0.485712 0.382683 0.490491 45 57.5 57.5 0 -1900 1 1 0 58.0302 54.2713 54.156 0.803016 0.427135 0.415597 0.490491 45 57.5 57.5 0 -1901 1 1 0 58.1623 53.6603 54.4698 0.816233 0.366027 0.446977 0.490491 45 57.5 57.5 0 -1902 1 1 0 58.2518 53.038 54.7623 0.825175 0.303801 0.476225 0.490491 45 57.5 57.5 0 -1903 1 1 0 57.4979 51.8743 56.3458 0.749786 0.187432 0.634579 0.490491 45 57.5 57.5 0 -1904 1 1 0 57.9265 52.1302 55.7125 0.79265 0.213023 0.571251 0.490491 45 57.5 57.5 0 -1905 1 1 0 57.9017 51.4741 55.949 0.79017 0.147413 0.594895 0.490491 45 57.5 57.5 0 -1906 1 1 0 58.3036 52.3723 55.0421 0.830359 0.237228 0.504209 0.490491 45 57.5 57.5 0 -1907 1 1 0 58.3081 51.7253 55.2913 0.830812 0.172532 0.529135 0.490491 45 57.5 57.5 0 -1908 1 1 0 58.2711 51.0649 55.5186 0.82711 0.106494 0.551859 0.490491 45 57.5 57.5 0 -1909 1 1 0 57.4534 53.2214 55.8369 0.745339 0.322141 0.583692 0.490491 45 57.5 57.5 0 -1910 1 1 0 57.9011 52.8032 55.4511 0.790112 0.280319 0.545109 0.490491 45 57.5 57.5 0 -1911 1 1 0 57.4944 52.5518 56.1093 0.749435 0.25518 0.610926 0.490491 45 57.5 57.5 0 -1912 1 1 0 54.1427 57.3501 55.3678 0.414272 0.735011 0.536784 0.490491 45 57.5 57.5 0 -1913 1 1 0 54.8521 57.0447 55.1797 0.485208 0.704471 0.51797 0.490491 45 57.5 57.5 0 -1914 1 1 0 55.5242 56.6961 54.9644 0.552418 0.669612 0.496441 0.490491 45 57.5 57.5 0 -1915 1 1 0 55.1338 56.4658 55.6425 0.513375 0.646578 0.564254 0.490491 45 57.5 57.5 0 -1916 1 1 0 54.4396 56.7898 55.8472 0.443957 0.678977 0.584716 0.490491 45 57.5 57.5 0 -1917 1 1 0 54.7092 56.1924 56.2831 0.470917 0.619242 0.628313 0.490491 45 57.5 57.5 0 -1918 1 1 0 56.1924 56.2831 54.7092 0.619242 0.628313 0.470917 0.490491 45 57.5 57.5 0 -1919 1 1 0 56.7898 55.8472 54.4396 0.678977 0.584716 0.443957 0.490491 45 57.5 57.5 0 -1920 1 1 0 56.4658 55.6425 55.1338 0.646578 0.564254 0.513375 0.490491 45 57.5 57.5 0 -1921 1 1 0 57.3501 55.3678 54.1427 0.735011 0.536784 0.414272 0.490491 45 57.5 57.5 0 -1922 1 1 0 57.0447 55.1797 54.8521 0.704471 0.51797 0.485208 0.490491 45 57.5 57.5 0 -1923 1 1 0 56.6961 54.9644 55.5242 0.669612 0.496441 0.552418 0.490491 45 57.5 57.5 0 -1924 1 1 0 54.9644 55.5242 56.6961 0.496441 0.552418 0.669612 0.490491 45 57.5 57.5 0 -1925 1 1 0 55.6425 55.1338 56.4658 0.564254 0.513375 0.646578 0.490491 45 57.5 57.5 0 -1926 1 1 0 55.1797 54.8521 57.0447 0.51797 0.485208 0.704471 0.490491 45 57.5 57.5 0 -1927 1 1 0 56.2831 54.7092 56.1924 0.628313 0.470917 0.619242 0.490491 45 57.5 57.5 0 -1928 1 1 0 55.8472 54.4396 56.7898 0.584716 0.443957 0.678977 0.490491 45 57.5 57.5 0 -1929 1 1 0 55.3678 54.1427 57.3501 0.536784 0.414272 0.735011 0.490491 45 57.5 57.5 0 -1930 1 1 0 55.8195 56.0748 55.4065 0.581952 0.607478 0.54065 0.490491 45 57.5 57.5 0 -1931 1 1 0 56.0748 55.4065 55.8195 0.607478 0.54065 0.581952 0.490491 45 57.5 57.5 0 -1932 1 1 0 55.4065 55.8195 56.0748 0.54065 0.581952 0.607478 0.490491 45 57.5 57.5 0 -1933 1 1 0 48.9351 55.5186 41.7289 -0.106494 0.551859 -0.82711 0.490491 45 57.5 57.5 0 -1934 1 1 0 48.5259 55.949 42.0983 -0.147413 0.594895 -0.79017 0.490491 45 57.5 57.5 0 -1935 1 1 0 48.1257 56.3458 42.5021 -0.187432 0.634579 -0.749786 0.490491 45 57.5 57.5 0 -1936 1 1 0 47.8698 55.7125 42.0735 -0.213023 0.571251 -0.79265 0.490491 45 57.5 57.5 0 -1937 1 1 0 48.2747 55.2913 41.6919 -0.172532 0.529135 -0.830812 0.490491 45 57.5 57.5 0 -1938 1 1 0 47.6277 55.0421 41.6964 -0.237228 0.504209 -0.830359 0.490491 45 57.5 57.5 0 -1939 1 1 0 47.711 56.7232 42.9602 -0.228899 0.672319 -0.703983 0.490491 45 57.5 57.5 0 -1940 1 1 0 47.3262 57.0524 43.4338 -0.267381 0.705236 -0.65662 0.490491 45 57.5 57.5 0 -1941 1 1 0 47.04 56.4741 42.9769 -0.296004 0.647412 -0.70231 0.490491 45 57.5 57.5 0 -1942 1 1 0 46.9479 57.3479 43.9426 -0.305212 0.734794 -0.605742 0.490491 45 57.5 57.5 0 -1943 1 1 0 46.5857 57.6041 44.4755 -0.341435 0.760406 -0.552454 0.490491 45 57.5 57.5 0 -1944 1 1 0 46.2825 57.0711 43.985 -0.371748 0.707107 -0.601501 0.490491 45 57.5 57.5 0 -1945 1 1 0 46.6531 56.7891 43.465 -0.334691 0.678913 -0.653497 0.490491 45 57.5 57.5 0 -1946 1 1 0 46.3841 56.1919 43.0296 -0.361591 0.619186 -0.697037 0.490491 45 57.5 57.5 0 -1947 1 1 0 46.0023 56.4945 43.5316 -0.399769 0.649448 -0.64684 0.490491 45 57.5 57.5 0 -1948 1 1 0 45.7467 55.8779 43.1181 -0.425325 0.587785 -0.688191 0.490491 45 57.5 57.5 0 -1949 1 1 0 46.962 54.7623 41.7482 -0.303801 0.476225 -0.825175 0.490491 45 57.5 57.5 0 -1950 1 1 0 46.5385 55.1612 42.1655 -0.346153 0.516122 -0.783452 0.490491 45 57.5 57.5 0 -1951 1 1 0 46.3397 54.4698 41.8377 -0.366027 0.446977 -0.816233 0.490491 45 57.5 57.5 0 -1952 1 1 0 46.1327 55.5337 42.6229 -0.38673 0.553372 -0.737712 0.490491 45 57.5 57.5 0 -1953 1 1 0 45.9171 54.8624 42.2742 -0.408286 0.48624 -0.772575 0.490491 45 57.5 57.5 0 -1954 1 1 0 45.5174 55.225 42.747 -0.448259 0.522499 -0.725299 0.490491 45 57.5 57.5 0 -1955 1 1 0 45.3157 54.5399 42.4206 -0.46843 0.45399 -0.757936 0.490491 45 57.5 57.5 0 -1956 1 1 0 45.7287 54.156 41.9698 -0.427135 0.415597 -0.803016 0.490491 45 57.5 57.5 0 -1957 1 1 0 45.1429 53.8268 42.141 -0.485712 0.382683 -0.785899 0.490491 45 57.5 57.5 0 -1958 1 1 0 47.4482 56.1093 42.5056 -0.25518 0.610926 -0.749435 0.490491 45 57.5 57.5 0 -1959 1 1 0 46.7786 55.8369 42.5466 -0.322141 0.583692 -0.745339 0.490491 45 57.5 57.5 0 -1960 1 1 0 47.1968 55.4511 42.0989 -0.280319 0.545109 -0.790112 0.490491 45 57.5 57.5 0 -1961 1 1 0 46.1732 57.859 45.1429 -0.382683 0.785899 -0.485712 0.490491 45 57.5 57.5 0 -1962 1 1 0 45.844 58.0302 45.7287 -0.415597 0.803016 -0.427135 0.490491 45 57.5 57.5 0 -1963 1 1 0 45.4601 57.5794 45.3157 -0.45399 0.757936 -0.46843 0.490491 45 57.5 57.5 0 -1964 1 1 0 45.5302 58.1623 46.3397 -0.446977 0.816233 -0.366027 0.490491 45 57.5 57.5 0 -1965 1 1 0 45.2377 58.2518 46.962 -0.476225 0.825175 -0.303801 0.490491 45 57.5 57.5 0 -1966 1 1 0 44.8388 57.8345 46.5385 -0.516122 0.783452 -0.346153 0.490491 45 57.5 57.5 0 -1967 1 1 0 45.1376 57.7258 45.9171 -0.48624 0.772575 -0.408286 0.490491 45 57.5 57.5 0 -1968 1 1 0 44.775 57.253 45.5174 -0.522499 0.725299 -0.448259 0.490491 45 57.5 57.5 0 -1969 1 1 0 44.4663 57.3771 46.1327 -0.553372 0.737712 -0.38673 0.490491 45 57.5 57.5 0 -1970 1 1 0 44.1221 56.8819 45.7467 -0.587785 0.688191 -0.425325 0.490491 45 57.5 57.5 0 -1971 1 1 0 44.9579 58.3036 47.6277 -0.504209 0.830359 -0.237228 0.490491 45 57.5 57.5 0 -1972 1 1 0 44.7087 58.3081 48.2747 -0.529135 0.830812 -0.172532 0.490491 45 57.5 57.5 0 -1973 1 1 0 44.2875 57.9265 47.8698 -0.571251 0.79265 -0.213023 0.490491 45 57.5 57.5 0 -1974 1 1 0 44.4814 58.2711 48.9351 -0.551859 0.82711 -0.106494 0.490491 45 57.5 57.5 0 -1975 1 1 0 44.051 57.9017 48.5259 -0.594895 0.79017 -0.147413 0.490491 45 57.5 57.5 0 -1976 1 1 0 43.6542 57.4979 48.1257 -0.634579 0.749786 -0.187432 0.490491 45 57.5 57.5 0 -1977 1 1 0 43.8081 56.9704 46.3841 -0.619186 0.697037 -0.361591 0.490491 45 57.5 57.5 0 -1978 1 1 0 43.5055 56.4684 46.0023 -0.649448 0.64684 -0.399769 0.490491 45 57.5 57.5 0 -1979 1 1 0 43.5259 57.0231 47.04 -0.647412 0.70231 -0.296004 0.490491 45 57.5 57.5 0 -1980 1 1 0 43.2109 56.535 46.6531 -0.678913 0.653497 -0.334691 0.490491 45 57.5 57.5 0 -1981 1 1 0 42.9289 56.015 46.2825 -0.707107 0.601501 -0.371748 0.490491 45 57.5 57.5 0 -1982 1 1 0 43.2768 57.0398 47.711 -0.672319 0.703983 -0.228899 0.490491 45 57.5 57.5 0 -1983 1 1 0 42.9476 56.5662 47.3262 -0.705236 0.65662 -0.267381 0.490491 45 57.5 57.5 0 -1984 1 1 0 42.6521 56.0574 46.9479 -0.734794 0.605742 -0.305212 0.490491 45 57.5 57.5 0 -1985 1 1 0 42.3959 55.5245 46.5857 -0.760406 0.552454 -0.341435 0.490491 45 57.5 57.5 0 -1986 1 1 0 44.5489 57.9011 47.1968 -0.545109 0.790112 -0.280319 0.490491 45 57.5 57.5 0 -1987 1 1 0 43.8907 57.4944 47.4482 -0.610926 0.749435 -0.25518 0.490491 45 57.5 57.5 0 -1988 1 1 0 44.1631 57.4534 46.7786 -0.583692 0.745339 -0.322141 0.490491 45 57.5 57.5 0 -1989 1 1 0 44.4755 53.4143 42.3959 -0.552454 0.341435 -0.760406 0.490491 45 57.5 57.5 0 -1990 1 1 0 43.985 53.7175 42.9289 -0.601501 0.371748 -0.707107 0.490491 45 57.5 57.5 0 -1991 1 1 0 43.9426 53.0521 42.6521 -0.605742 0.305212 -0.734794 0.490491 45 57.5 57.5 0 -1992 1 1 0 43.5316 53.9977 43.5055 -0.64684 0.399769 -0.649448 0.490491 45 57.5 57.5 0 -1993 1 1 0 43.465 53.3469 43.2109 -0.653497 0.334691 -0.678913 0.490491 45 57.5 57.5 0 -1994 1 1 0 43.1181 54.2533 44.1221 -0.688191 0.425325 -0.587785 0.490491 45 57.5 57.5 0 -1995 1 1 0 43.0296 53.6159 43.8081 -0.697037 0.361591 -0.619186 0.490491 45 57.5 57.5 0 -1996 1 1 0 42.9769 52.96 43.5259 -0.70231 0.296004 -0.647412 0.490491 45 57.5 57.5 0 -1997 1 1 0 43.4338 52.6738 42.9476 -0.65662 0.267381 -0.705236 0.490491 45 57.5 57.5 0 -1998 1 1 0 42.9602 52.289 43.2768 -0.703983 0.228899 -0.672319 0.490491 45 57.5 57.5 0 -1999 1 1 0 42.747 54.4826 44.775 -0.725299 0.448259 -0.522499 0.490491 45 57.5 57.5 0 -2000 1 1 0 42.6229 53.8673 44.4663 -0.737712 0.38673 -0.553372 0.490491 45 57.5 57.5 0 -2001 1 1 0 42.4206 54.6843 45.4601 -0.757936 0.46843 -0.45399 0.490491 45 57.5 57.5 0 -2002 1 1 0 42.2742 54.0829 45.1376 -0.772575 0.408286 -0.48624 0.490491 45 57.5 57.5 0 -2003 1 1 0 42.1655 53.4615 44.8388 -0.783452 0.346153 -0.516122 0.490491 45 57.5 57.5 0 -2004 1 1 0 42.141 54.8571 46.1732 -0.785899 0.485712 -0.382683 0.490491 45 57.5 57.5 0 -2005 1 1 0 41.9698 54.2713 45.844 -0.803016 0.427135 -0.415597 0.490491 45 57.5 57.5 0 -2006 1 1 0 41.8377 53.6603 45.5302 -0.816233 0.366027 -0.446977 0.490491 45 57.5 57.5 0 -2007 1 1 0 41.7482 53.038 45.2377 -0.825175 0.303801 -0.476225 0.490491 45 57.5 57.5 0 -2008 1 1 0 42.5021 51.8743 43.6542 -0.749786 0.187432 -0.634579 0.490491 45 57.5 57.5 0 -2009 1 1 0 42.0735 52.1302 44.2875 -0.79265 0.213023 -0.571251 0.490491 45 57.5 57.5 0 -2010 1 1 0 42.0983 51.4741 44.051 -0.79017 0.147413 -0.594895 0.490491 45 57.5 57.5 0 -2011 1 1 0 41.6964 52.3723 44.9579 -0.830359 0.237228 -0.504209 0.490491 45 57.5 57.5 0 -2012 1 1 0 41.6919 51.7253 44.7087 -0.830812 0.172532 -0.529135 0.490491 45 57.5 57.5 0 -2013 1 1 0 41.7289 51.0649 44.4814 -0.82711 0.106494 -0.551859 0.490491 45 57.5 57.5 0 -2014 1 1 0 42.5466 53.2214 44.1631 -0.745339 0.322141 -0.583692 0.490491 45 57.5 57.5 0 -2015 1 1 0 42.0989 52.8032 44.5489 -0.790112 0.280319 -0.545109 0.490491 45 57.5 57.5 0 -2016 1 1 0 42.5056 52.5518 43.8907 -0.749435 0.25518 -0.610926 0.490491 45 57.5 57.5 0 -2017 1 1 0 45.8573 57.3501 44.6322 -0.414272 0.735011 -0.536784 0.490491 45 57.5 57.5 0 -2018 1 1 0 45.1479 57.0447 44.8203 -0.485208 0.704471 -0.51797 0.490491 45 57.5 57.5 0 -2019 1 1 0 44.4758 56.6961 45.0356 -0.552418 0.669612 -0.496441 0.490491 45 57.5 57.5 0 -2020 1 1 0 44.8662 56.4658 44.3575 -0.513375 0.646578 -0.564254 0.490491 45 57.5 57.5 0 -2021 1 1 0 45.5604 56.7898 44.1528 -0.443957 0.678977 -0.584716 0.490491 45 57.5 57.5 0 -2022 1 1 0 45.2908 56.1924 43.7169 -0.470917 0.619242 -0.628313 0.490491 45 57.5 57.5 0 -2023 1 1 0 43.8076 56.2831 45.2908 -0.619242 0.628313 -0.470917 0.490491 45 57.5 57.5 0 -2024 1 1 0 43.2102 55.8472 45.5604 -0.678977 0.584716 -0.443957 0.490491 45 57.5 57.5 0 -2025 1 1 0 43.5342 55.6425 44.8662 -0.646578 0.564254 -0.513375 0.490491 45 57.5 57.5 0 -2026 1 1 0 42.6499 55.3678 45.8573 -0.735011 0.536784 -0.414272 0.490491 45 57.5 57.5 0 -2027 1 1 0 42.9553 55.1797 45.1479 -0.704471 0.51797 -0.485208 0.490491 45 57.5 57.5 0 -2028 1 1 0 43.3039 54.9644 44.4758 -0.669612 0.496441 -0.552418 0.490491 45 57.5 57.5 0 -2029 1 1 0 45.0356 55.5242 43.3039 -0.496441 0.552418 -0.669612 0.490491 45 57.5 57.5 0 -2030 1 1 0 44.3575 55.1338 43.5342 -0.564254 0.513375 -0.646578 0.490491 45 57.5 57.5 0 -2031 1 1 0 44.8203 54.8521 42.9553 -0.51797 0.485208 -0.704471 0.490491 45 57.5 57.5 0 -2032 1 1 0 43.7169 54.7092 43.8076 -0.628313 0.470917 -0.619242 0.490491 45 57.5 57.5 0 -2033 1 1 0 44.1528 54.4396 43.2102 -0.584716 0.443957 -0.678977 0.490491 45 57.5 57.5 0 -2034 1 1 0 44.6322 54.1427 42.6499 -0.536784 0.414272 -0.735011 0.490491 45 57.5 57.5 0 -2035 1 1 0 44.1805 56.0748 44.5935 -0.581952 0.607478 -0.54065 0.490491 45 57.5 57.5 0 -2036 1 1 0 43.9252 55.4065 44.1805 -0.607478 0.54065 -0.581952 0.490491 45 57.5 57.5 0 -2037 1 1 0 44.5935 55.8195 43.9252 -0.54065 0.581952 -0.607478 0.490491 45 57.5 57.5 0 -2038 1 1 0 51.0649 55.5186 41.7289 0.106494 0.551859 -0.82711 0.490491 45 57.5 57.5 0 -2039 1 1 0 51.7253 55.2913 41.6919 0.172532 0.529135 -0.830812 0.490491 45 57.5 57.5 0 -2040 1 1 0 52.3723 55.0421 41.6964 0.237228 0.504209 -0.830359 0.490491 45 57.5 57.5 0 -2041 1 1 0 52.1302 55.7125 42.0735 0.213023 0.571251 -0.79265 0.490491 45 57.5 57.5 0 -2042 1 1 0 51.4741 55.949 42.0983 0.147413 0.594895 -0.79017 0.490491 45 57.5 57.5 0 -2043 1 1 0 51.8743 56.3458 42.5021 0.187432 0.634579 -0.749786 0.490491 45 57.5 57.5 0 -2044 1 1 0 53.038 54.7623 41.7482 0.303801 0.476225 -0.825175 0.490491 45 57.5 57.5 0 -2045 1 1 0 53.6603 54.4698 41.8377 0.366027 0.446977 -0.816233 0.490491 45 57.5 57.5 0 -2046 1 1 0 53.4615 55.1612 42.1655 0.346153 0.516122 -0.783452 0.490491 45 57.5 57.5 0 -2047 1 1 0 54.2713 54.156 41.9698 0.427135 0.415597 -0.803016 0.490491 45 57.5 57.5 0 -2048 1 1 0 54.8571 53.8268 42.141 0.485712 0.382683 -0.785899 0.490491 45 57.5 57.5 0 -2049 1 1 0 54.6843 54.5399 42.4206 0.46843 0.45399 -0.757936 0.490491 45 57.5 57.5 0 -2050 1 1 0 54.0829 54.8624 42.2742 0.408286 0.48624 -0.772575 0.490491 45 57.5 57.5 0 -2051 1 1 0 53.8673 55.5337 42.6229 0.38673 0.553372 -0.737712 0.490491 45 57.5 57.5 0 -2052 1 1 0 54.4826 55.225 42.747 0.448259 0.522499 -0.725299 0.490491 45 57.5 57.5 0 -2053 1 1 0 54.2533 55.8779 43.1181 0.425325 0.587785 -0.688191 0.490491 45 57.5 57.5 0 -2054 1 1 0 52.289 56.7232 42.9602 0.228899 0.672319 -0.703983 0.490491 45 57.5 57.5 0 -2055 1 1 0 52.96 56.4741 42.9769 0.296004 0.647412 -0.70231 0.490491 45 57.5 57.5 0 -2056 1 1 0 52.6738 57.0524 43.4338 0.267381 0.705236 -0.65662 0.490491 45 57.5 57.5 0 -2057 1 1 0 53.6159 56.1919 43.0296 0.361591 0.619186 -0.697037 0.490491 45 57.5 57.5 0 -2058 1 1 0 53.3469 56.7891 43.465 0.334691 0.678913 -0.653497 0.490491 45 57.5 57.5 0 -2059 1 1 0 53.9977 56.4945 43.5316 0.399769 0.649448 -0.64684 0.490491 45 57.5 57.5 0 -2060 1 1 0 53.7175 57.0711 43.985 0.371748 0.707107 -0.601501 0.490491 45 57.5 57.5 0 -2061 1 1 0 53.0521 57.3479 43.9426 0.305212 0.734794 -0.605742 0.490491 45 57.5 57.5 0 -2062 1 1 0 53.4143 57.6041 44.4755 0.341435 0.760406 -0.552454 0.490491 45 57.5 57.5 0 -2063 1 1 0 52.8032 55.4511 42.0989 0.280319 0.545109 -0.790112 0.490491 45 57.5 57.5 0 -2064 1 1 0 53.2214 55.8369 42.5466 0.322141 0.583692 -0.745339 0.490491 45 57.5 57.5 0 -2065 1 1 0 52.5518 56.1093 42.5056 0.25518 0.610926 -0.749435 0.490491 45 57.5 57.5 0 -2066 1 1 0 55.5245 53.4143 42.3959 0.552454 0.341435 -0.760406 0.490491 45 57.5 57.5 0 -2067 1 1 0 56.0574 53.0521 42.6521 0.605742 0.305212 -0.734794 0.490491 45 57.5 57.5 0 -2068 1 1 0 56.015 53.7175 42.9289 0.601501 0.371748 -0.707107 0.490491 45 57.5 57.5 0 -2069 1 1 0 56.5662 52.6738 42.9476 0.65662 0.267381 -0.705236 0.490491 45 57.5 57.5 0 -2070 1 1 0 57.0398 52.289 43.2768 0.703983 0.228899 -0.672319 0.490491 45 57.5 57.5 0 -2071 1 1 0 57.0231 52.96 43.5259 0.70231 0.296004 -0.647412 0.490491 45 57.5 57.5 0 -2072 1 1 0 56.535 53.3469 43.2109 0.653497 0.334691 -0.678913 0.490491 45 57.5 57.5 0 -2073 1 1 0 56.4684 53.9977 43.5055 0.64684 0.399769 -0.649448 0.490491 45 57.5 57.5 0 -2074 1 1 0 56.9704 53.6159 43.8081 0.697037 0.361591 -0.619186 0.490491 45 57.5 57.5 0 -2075 1 1 0 56.8819 54.2533 44.1221 0.688191 0.425325 -0.587785 0.490491 45 57.5 57.5 0 -2076 1 1 0 57.4979 51.8743 43.6542 0.749786 0.187432 -0.634579 0.490491 45 57.5 57.5 0 -2077 1 1 0 57.9017 51.4741 44.051 0.79017 0.147413 -0.594895 0.490491 45 57.5 57.5 0 -2078 1 1 0 57.9265 52.1302 44.2875 0.79265 0.213023 -0.571251 0.490491 45 57.5 57.5 0 -2079 1 1 0 58.2711 51.0649 44.4814 0.82711 0.106494 -0.551859 0.490491 45 57.5 57.5 0 -2080 1 1 0 58.3081 51.7253 44.7087 0.830812 0.172532 -0.529135 0.490491 45 57.5 57.5 0 -2081 1 1 0 58.3036 52.3723 44.9579 0.830359 0.237228 -0.504209 0.490491 45 57.5 57.5 0 -2082 1 1 0 57.3771 53.8673 44.4663 0.737712 0.38673 -0.553372 0.490491 45 57.5 57.5 0 -2083 1 1 0 57.253 54.4826 44.775 0.725299 0.448259 -0.522499 0.490491 45 57.5 57.5 0 -2084 1 1 0 57.8345 53.4615 44.8388 0.783452 0.346153 -0.516122 0.490491 45 57.5 57.5 0 -2085 1 1 0 57.7258 54.0829 45.1376 0.772575 0.408286 -0.48624 0.490491 45 57.5 57.5 0 -2086 1 1 0 57.5794 54.6843 45.4601 0.757936 0.46843 -0.45399 0.490491 45 57.5 57.5 0 -2087 1 1 0 58.2518 53.038 45.2377 0.825175 0.303801 -0.476225 0.490491 45 57.5 57.5 0 -2088 1 1 0 58.1623 53.6603 45.5302 0.816233 0.366027 -0.446977 0.490491 45 57.5 57.5 0 -2089 1 1 0 58.0302 54.2713 45.844 0.803016 0.427135 -0.415597 0.490491 45 57.5 57.5 0 -2090 1 1 0 57.859 54.8571 46.1732 0.785899 0.485712 -0.382683 0.490491 45 57.5 57.5 0 -2091 1 1 0 57.4944 52.5518 43.8907 0.749435 0.25518 -0.610926 0.490491 45 57.5 57.5 0 -2092 1 1 0 57.9011 52.8032 44.5489 0.790112 0.280319 -0.545109 0.490491 45 57.5 57.5 0 -2093 1 1 0 57.4534 53.2214 44.1631 0.745339 0.322141 -0.583692 0.490491 45 57.5 57.5 0 -2094 1 1 0 53.8268 57.859 45.1429 0.382683 0.785899 -0.485712 0.490491 45 57.5 57.5 0 -2095 1 1 0 54.5399 57.5794 45.3157 0.45399 0.757936 -0.46843 0.490491 45 57.5 57.5 0 -2096 1 1 0 54.156 58.0302 45.7287 0.415597 0.803016 -0.427135 0.490491 45 57.5 57.5 0 -2097 1 1 0 55.225 57.253 45.5174 0.522499 0.725299 -0.448259 0.490491 45 57.5 57.5 0 -2098 1 1 0 54.8624 57.7258 45.9171 0.48624 0.772575 -0.408286 0.490491 45 57.5 57.5 0 -2099 1 1 0 55.8779 56.8819 45.7467 0.587785 0.688191 -0.425325 0.490491 45 57.5 57.5 0 -2100 1 1 0 55.5337 57.3771 46.1327 0.553372 0.737712 -0.38673 0.490491 45 57.5 57.5 0 -2101 1 1 0 55.1612 57.8345 46.5385 0.516122 0.783452 -0.346153 0.490491 45 57.5 57.5 0 -2102 1 1 0 54.4698 58.1623 46.3397 0.446977 0.816233 -0.366027 0.490491 45 57.5 57.5 0 -2103 1 1 0 54.7623 58.2518 46.962 0.476225 0.825175 -0.303801 0.490491 45 57.5 57.5 0 -2104 1 1 0 56.4945 56.4684 46.0023 0.649448 0.64684 -0.399769 0.490491 45 57.5 57.5 0 -2105 1 1 0 56.1919 56.9704 46.3841 0.619186 0.697037 -0.361591 0.490491 45 57.5 57.5 0 -2106 1 1 0 57.0711 56.015 46.2825 0.707107 0.601501 -0.371748 0.490491 45 57.5 57.5 0 -2107 1 1 0 56.7891 56.535 46.6531 0.678913 0.653497 -0.334691 0.490491 45 57.5 57.5 0 -2108 1 1 0 56.4741 57.0231 47.04 0.647412 0.70231 -0.296004 0.490491 45 57.5 57.5 0 -2109 1 1 0 57.6041 55.5245 46.5857 0.760406 0.552454 -0.341435 0.490491 45 57.5 57.5 0 -2110 1 1 0 57.3479 56.0574 46.9479 0.734794 0.605742 -0.305212 0.490491 45 57.5 57.5 0 -2111 1 1 0 57.0524 56.5662 47.3262 0.705236 0.65662 -0.267381 0.490491 45 57.5 57.5 0 -2112 1 1 0 56.7232 57.0398 47.711 0.672319 0.703983 -0.228899 0.490491 45 57.5 57.5 0 -2113 1 1 0 55.0421 58.3036 47.6277 0.504209 0.830359 -0.237228 0.490491 45 57.5 57.5 0 -2114 1 1 0 55.7125 57.9265 47.8698 0.571251 0.79265 -0.213023 0.490491 45 57.5 57.5 0 -2115 1 1 0 55.2913 58.3081 48.2747 0.529135 0.830812 -0.172532 0.490491 45 57.5 57.5 0 -2116 1 1 0 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48.2692 0.516121 -0.783452 -0.346153 0.489345 45 57.5 1 0.2 +588 1 1 1 52.9389 46.559 47.8734 0.587785 -0.688191 -0.425325 0.489345 45 57.5 1 0.2 +589 1 1 -1 52.8563 46.0368 48.9349 0.571252 -0.792649 -0.213023 0.489345 45 57.5 1 0.2 +590 1 1 1 53.2371 46.4884 48.52 0.647412 -0.70231 -0.296004 0.489345 45 57.5 1 0.2 +591 1 1 -1 53.5355 46.9925 48.1413 0.707107 -0.601501 -0.371748 0.489345 45 57.5 1 0.2 +592 1 1 1 53.0075 48.1413 46.4645 0.601501 -0.371748 -0.707107 0.489345 45 57.5 1 0.2 +593 1 1 -1 53.441 47.8734 47.0611 0.688191 -0.425325 -0.587785 0.489345 45 57.5 1 0.2 +594 1 1 1 53.5116 48.52 46.7629 0.70231 -0.296004 -0.647412 0.489345 45 57.5 1 0.2 +595 1 1 -1 53.7897 47.6579 47.73 0.757936 -0.468429 -0.45399 0.489345 45 57.5 1 0.2 +596 1 1 1 53.9173 48.2692 47.4194 0.783452 -0.346153 -0.516121 0.489345 45 57.5 1 0.2 +597 1 1 -1 53.9632 48.9349 47.1437 0.792649 -0.213023 -0.571252 0.489345 45 57.5 1 0.2 +598 1 1 1 52.5669 46.7671 47.1787 0.513375 -0.646578 -0.564254 0.489345 45 57.5 1 0.2 +599 1 1 -1 53.2329 47.1787 47.4331 0.646578 -0.564254 -0.513375 0.489345 45 57.5 1 0.2 +600 1 1 1 52.8213 47.4331 46.7671 0.564254 -0.513375 -0.646578 0.489345 45 57.5 1 0.2 +601 1 1 -1 48.9349 47.1437 53.9632 -0.213023 -0.571252 0.792649 0.489345 45 57.5 1 0.2 +602 1 1 1 48.52 46.7629 53.5116 -0.296004 -0.647412 0.70231 0.489345 45 57.5 1 0.2 +603 1 1 -1 48.1413 46.4645 53.0075 -0.371748 -0.707107 0.601501 0.489345 45 57.5 1 0.2 +604 1 1 1 47.8734 47.0611 53.441 -0.425325 -0.587785 0.688191 0.489345 45 57.5 1 0.2 +605 1 1 -1 48.2692 47.4194 53.9173 -0.346153 -0.516121 0.783452 0.489345 45 57.5 1 0.2 +606 1 1 1 47.6579 47.73 53.7897 -0.468429 -0.45399 0.757936 0.489345 45 57.5 1 0.2 +607 1 1 -1 47.73 46.2103 52.3421 -0.45399 -0.757936 0.468429 0.489345 45 57.5 1 0.2 +608 1 1 1 47.4194 46.0827 51.7308 -0.516121 -0.783452 0.346153 0.489345 45 57.5 1 0.2 +609 1 1 -1 47.0611 46.559 52.1266 -0.587785 -0.688191 0.425325 0.489345 45 57.5 1 0.2 +610 1 1 1 47.1437 46.0368 51.0651 -0.571252 -0.792649 0.213023 0.489345 45 57.5 1 0.2 +611 1 1 -1 46.7629 46.4884 51.48 -0.647412 -0.70231 0.296004 0.489345 45 57.5 1 0.2 +612 1 1 1 46.4645 46.9925 51.8587 -0.707107 -0.601501 0.371748 0.489345 45 57.5 1 0.2 +613 1 1 -1 46.9925 48.1413 53.5355 -0.601501 -0.371748 0.707107 0.489345 45 57.5 1 0.2 +614 1 1 1 46.559 47.8734 52.9389 -0.688191 -0.425325 0.587785 0.489345 45 57.5 1 0.2 +615 1 1 -1 46.4884 48.52 53.2371 -0.70231 -0.296004 0.647412 0.489345 45 57.5 1 0.2 +616 1 1 1 46.2103 47.6579 52.27 -0.757936 -0.468429 0.45399 0.489345 45 57.5 1 0.2 +617 1 1 -1 46.0827 48.2692 52.5806 -0.783452 -0.346153 0.516121 0.489345 45 57.5 1 0.2 +618 1 1 1 46.0368 48.9349 52.8563 -0.792649 -0.213023 0.571252 0.489345 45 57.5 1 0.2 +619 1 1 -1 47.4331 46.7671 52.8213 -0.513375 -0.646578 0.564254 0.489345 45 57.5 1 0.2 +620 1 1 1 46.7671 47.1787 52.5669 -0.646578 -0.564254 0.513375 0.489345 45 57.5 1 0.2 +621 1 1 -1 47.1787 47.4331 53.2329 -0.564254 -0.513375 0.646578 0.489345 45 57.5 1 0.2 +622 1 1 1 51.0651 47.1437 53.9632 0.213023 -0.571252 0.792649 0.489345 45 57.5 1 0.2 +623 1 1 -1 51.7308 47.4194 53.9173 0.346153 -0.516121 0.783452 0.489345 45 57.5 1 0.2 +624 1 1 1 52.3421 47.73 53.7897 0.468429 -0.45399 0.757936 0.489345 45 57.5 1 0.2 +625 1 1 -1 52.1266 47.0611 53.441 0.425325 -0.587785 0.688191 0.489345 45 57.5 1 0.2 +626 1 1 1 51.48 46.7629 53.5116 0.296004 -0.647412 0.70231 0.489345 45 57.5 1 0.2 +627 1 1 -1 51.8587 46.4645 53.0075 0.371748 -0.707107 0.601501 0.489345 45 57.5 1 0.2 +628 1 1 1 53.0075 48.1413 53.5355 0.601501 -0.371748 0.707107 0.489345 45 57.5 1 0.2 +629 1 1 -1 53.5116 48.52 53.2371 0.70231 -0.296004 0.647412 0.489345 45 57.5 1 0.2 +630 1 1 1 53.441 47.8734 52.9389 0.688191 -0.425325 0.587785 0.489345 45 57.5 1 0.2 +631 1 1 -1 53.9632 48.9349 52.8563 0.792649 -0.213023 0.571252 0.489345 45 57.5 1 0.2 +632 1 1 1 53.9173 48.2692 52.5806 0.783452 -0.346153 0.516121 0.489345 45 57.5 1 0.2 +633 1 1 -1 53.7897 47.6579 52.27 0.757936 -0.468429 0.45399 0.489345 45 57.5 1 0.2 +634 1 1 1 52.27 46.2103 52.3421 0.45399 -0.757936 0.468429 0.489345 45 57.5 1 0.2 +635 1 1 -1 52.9389 46.559 52.1266 0.587785 -0.688191 0.425325 0.489345 45 57.5 1 0.2 +636 1 1 1 52.5806 46.0827 51.7308 0.516121 -0.783452 0.346153 0.489345 45 57.5 1 0.2 +637 1 1 -1 53.5355 46.9925 51.8587 0.707107 -0.601501 0.371748 0.489345 45 57.5 1 0.2 +638 1 1 1 53.2371 46.4884 51.48 0.647412 -0.70231 0.296004 0.489345 45 57.5 1 0.2 +639 1 1 -1 52.8563 46.0368 51.0651 0.571252 -0.792649 0.213023 0.489345 45 57.5 1 0.2 +640 1 1 1 52.8213 47.4331 53.2329 0.564254 -0.513375 0.646578 0.489345 45 57.5 1 0.2 +641 1 1 -1 53.2329 47.1787 52.5669 0.646578 -0.564254 0.513375 0.489345 45 57.5 1 0.2 +642 1 1 1 52.5669 46.7671 52.8213 0.513375 -0.646578 0.564254 0.489345 45 57.5 1 0.2 +643 2 2 1 50 50 57 0 0 1 0.489345 45 57.5 80 0 diff --git a/examples/PACKAGES/dielectric/in.nopbc b/examples/PACKAGES/dielectric/in.nopbc index cbb0d45377..724ad8456a 100644 --- a/examples/PACKAGES/dielectric/in.nopbc +++ b/examples/PACKAGES/dielectric/in.nopbc @@ -18,7 +18,7 @@ read_data ${data} group interface type 1 group ions type 2 3 -pair_style lj/cut/coul/cut/dielectric 1.122 20.0 +pair_style lj/cut/coul/cut/dielectric 1.122 12.0 pair_coeff * * 1.0 1.0 pair_coeff 1 1 0.0 1.0 @@ -27,7 +27,7 @@ neigh_modify one 5000 #compute ef all efield/atom #dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] # -#dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] #dump_modify 1 sort id fix 1 ions nve diff --git a/src/DIELECTRIC/fix_polarize_functional.cpp b/src/DIELECTRIC/fix_polarize_functional.cpp index d751bcd6ce..a0dc034818 100644 --- a/src/DIELECTRIC/fix_polarize_functional.cpp +++ b/src/DIELECTRIC/fix_polarize_functional.cpp @@ -502,11 +502,11 @@ int FixPolarizeFunctional::modify_param(int narg, char **arg) int set_charge = 0; double ediff = utils::numeric(FLERR, arg[iarg + 1], false, lmp); double emean = utils::numeric(FLERR, arg[iarg + 2], false, lmp); - if (strcmp(arg[iarg + 3], "nullptr") != 0) + if (strcmp(arg[iarg + 3], "NULL") != 0) epsiloni = utils::numeric(FLERR, arg[iarg + 3], false, lmp); - if (strcmp(arg[iarg + 4], "nullptr") != 0) + if (strcmp(arg[iarg + 4], "NULL") != 0) areai = utils::numeric(FLERR, arg[iarg + 4], false, lmp); - if (strcmp(arg[iarg + 5], "nullptr") != 0) { + if (strcmp(arg[iarg + 5], "NULL") != 0) { q_unscaled = utils::numeric(FLERR, arg[iarg + 5], false, lmp); set_charge = 1; } From b65623ef1fa281c15d13cb40dfa7eac945216eec Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Tue, 7 Mar 2023 11:57:49 -0600 Subject: [PATCH 087/109] Added back comments to data.sphere --- examples/PACKAGES/dielectric/data.sphere | 1288 +++++++++++----------- 1 file changed, 644 insertions(+), 644 deletions(-) diff --git a/examples/PACKAGES/dielectric/data.sphere b/examples/PACKAGES/dielectric/data.sphere index ede3849635..0c22c2d560 100644 --- a/examples/PACKAGES/dielectric/data.sphere +++ b/examples/PACKAGES/dielectric/data.sphere @@ -1,4 +1,4 @@ -LAMMPS data file: sphere radius = 5; ion distance to center = 7, epsilon inside = 35 outside = 80 +LAMMPS data file: a single ion near a dielectric sphere (radius = 5); ion distance to sphere center = 7; epsilon inside sphere = 35 outside = 80 643 atoms 3 atom types @@ -14,648 +14,648 @@ Masses 2 1 3 1 -Atoms # dielectric +Atoms # dielectric: id mol type q x y z normx normy normz area_per_patch ed em epsilon mean_curvature -1 1 1 -1 50 52.6287 45.7467 0 0.525731 -0.850651 0.489345 45 57.5 1 0.2 -2 1 1 1 50.4054 53.0782 46.0808 0.0810867 0.615642 -0.783843 0.489345 45 57.5 1 0.2 -3 1 1 -1 49.5946 53.0782 46.0808 -0.0810867 0.615642 -0.783843 0.489345 45 57.5 1 0.2 -4 1 1 1 50.8031 53.4689 46.4898 0.160622 0.693781 -0.702046 0.489345 45 57.5 1 0.2 -5 1 1 -1 50 53.5145 46.4436 0 0.702907 -0.711282 0.489345 45 57.5 1 0.2 -6 1 1 1 49.1969 53.4689 46.4898 -0.160622 0.693781 -0.702046 0.489345 45 57.5 1 0.2 -7 1 1 -1 51.1854 53.7933 46.9659 0.237086 0.758653 -0.606824 0.489345 45 57.5 1 0.2 -8 1 1 1 50.4057 53.901 46.8988 0.0811424 0.780205 -0.620239 0.489345 45 57.5 1 0.2 -9 1 1 -1 51.5451 54.0451 47.5 0.309017 0.809017 -0.499999 0.489345 45 57.5 1 0.2 -10 1 1 1 50.7822 54.2009 47.4037 0.156435 0.840178 -0.519258 0.489345 45 57.5 1 0.2 -11 1 1 -1 50 54.2533 47.3713 0 0.850651 -0.52573 0.489345 45 57.5 1 0.2 -12 1 1 1 49.5943 53.901 46.8988 -0.0811424 0.780205 -0.620239 0.489345 45 57.5 1 0.2 -13 1 1 -1 48.8146 53.7933 46.9659 -0.237086 0.758653 -0.606824 0.489345 45 57.5 1 0.2 -14 1 1 1 49.2178 54.2009 47.4037 -0.156435 0.840178 -0.519258 0.489345 45 57.5 1 0.2 -15 1 1 -1 48.4549 54.0451 47.5 -0.309017 0.809017 -0.499999 0.489345 45 57.5 1 0.2 -16 1 1 1 51.8752 54.2196 48.0819 0.375038 0.843912 -0.383614 0.489345 45 57.5 1 0.2 -17 1 1 -1 51.1934 54.455 48.0691 0.238678 0.891006 -0.386187 0.489345 45 57.5 1 0.2 -18 1 1 1 52.1694 54.3133 48.7005 0.433888 0.862669 -0.259892 0.489345 45 57.5 1 0.2 -19 1 1 -1 51.5063 54.5812 48.6796 0.301259 0.916244 -0.264082 0.489345 45 57.5 1 0.2 -20 1 1 1 50.8123 54.7553 48.6857 0.16246 0.951056 -0.262865 0.489345 45 57.5 1 0.2 -21 1 1 -1 52.4222 54.3246 49.344 0.484441 0.864929 -0.1312 0.489345 45 57.5 1 0.2 -22 1 1 1 51.7911 54.6215 49.3417 0.358229 0.924304 -0.131656 0.489345 45 57.5 1 0.2 -23 1 1 -1 52.6287 54.2533 50 0.525731 0.850651 0 0.489345 45 57.5 1 0.2 -24 1 1 1 52.0168 54.5752 50 0.403355 0.915043 0 0.489345 45 57.5 1 0.2 -25 1 1 -1 51.3663 54.8097 50 0.273267 0.961938 0 0.489345 45 57.5 1 0.2 -26 1 1 1 51.1006 54.832 49.336 0.220117 0.966393 -0.132793 0.489345 45 57.5 1 0.2 -27 1 1 -1 50.4112 54.9384 49.3346 0.0822426 0.987688 -0.133071 0.489345 45 57.5 1 0.2 -28 1 1 1 50.6898 54.9522 50 0.137952 0.990439 0 0.489345 45 57.5 1 0.2 -29 1 1 -1 50 55 50 0 1 0 0.489345 45 57.5 1 0.2 -30 1 1 1 48.8066 54.455 48.0691 -0.238678 0.891006 -0.386187 0.489345 45 57.5 1 0.2 -31 1 1 -1 48.1248 54.2196 48.0819 -0.375038 0.843912 -0.383614 0.489345 45 57.5 1 0.2 -32 1 1 1 49.1877 54.7553 48.6857 -0.16246 0.951056 -0.262865 0.489345 45 57.5 1 0.2 -33 1 1 -1 48.4937 54.5812 48.6796 -0.301259 0.916244 -0.264082 0.489345 45 57.5 1 0.2 -34 1 1 1 47.8306 54.3133 48.7005 -0.433888 0.862669 -0.259892 0.489345 45 57.5 1 0.2 -35 1 1 -1 49.5888 54.9384 49.3346 -0.0822426 0.987688 -0.133071 0.489345 45 57.5 1 0.2 -36 1 1 1 48.8994 54.832 49.336 -0.220117 0.966393 -0.132793 0.489345 45 57.5 1 0.2 -37 1 1 -1 49.3102 54.9522 50 -0.137952 0.990439 0 0.489345 45 57.5 1 0.2 -38 1 1 1 48.6337 54.8097 50 -0.273267 0.961938 0 0.489345 45 57.5 1 0.2 -39 1 1 -1 48.2089 54.6215 49.3417 -0.358229 0.924304 -0.131656 0.489345 45 57.5 1 0.2 -40 1 1 1 47.5778 54.3246 49.344 -0.484441 0.864929 -0.1312 0.489345 45 57.5 1 0.2 -41 1 1 -1 47.9832 54.5752 50 -0.403355 0.915043 0 0.489345 45 57.5 1 0.2 -42 1 1 1 47.3713 54.2533 50 -0.525731 0.850651 0 0.489345 45 57.5 1 0.2 -43 1 1 -1 50.4116 54.5649 48.002 0.0823234 0.912983 -0.399606 0.489345 45 57.5 1 0.2 -44 1 1 1 50 54.8193 48.668 0 0.963861 -0.266405 0.489345 45 57.5 1 0.2 -45 1 1 -1 49.5884 54.5649 48.002 -0.0823234 0.912983 -0.399606 0.489345 45 57.5 1 0.2 -46 1 1 1 50 52.6287 54.2533 0 0.525731 0.850651 0.489345 45 57.5 1 0.2 -47 1 1 -1 49.5946 53.0782 53.9192 -0.0810867 0.615642 0.783843 0.489345 45 57.5 1 0.2 -48 1 1 1 50.4054 53.0782 53.9192 0.0810867 0.615642 0.783843 0.489345 45 57.5 1 0.2 -49 1 1 -1 49.1969 53.4689 53.5102 -0.160622 0.693781 0.702046 0.489345 45 57.5 1 0.2 -50 1 1 1 50 53.5145 53.5564 0 0.702907 0.711282 0.489345 45 57.5 1 0.2 -51 1 1 -1 50.8031 53.4689 53.5102 0.160622 0.693781 0.702046 0.489345 45 57.5 1 0.2 -52 1 1 1 48.8146 53.7933 53.0341 -0.237086 0.758653 0.606824 0.489345 45 57.5 1 0.2 -53 1 1 -1 49.5943 53.901 53.1012 -0.0811424 0.780205 0.620239 0.489345 45 57.5 1 0.2 -54 1 1 1 48.4549 54.0451 52.5 -0.309017 0.809017 0.499999 0.489345 45 57.5 1 0.2 -55 1 1 -1 49.2178 54.2009 52.5963 -0.156435 0.840178 0.519258 0.489345 45 57.5 1 0.2 -56 1 1 1 50 54.2533 52.6287 0 0.850651 0.52573 0.489345 45 57.5 1 0.2 -57 1 1 -1 50.4057 53.901 53.1012 0.0811424 0.780205 0.620239 0.489345 45 57.5 1 0.2 -58 1 1 1 51.1854 53.7933 53.0341 0.237086 0.758653 0.606824 0.489345 45 57.5 1 0.2 -59 1 1 -1 50.7822 54.2009 52.5963 0.156435 0.840178 0.519258 0.489345 45 57.5 1 0.2 -60 1 1 1 51.5451 54.0451 52.5 0.309017 0.809017 0.499999 0.489345 45 57.5 1 0.2 -61 1 1 -1 48.1248 54.2196 51.9181 -0.375038 0.843912 0.383614 0.489345 45 57.5 1 0.2 -62 1 1 1 48.8066 54.455 51.9309 -0.238678 0.891006 0.386187 0.489345 45 57.5 1 0.2 -63 1 1 -1 47.8306 54.3133 51.2995 -0.433888 0.862669 0.259892 0.489345 45 57.5 1 0.2 -64 1 1 1 48.4937 54.5812 51.3204 -0.301259 0.916244 0.264082 0.489345 45 57.5 1 0.2 -65 1 1 -1 49.1877 54.7553 51.3143 -0.16246 0.951056 0.262865 0.489345 45 57.5 1 0.2 -66 1 1 1 47.5778 54.3246 50.656 -0.484441 0.864929 0.1312 0.489345 45 57.5 1 0.2 -67 1 1 -1 48.2089 54.6215 50.6583 -0.358229 0.924304 0.131656 0.489345 45 57.5 1 0.2 -68 1 1 1 48.8994 54.832 50.664 -0.220117 0.966393 0.132793 0.489345 45 57.5 1 0.2 -69 1 1 -1 49.5888 54.9384 50.6654 -0.0822426 0.987688 0.133071 0.489345 45 57.5 1 0.2 -70 1 1 1 51.1934 54.455 51.9309 0.238678 0.891006 0.386187 0.489345 45 57.5 1 0.2 -71 1 1 -1 51.8752 54.2196 51.9181 0.375038 0.843912 0.383614 0.489345 45 57.5 1 0.2 -72 1 1 1 50.8123 54.7553 51.3143 0.16246 0.951056 0.262865 0.489345 45 57.5 1 0.2 -73 1 1 -1 51.5063 54.5812 51.3204 0.301259 0.916244 0.264082 0.489345 45 57.5 1 0.2 -74 1 1 1 52.1694 54.3133 51.2995 0.433888 0.862669 0.259892 0.489345 45 57.5 1 0.2 -75 1 1 -1 50.4112 54.9384 50.6654 0.0822426 0.987688 0.133071 0.489345 45 57.5 1 0.2 -76 1 1 1 51.1006 54.832 50.664 0.220117 0.966393 0.132793 0.489345 45 57.5 1 0.2 -77 1 1 -1 51.7911 54.6215 50.6583 0.358229 0.924304 0.131656 0.489345 45 57.5 1 0.2 -78 1 1 1 52.4222 54.3246 50.656 0.484441 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45.4351 48.002 49.5884 -0.912983 -0.399606 -0.0823234 0.489345 45 57.5 57.5 0.2 +396 1 1 1 45.1807 48.668 50 -0.963861 -0.266405 0 0.489345 45 57.5 57.5 0.2 +397 1 1 -1 45.4351 48.002 50.4116 -0.912983 -0.399606 0.0823234 0.489345 45 57.5 57.5 0.2 +398 1 1 1 53.0782 53.9192 49.5946 0.615642 0.783843 -0.0810867 0.489345 45 57.5 57.5 0.2 +399 1 1 -1 53.0782 53.9192 50.4054 0.615642 0.783843 0.0810867 0.489345 45 57.5 57.5 0.2 +400 1 1 1 53.4689 53.5102 49.1969 0.693781 0.702046 -0.160622 0.489345 45 57.5 57.5 0.2 +401 1 1 -1 53.5145 53.5564 50 0.702907 0.711282 0 0.489345 45 57.5 57.5 0.2 +402 1 1 1 53.4689 53.5102 50.8031 0.693781 0.702046 0.160622 0.489345 45 57.5 57.5 0.2 +403 1 1 -1 53.7933 53.0341 48.8146 0.758653 0.606824 -0.237086 0.489345 45 57.5 57.5 0.2 +404 1 1 1 53.901 53.1012 49.5943 0.780205 0.620239 -0.0811424 0.489345 45 57.5 57.5 0.2 +405 1 1 -1 54.0451 52.5 48.4549 0.809017 0.499999 -0.309017 0.489345 45 57.5 57.5 0.2 +406 1 1 1 54.2009 52.5963 49.2178 0.840178 0.519258 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1 1 1 54.6215 50.6583 48.2089 0.924304 0.131656 -0.358229 0.489345 45 57.5 57.5 0.2 +419 1 1 -1 54.5752 50 47.9832 0.915043 0 -0.403355 0.489345 45 57.5 57.5 0.2 +420 1 1 1 54.8097 50 48.6337 0.961938 0 -0.273267 0.489345 45 57.5 57.5 0.2 +421 1 1 -1 54.832 50.664 48.8994 0.966393 0.132793 -0.220117 0.489345 45 57.5 57.5 0.2 +422 1 1 1 54.9384 50.6654 49.5888 0.987688 0.133071 -0.0822426 0.489345 45 57.5 57.5 0.2 +423 1 1 -1 54.9522 50 49.3102 0.990439 0 -0.137952 0.489345 45 57.5 57.5 0.2 +424 1 1 1 55 50 50 1 0 0 0.489345 45 57.5 57.5 0.2 +425 1 1 -1 54.455 51.9309 51.1934 0.891006 0.386187 0.238678 0.489345 45 57.5 57.5 0.2 +426 1 1 1 54.2196 51.9181 51.8752 0.843912 0.383614 0.375038 0.489345 45 57.5 57.5 0.2 +427 1 1 -1 54.7553 51.3143 50.8123 0.951056 0.262865 0.16246 0.489345 45 57.5 57.5 0.2 +428 1 1 1 54.5812 51.3204 51.5063 0.916244 0.264082 0.301259 0.489345 45 57.5 57.5 0.2 +429 1 1 -1 54.3133 51.2995 52.1694 0.862669 0.259892 0.433888 0.489345 45 57.5 57.5 0.2 +430 1 1 1 54.9384 50.6654 50.4112 0.987688 0.133071 0.0822426 0.489345 45 57.5 57.5 0.2 +431 1 1 -1 54.832 50.664 51.1006 0.966393 0.132793 0.220117 0.489345 45 57.5 57.5 0.2 +432 1 1 1 54.9522 50 50.6898 0.990439 0 0.137952 0.489345 45 57.5 57.5 0.2 +433 1 1 -1 54.8097 50 51.3663 0.961938 0 0.273267 0.489345 45 57.5 57.5 0.2 +434 1 1 1 54.6215 50.6583 51.7911 0.924304 0.131656 0.358229 0.489345 45 57.5 57.5 0.2 +435 1 1 -1 54.3246 50.656 52.4222 0.864929 0.1312 0.484441 0.489345 45 57.5 57.5 0.2 +436 1 1 1 54.5752 50 52.0168 0.915043 0 0.403355 0.489345 45 57.5 57.5 0.2 +437 1 1 -1 54.5649 51.998 49.5884 0.912983 0.399606 -0.0823234 0.489345 45 57.5 57.5 0.2 +438 1 1 1 54.8193 51.332 50 0.963861 0.266405 0 0.489345 45 57.5 57.5 0.2 +439 1 1 -1 54.5649 51.998 50.4116 0.912983 0.399606 0.0823234 0.489345 45 57.5 57.5 0.2 +440 1 1 1 53.0782 46.0808 50.4054 0.615642 -0.783843 0.0810867 0.489345 45 57.5 57.5 0.2 +441 1 1 -1 53.0782 46.0808 49.5946 0.615642 -0.783843 -0.0810867 0.489345 45 57.5 57.5 0.2 +442 1 1 1 53.4689 46.4898 50.8031 0.693781 -0.702046 0.160622 0.489345 45 57.5 57.5 0.2 +443 1 1 -1 53.5145 46.4436 50 0.702907 -0.711282 0 0.489345 45 57.5 57.5 0.2 +444 1 1 1 53.4689 46.4898 49.1969 0.693781 -0.702046 -0.160622 0.489345 45 57.5 57.5 0.2 +445 1 1 -1 53.7933 46.9659 51.1854 0.758653 -0.606824 0.237086 0.489345 45 57.5 57.5 0.2 +446 1 1 1 53.901 46.8988 50.4057 0.780205 -0.620239 0.0811424 0.489345 45 57.5 57.5 0.2 +447 1 1 -1 54.0451 47.5 51.5451 0.809017 -0.499999 0.309017 0.489345 45 57.5 57.5 0.2 +448 1 1 1 54.2009 47.4037 50.7822 0.840178 -0.519258 0.156435 0.489345 45 57.5 57.5 0.2 +449 1 1 -1 54.2533 47.3713 50 0.850651 -0.52573 0 0.489345 45 57.5 57.5 0.2 +450 1 1 1 53.901 46.8988 49.5943 0.780205 -0.620239 -0.0811424 0.489345 45 57.5 57.5 0.2 +451 1 1 -1 53.7933 46.9659 48.8146 0.758653 -0.606824 -0.237086 0.489345 45 57.5 57.5 0.2 +452 1 1 1 54.2009 47.4037 49.2178 0.840178 -0.519258 -0.156435 0.489345 45 57.5 57.5 0.2 +453 1 1 -1 54.0451 47.5 48.4549 0.809017 -0.499999 -0.309017 0.489345 45 57.5 57.5 0.2 +454 1 1 1 54.2196 48.0819 51.8752 0.843912 -0.383614 0.375038 0.489345 45 57.5 57.5 0.2 +455 1 1 -1 54.455 48.0691 51.1934 0.891006 -0.386187 0.238678 0.489345 45 57.5 57.5 0.2 +456 1 1 1 54.3133 48.7005 52.1694 0.862669 -0.259892 0.433888 0.489345 45 57.5 57.5 0.2 +457 1 1 -1 54.5812 48.6796 51.5063 0.916244 -0.264082 0.301259 0.489345 45 57.5 57.5 0.2 +458 1 1 1 54.7553 48.6857 50.8123 0.951056 -0.262865 0.16246 0.489345 45 57.5 57.5 0.2 +459 1 1 -1 54.3246 49.344 52.4222 0.864929 -0.1312 0.484441 0.489345 45 57.5 57.5 0.2 +460 1 1 1 54.6215 49.3417 51.7911 0.924304 -0.131656 0.358229 0.489345 45 57.5 57.5 0.2 +461 1 1 -1 54.832 49.336 51.1006 0.966393 -0.132793 0.220117 0.489345 45 57.5 57.5 0.2 +462 1 1 1 54.9384 49.3346 50.4112 0.987688 -0.133071 0.0822426 0.489345 45 57.5 57.5 0.2 +463 1 1 -1 54.455 48.0691 48.8066 0.891006 -0.386187 -0.238678 0.489345 45 57.5 57.5 0.2 +464 1 1 1 54.2196 48.0819 48.1248 0.843912 -0.383614 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57.5 57.5 0.2 +476 1 1 1 48.2692 52.5806 53.9173 -0.346153 0.516121 0.783452 0.489345 45 57.5 57.5 0.2 +477 1 1 -1 47.6579 52.27 53.7897 -0.468429 0.45399 0.757936 0.489345 45 57.5 57.5 0.2 +478 1 1 1 47.8734 52.9389 53.441 -0.425325 0.587785 0.688191 0.489345 45 57.5 57.5 0.2 +479 1 1 -1 48.52 53.2371 53.5116 -0.296004 0.647412 0.70231 0.489345 45 57.5 57.5 0.2 +480 1 1 1 48.1413 53.5355 53.0075 -0.371748 0.707107 0.601501 0.489345 45 57.5 57.5 0.2 +481 1 1 -1 46.9925 51.8587 53.5355 -0.601501 0.371748 0.707107 0.489345 45 57.5 57.5 0.2 +482 1 1 1 46.4884 51.48 53.2371 -0.70231 0.296004 0.647412 0.489345 45 57.5 57.5 0.2 +483 1 1 -1 46.559 52.1266 52.9389 -0.688191 0.425325 0.587785 0.489345 45 57.5 57.5 0.2 +484 1 1 1 46.0368 51.0651 52.8563 -0.792649 0.213023 0.571252 0.489345 45 57.5 57.5 0.2 +485 1 1 -1 46.0827 51.7308 52.5806 -0.783452 0.346153 0.516121 0.489345 45 57.5 57.5 0.2 +486 1 1 1 46.2103 52.3421 52.27 -0.757936 0.468429 0.45399 0.489345 45 57.5 57.5 0.2 +487 1 1 -1 47.73 53.7897 52.3421 -0.45399 0.757936 0.468429 0.489345 45 57.5 57.5 0.2 +488 1 1 1 47.0611 53.441 52.1266 -0.587785 0.688191 0.425325 0.489345 45 57.5 57.5 0.2 +489 1 1 -1 47.4194 53.9173 51.7308 -0.516121 0.783452 0.346153 0.489345 45 57.5 57.5 0.2 +490 1 1 1 46.4645 53.0075 51.8587 -0.707107 0.601501 0.371748 0.489345 45 57.5 57.5 0.2 +491 1 1 -1 46.7629 53.5116 51.48 -0.647412 0.70231 0.296004 0.489345 45 57.5 57.5 0.2 +492 1 1 1 47.1437 53.9632 51.0651 -0.571252 0.792649 0.213023 0.489345 45 57.5 57.5 0.2 +493 1 1 -1 47.1787 52.5669 53.2329 -0.564254 0.513375 0.646578 0.489345 45 57.5 57.5 0.2 +494 1 1 1 46.7671 52.8213 52.5669 -0.646578 0.564254 0.513375 0.489345 45 57.5 57.5 0.2 +495 1 1 -1 47.4331 53.2329 52.8213 -0.513375 0.646578 0.564254 0.489345 45 57.5 57.5 0.2 +496 1 1 1 51.0651 52.8563 53.9632 0.213023 0.571252 0.792649 0.489345 45 57.5 57.5 0.2 +497 1 1 -1 51.48 53.2371 53.5116 0.296004 0.647412 0.70231 0.489345 45 57.5 57.5 0.2 +498 1 1 1 51.8587 53.5355 53.0075 0.371748 0.707107 0.601501 0.489345 45 57.5 57.5 0.2 +499 1 1 -1 52.1266 52.9389 53.441 0.425325 0.587785 0.688191 0.489345 45 57.5 57.5 0.2 +500 1 1 1 51.7308 52.5806 53.9173 0.346153 0.516121 0.783452 0.489345 45 57.5 57.5 0.2 +501 1 1 -1 52.3421 52.27 53.7897 0.468429 0.45399 0.757936 0.489345 45 57.5 57.5 0.2 +502 1 1 1 52.27 53.7897 52.3421 0.45399 0.757936 0.468429 0.489345 45 57.5 57.5 0.2 +503 1 1 -1 52.5806 53.9173 51.7308 0.516121 0.783452 0.346153 0.489345 45 57.5 57.5 0.2 +504 1 1 1 52.9389 53.441 52.1266 0.587785 0.688191 0.425325 0.489345 45 57.5 57.5 0.2 +505 1 1 -1 52.8563 53.9632 51.0651 0.571252 0.792649 0.213023 0.489345 45 57.5 57.5 0.2 +506 1 1 1 53.2371 53.5116 51.48 0.647412 0.70231 0.296004 0.489345 45 57.5 57.5 0.2 +507 1 1 -1 53.5355 53.0075 51.8587 0.707107 0.601501 0.371748 0.489345 45 57.5 57.5 0.2 +508 1 1 1 53.0075 51.8587 53.5355 0.601501 0.371748 0.707107 0.489345 45 57.5 57.5 0.2 +509 1 1 -1 53.441 52.1266 52.9389 0.688191 0.425325 0.587785 0.489345 45 57.5 57.5 0.2 +510 1 1 1 53.5116 51.48 53.2371 0.70231 0.296004 0.647412 0.489345 45 57.5 57.5 0.2 +511 1 1 -1 53.7897 52.3421 52.27 0.757936 0.468429 0.45399 0.489345 45 57.5 57.5 0.2 +512 1 1 1 53.9173 51.7308 52.5806 0.783452 0.346153 0.516121 0.489345 45 57.5 57.5 0.2 +513 1 1 -1 53.9632 51.0651 52.8563 0.792649 0.213023 0.571252 0.489345 45 57.5 57.5 0.2 +514 1 1 1 52.5669 53.2329 52.8213 0.513375 0.646578 0.564254 0.489345 45 57.5 57.5 0.2 +515 1 1 -1 53.2329 52.8213 52.5669 0.646578 0.564254 0.513375 0.489345 45 57.5 57.5 0.2 +516 1 1 1 52.8213 52.5669 53.2329 0.564254 0.513375 0.646578 0.489345 45 57.5 57.5 0.2 +517 1 1 -1 48.9349 52.8563 46.0368 -0.213023 0.571252 -0.792649 0.489345 45 57.5 57.5 0.2 +518 1 1 1 48.52 53.2371 46.4884 -0.296004 0.647412 -0.70231 0.489345 45 57.5 57.5 0.2 +519 1 1 -1 48.1413 53.5355 46.9925 -0.371748 0.707107 -0.601501 0.489345 45 57.5 57.5 0.2 +520 1 1 1 47.8734 52.9389 46.559 -0.425325 0.587785 -0.688191 0.489345 45 57.5 57.5 0.2 +521 1 1 -1 48.2692 52.5806 46.0827 -0.346153 0.516121 -0.783452 0.489345 45 57.5 57.5 0.2 +522 1 1 1 47.6579 52.27 46.2103 -0.468429 0.45399 -0.757936 0.489345 45 57.5 57.5 0.2 +523 1 1 -1 47.73 53.7897 47.6579 -0.45399 0.757936 -0.468429 0.489345 45 57.5 57.5 0.2 +524 1 1 1 47.4194 53.9173 48.2692 -0.516121 0.783452 -0.346153 0.489345 45 57.5 57.5 0.2 +525 1 1 -1 47.0611 53.441 47.8734 -0.587785 0.688191 -0.425325 0.489345 45 57.5 57.5 0.2 +526 1 1 1 47.1437 53.9632 48.9349 -0.571252 0.792649 -0.213023 0.489345 45 57.5 57.5 0.2 +527 1 1 -1 46.7629 53.5116 48.52 -0.647412 0.70231 -0.296004 0.489345 45 57.5 57.5 0.2 +528 1 1 1 46.4645 53.0075 48.1413 -0.707107 0.601501 -0.371748 0.489345 45 57.5 57.5 0.2 +529 1 1 -1 46.9925 51.8587 46.4645 -0.601501 0.371748 -0.707107 0.489345 45 57.5 57.5 0.2 +530 1 1 1 46.559 52.1266 47.0611 -0.688191 0.425325 -0.587785 0.489345 45 57.5 57.5 0.2 +531 1 1 -1 46.4884 51.48 46.7629 -0.70231 0.296004 -0.647412 0.489345 45 57.5 57.5 0.2 +532 1 1 1 46.2103 52.3421 47.73 -0.757936 0.468429 -0.45399 0.489345 45 57.5 57.5 0.2 +533 1 1 -1 46.0827 51.7308 47.4194 -0.783452 0.346153 -0.516121 0.489345 45 57.5 57.5 0.2 +534 1 1 1 46.0368 51.0651 47.1437 -0.792649 0.213023 -0.571252 0.489345 45 57.5 57.5 0.2 +535 1 1 -1 47.4331 53.2329 47.1787 -0.513375 0.646578 -0.564254 0.489345 45 57.5 57.5 0.2 +536 1 1 1 46.7671 52.8213 47.4331 -0.646578 0.564254 -0.513375 0.489345 45 57.5 57.5 0.2 +537 1 1 -1 47.1787 52.5669 46.7671 -0.564254 0.513375 -0.646578 0.489345 45 57.5 57.5 0.2 +538 1 1 1 51.0651 52.8563 46.0368 0.213023 0.571252 -0.792649 0.489345 45 57.5 57.5 0.2 +539 1 1 -1 51.7308 52.5806 46.0827 0.346153 0.516121 -0.783452 0.489345 45 57.5 57.5 0.2 +540 1 1 1 52.3421 52.27 46.2103 0.468429 0.45399 -0.757936 0.489345 45 57.5 57.5 0.2 +541 1 1 -1 52.1266 52.9389 46.559 0.425325 0.587785 -0.688191 0.489345 45 57.5 57.5 0.2 +542 1 1 1 51.48 53.2371 46.4884 0.296004 0.647412 -0.70231 0.489345 45 57.5 57.5 0.2 +543 1 1 -1 51.8587 53.5355 46.9925 0.371748 0.707107 -0.601501 0.489345 45 57.5 57.5 0.2 +544 1 1 1 53.0075 51.8587 46.4645 0.601501 0.371748 -0.707107 0.489345 45 57.5 57.5 0.2 +545 1 1 -1 53.5116 51.48 46.7629 0.70231 0.296004 -0.647412 0.489345 45 57.5 57.5 0.2 +546 1 1 1 53.441 52.1266 47.0611 0.688191 0.425325 -0.587785 0.489345 45 57.5 57.5 0.2 +547 1 1 -1 53.9632 51.0651 47.1437 0.792649 0.213023 -0.571252 0.489345 45 57.5 57.5 0.2 +548 1 1 1 53.9173 51.7308 47.4194 0.783452 0.346153 -0.516121 0.489345 45 57.5 57.5 0.2 +549 1 1 -1 53.7897 52.3421 47.73 0.757936 0.468429 -0.45399 0.489345 45 57.5 57.5 0.2 +550 1 1 1 52.27 53.7897 47.6579 0.45399 0.757936 -0.468429 0.489345 45 57.5 57.5 0.2 +551 1 1 -1 52.9389 53.441 47.8734 0.587785 0.688191 -0.425325 0.489345 45 57.5 57.5 0.2 +552 1 1 1 52.5806 53.9173 48.2692 0.516121 0.783452 -0.346153 0.489345 45 57.5 57.5 0.2 +553 1 1 -1 53.5355 53.0075 48.1413 0.707107 0.601501 -0.371748 0.489345 45 57.5 57.5 0.2 +554 1 1 1 53.2371 53.5116 48.52 0.647412 0.70231 -0.296004 0.489345 45 57.5 57.5 0.2 +555 1 1 -1 52.8563 53.9632 48.9349 0.571252 0.792649 -0.213023 0.489345 45 57.5 57.5 0.2 +556 1 1 1 52.8213 52.5669 46.7671 0.564254 0.513375 -0.646578 0.489345 45 57.5 57.5 0.2 +557 1 1 -1 53.2329 52.8213 47.4331 0.646578 0.564254 -0.513375 0.489345 45 57.5 57.5 0.2 +558 1 1 1 52.5669 53.2329 47.1787 0.513375 0.646578 -0.564254 0.489345 45 57.5 57.5 0.2 +559 1 1 -1 48.9349 47.1437 46.0368 -0.213023 -0.571252 -0.792649 0.489345 45 57.5 57.5 0.2 +560 1 1 1 48.2692 47.4194 46.0827 -0.346153 -0.516121 -0.783452 0.489345 45 57.5 57.5 0.2 +561 1 1 -1 47.6579 47.73 46.2103 -0.468429 -0.45399 -0.757936 0.489345 45 57.5 57.5 0.2 +562 1 1 1 47.8734 47.0611 46.559 -0.425325 -0.587785 -0.688191 0.489345 45 57.5 57.5 0.2 +563 1 1 -1 48.52 46.7629 46.4884 -0.296004 -0.647412 -0.70231 0.489345 45 57.5 57.5 0.2 +564 1 1 1 48.1413 46.4645 46.9925 -0.371748 -0.707107 -0.601501 0.489345 45 57.5 57.5 0.2 +565 1 1 -1 46.9925 48.1413 46.4645 -0.601501 -0.371748 -0.707107 0.489345 45 57.5 57.5 0.2 +566 1 1 1 46.4884 48.52 46.7629 -0.70231 -0.296004 -0.647412 0.489345 45 57.5 57.5 0.2 +567 1 1 -1 46.559 47.8734 47.0611 -0.688191 -0.425325 -0.587785 0.489345 45 57.5 57.5 0.2 +568 1 1 1 46.0368 48.9349 47.1437 -0.792649 -0.213023 -0.571252 0.489345 45 57.5 57.5 0.2 +569 1 1 -1 46.0827 48.2692 47.4194 -0.783452 -0.346153 -0.516121 0.489345 45 57.5 57.5 0.2 +570 1 1 1 46.2103 47.6579 47.73 -0.757936 -0.468429 -0.45399 0.489345 45 57.5 57.5 0.2 +571 1 1 -1 47.73 46.2103 47.6579 -0.45399 -0.757936 -0.468429 0.489345 45 57.5 57.5 0.2 +572 1 1 1 47.0611 46.559 47.8734 -0.587785 -0.688191 -0.425325 0.489345 45 57.5 57.5 0.2 +573 1 1 -1 47.4194 46.0827 48.2692 -0.516121 -0.783452 -0.346153 0.489345 45 57.5 57.5 0.2 +574 1 1 1 46.4645 46.9925 48.1413 -0.707107 -0.601501 -0.371748 0.489345 45 57.5 57.5 0.2 +575 1 1 -1 46.7629 46.4884 48.52 -0.647412 -0.70231 -0.296004 0.489345 45 57.5 57.5 0.2 +576 1 1 1 47.1437 46.0368 48.9349 -0.571252 -0.792649 -0.213023 0.489345 45 57.5 57.5 0.2 +577 1 1 -1 47.1787 47.4331 46.7671 -0.564254 -0.513375 -0.646578 0.489345 45 57.5 57.5 0.2 +578 1 1 1 46.7671 47.1787 47.4331 -0.646578 -0.564254 -0.513375 0.489345 45 57.5 57.5 0.2 +579 1 1 -1 47.4331 46.7671 47.1787 -0.513375 -0.646578 -0.564254 0.489345 45 57.5 57.5 0.2 +580 1 1 1 51.0651 47.1437 46.0368 0.213023 -0.571252 -0.792649 0.489345 45 57.5 57.5 0.2 +581 1 1 -1 51.48 46.7629 46.4884 0.296004 -0.647412 -0.70231 0.489345 45 57.5 57.5 0.2 +582 1 1 1 51.8587 46.4645 46.9925 0.371748 -0.707107 -0.601501 0.489345 45 57.5 57.5 0.2 +583 1 1 -1 52.1266 47.0611 46.559 0.425325 -0.587785 -0.688191 0.489345 45 57.5 57.5 0.2 +584 1 1 1 51.7308 47.4194 46.0827 0.346153 -0.516121 -0.783452 0.489345 45 57.5 57.5 0.2 +585 1 1 -1 52.3421 47.73 46.2103 0.468429 -0.45399 -0.757936 0.489345 45 57.5 57.5 0.2 +586 1 1 1 52.27 46.2103 47.6579 0.45399 -0.757936 -0.468429 0.489345 45 57.5 57.5 0.2 +587 1 1 -1 52.5806 46.0827 48.2692 0.516121 -0.783452 -0.346153 0.489345 45 57.5 57.5 0.2 +588 1 1 1 52.9389 46.559 47.8734 0.587785 -0.688191 -0.425325 0.489345 45 57.5 57.5 0.2 +589 1 1 -1 52.8563 46.0368 48.9349 0.571252 -0.792649 -0.213023 0.489345 45 57.5 57.5 0.2 +590 1 1 1 53.2371 46.4884 48.52 0.647412 -0.70231 -0.296004 0.489345 45 57.5 57.5 0.2 +591 1 1 -1 53.5355 46.9925 48.1413 0.707107 -0.601501 -0.371748 0.489345 45 57.5 57.5 0.2 +592 1 1 1 53.0075 48.1413 46.4645 0.601501 -0.371748 -0.707107 0.489345 45 57.5 57.5 0.2 +593 1 1 -1 53.441 47.8734 47.0611 0.688191 -0.425325 -0.587785 0.489345 45 57.5 57.5 0.2 +594 1 1 1 53.5116 48.52 46.7629 0.70231 -0.296004 -0.647412 0.489345 45 57.5 57.5 0.2 +595 1 1 -1 53.7897 47.6579 47.73 0.757936 -0.468429 -0.45399 0.489345 45 57.5 57.5 0.2 +596 1 1 1 53.9173 48.2692 47.4194 0.783452 -0.346153 -0.516121 0.489345 45 57.5 57.5 0.2 +597 1 1 -1 53.9632 48.9349 47.1437 0.792649 -0.213023 -0.571252 0.489345 45 57.5 57.5 0.2 +598 1 1 1 52.5669 46.7671 47.1787 0.513375 -0.646578 -0.564254 0.489345 45 57.5 57.5 0.2 +599 1 1 -1 53.2329 47.1787 47.4331 0.646578 -0.564254 -0.513375 0.489345 45 57.5 57.5 0.2 +600 1 1 1 52.8213 47.4331 46.7671 0.564254 -0.513375 -0.646578 0.489345 45 57.5 57.5 0.2 +601 1 1 -1 48.9349 47.1437 53.9632 -0.213023 -0.571252 0.792649 0.489345 45 57.5 57.5 0.2 +602 1 1 1 48.52 46.7629 53.5116 -0.296004 -0.647412 0.70231 0.489345 45 57.5 57.5 0.2 +603 1 1 -1 48.1413 46.4645 53.0075 -0.371748 -0.707107 0.601501 0.489345 45 57.5 57.5 0.2 +604 1 1 1 47.8734 47.0611 53.441 -0.425325 -0.587785 0.688191 0.489345 45 57.5 57.5 0.2 +605 1 1 -1 48.2692 47.4194 53.9173 -0.346153 -0.516121 0.783452 0.489345 45 57.5 57.5 0.2 +606 1 1 1 47.6579 47.73 53.7897 -0.468429 -0.45399 0.757936 0.489345 45 57.5 57.5 0.2 +607 1 1 -1 47.73 46.2103 52.3421 -0.45399 -0.757936 0.468429 0.489345 45 57.5 57.5 0.2 +608 1 1 1 47.4194 46.0827 51.7308 -0.516121 -0.783452 0.346153 0.489345 45 57.5 57.5 0.2 +609 1 1 -1 47.0611 46.559 52.1266 -0.587785 -0.688191 0.425325 0.489345 45 57.5 57.5 0.2 +610 1 1 1 47.1437 46.0368 51.0651 -0.571252 -0.792649 0.213023 0.489345 45 57.5 57.5 0.2 +611 1 1 -1 46.7629 46.4884 51.48 -0.647412 -0.70231 0.296004 0.489345 45 57.5 57.5 0.2 +612 1 1 1 46.4645 46.9925 51.8587 -0.707107 -0.601501 0.371748 0.489345 45 57.5 57.5 0.2 +613 1 1 -1 46.9925 48.1413 53.5355 -0.601501 -0.371748 0.707107 0.489345 45 57.5 57.5 0.2 +614 1 1 1 46.559 47.8734 52.9389 -0.688191 -0.425325 0.587785 0.489345 45 57.5 57.5 0.2 +615 1 1 -1 46.4884 48.52 53.2371 -0.70231 -0.296004 0.647412 0.489345 45 57.5 57.5 0.2 +616 1 1 1 46.2103 47.6579 52.27 -0.757936 -0.468429 0.45399 0.489345 45 57.5 57.5 0.2 +617 1 1 -1 46.0827 48.2692 52.5806 -0.783452 -0.346153 0.516121 0.489345 45 57.5 57.5 0.2 +618 1 1 1 46.0368 48.9349 52.8563 -0.792649 -0.213023 0.571252 0.489345 45 57.5 57.5 0.2 +619 1 1 -1 47.4331 46.7671 52.8213 -0.513375 -0.646578 0.564254 0.489345 45 57.5 57.5 0.2 +620 1 1 1 46.7671 47.1787 52.5669 -0.646578 -0.564254 0.513375 0.489345 45 57.5 57.5 0.2 +621 1 1 -1 47.1787 47.4331 53.2329 -0.564254 -0.513375 0.646578 0.489345 45 57.5 57.5 0.2 +622 1 1 1 51.0651 47.1437 53.9632 0.213023 -0.571252 0.792649 0.489345 45 57.5 57.5 0.2 +623 1 1 -1 51.7308 47.4194 53.9173 0.346153 -0.516121 0.783452 0.489345 45 57.5 57.5 0.2 +624 1 1 1 52.3421 47.73 53.7897 0.468429 -0.45399 0.757936 0.489345 45 57.5 57.5 0.2 +625 1 1 -1 52.1266 47.0611 53.441 0.425325 -0.587785 0.688191 0.489345 45 57.5 57.5 0.2 +626 1 1 1 51.48 46.7629 53.5116 0.296004 -0.647412 0.70231 0.489345 45 57.5 57.5 0.2 +627 1 1 -1 51.8587 46.4645 53.0075 0.371748 -0.707107 0.601501 0.489345 45 57.5 57.5 0.2 +628 1 1 1 53.0075 48.1413 53.5355 0.601501 -0.371748 0.707107 0.489345 45 57.5 57.5 0.2 +629 1 1 -1 53.5116 48.52 53.2371 0.70231 -0.296004 0.647412 0.489345 45 57.5 57.5 0.2 +630 1 1 1 53.441 47.8734 52.9389 0.688191 -0.425325 0.587785 0.489345 45 57.5 57.5 0.2 +631 1 1 -1 53.9632 48.9349 52.8563 0.792649 -0.213023 0.571252 0.489345 45 57.5 57.5 0.2 +632 1 1 1 53.9173 48.2692 52.5806 0.783452 -0.346153 0.516121 0.489345 45 57.5 57.5 0.2 +633 1 1 -1 53.7897 47.6579 52.27 0.757936 -0.468429 0.45399 0.489345 45 57.5 57.5 0.2 +634 1 1 1 52.27 46.2103 52.3421 0.45399 -0.757936 0.468429 0.489345 45 57.5 57.5 0.2 +635 1 1 -1 52.9389 46.559 52.1266 0.587785 -0.688191 0.425325 0.489345 45 57.5 57.5 0.2 +636 1 1 1 52.5806 46.0827 51.7308 0.516121 -0.783452 0.346153 0.489345 45 57.5 57.5 0.2 +637 1 1 -1 53.5355 46.9925 51.8587 0.707107 -0.601501 0.371748 0.489345 45 57.5 57.5 0.2 +638 1 1 1 53.2371 46.4884 51.48 0.647412 -0.70231 0.296004 0.489345 45 57.5 57.5 0.2 +639 1 1 -1 52.8563 46.0368 51.0651 0.571252 -0.792649 0.213023 0.489345 45 57.5 57.5 0.2 +640 1 1 1 52.8213 47.4331 53.2329 0.564254 -0.513375 0.646578 0.489345 45 57.5 57.5 0.2 +641 1 1 -1 53.2329 47.1787 52.5669 0.646578 -0.564254 0.513375 0.489345 45 57.5 57.5 0.2 +642 1 1 1 52.5669 46.7671 52.8213 0.513375 -0.646578 0.564254 0.489345 45 57.5 57.5 0.2 643 2 2 1 50 50 57 0 0 1 0.489345 45 57.5 80 0 From a3c90296648f56c698f42b2caf3157a5513ba1c6 Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Tue, 7 Mar 2023 12:02:56 -0600 Subject: [PATCH 088/109] Reverted the cutoff to 20.0 for in.nopbc --- examples/PACKAGES/dielectric/in.nopbc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/PACKAGES/dielectric/in.nopbc b/examples/PACKAGES/dielectric/in.nopbc index 724ad8456a..e6f63f3444 100644 --- a/examples/PACKAGES/dielectric/in.nopbc +++ b/examples/PACKAGES/dielectric/in.nopbc @@ -18,7 +18,7 @@ read_data ${data} group interface type 1 group ions type 2 3 -pair_style lj/cut/coul/cut/dielectric 1.122 12.0 +pair_style lj/cut/coul/cut/dielectric 1.122 20.0 pair_coeff * * 1.0 1.0 pair_coeff 1 1 0.0 1.0 From ce1956e60b198063b519cdfe53ec90f55aad7976 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Mar 2023 13:43:27 -0500 Subject: [PATCH 089/109] avoid linking errors due to nvcc wrapper warning silencing. --- cmake/CMakeLists.txt | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index a6956f5f5d..41229e9cd6 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -538,7 +538,10 @@ set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine separate_arguments(CMAKE_TUNE_FLAGS) foreach(_FLAG ${CMAKE_TUNE_FLAGS}) target_compile_options(lammps PRIVATE ${_FLAG}) - target_compile_options(lmp PRIVATE ${_FLAG}) + # skip these flags when linking the main executable + if(NOT (("${_FLAG}" STREQUAL "-Xcudafe") OR (("${_FLAG}" STREQUAL "--diag_suppress=unrecognized_pragma")))) + target_compile_options(lmp PRIVATE ${_FLAG}) + endif() endforeach() ######################################################################## # Basic system tests (standard libraries, headers, functions, types) # From 4ed49d2f21ffe6a65d022d46906ff9c82ec1ec7a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Mar 2023 13:44:34 -0500 Subject: [PATCH 090/109] make Input::file(const char *) function safe for passing a null pointer --- src/input.cpp | 23 ++++++++++++----------- src/library.cpp | 3 +-- 2 files changed, 13 insertions(+), 13 deletions(-) diff --git a/src/input.cpp b/src/input.cpp index e653704ae3..ef0433dc99 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -327,15 +327,14 @@ void Input::file(const char *filename) // call to file() will close filename and decrement nfile if (me == 0) { - if (nfile == maxfile) - error->one(FLERR,"Too many nested levels of input scripts"); + if (nfile == maxfile) error->one(FLERR,"Too many nested levels of input scripts"); - infile = fopen(filename,"r"); - if (infile == nullptr) - error->one(FLERR,"Cannot open input script {}: {}", - filename, utils::getsyserror()); - - infiles[nfile++] = infile; + if (filename) { + infile = fopen(filename,"r"); + if (infile == nullptr) + error->one(FLERR,"Cannot open input script {}: {}", filename, utils::getsyserror()); + infiles[nfile++] = infile; + } } // process contents of file @@ -343,9 +342,11 @@ void Input::file(const char *filename) file(); if (me == 0) { - fclose(infile); - nfile--; - infile = infiles[nfile-1]; + if (filename) { + fclose(infile); + nfile--; + infile = infiles[nfile-1]; + } } } diff --git a/src/library.cpp b/src/library.cpp index 7fcc22ef17..9f817a1199 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -532,8 +532,7 @@ void lammps_file(void *handle, const char *filename) BEGIN_CAPTURE { if (lmp->update->whichflag != 0) - lmp->error->all(FLERR,"Library error: issuing LAMMPS commands " - "during a run is not allowed."); + lmp->error->all(FLERR, "Library error: issuing LAMMPS commands during a run is not allowed"); else lmp->input->file(filename); } From 19a3e2f6b3229f84a8ade829e56eeed477dec904 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Mar 2023 13:47:09 -0500 Subject: [PATCH 091/109] CUDA 12 is now tested --- cmake/Modules/Packages/GPU.cmake | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/cmake/Modules/Packages/GPU.cmake b/cmake/Modules/Packages/GPU.cmake index 8ac1decc86..22b0bec798 100644 --- a/cmake/Modules/Packages/GPU.cmake +++ b/cmake/Modules/Packages/GPU.cmake @@ -98,9 +98,11 @@ if(GPU_API STREQUAL "CUDA") # comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported if(CUDA_VERSION VERSION_LESS 8.0) message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required") - elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0") + elseif(CUDA_VERSION VERSION_GREATER_EQUAL "13.0") message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk") set(GPU_CUDA_GENCODE "-arch=all") + elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0") + set(GPU_CUDA_GENCODE "-arch=all") else() # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2 if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0")) From 2a3d0458d5e0465f6bb5a127f265c56d1b88dc0c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Mar 2023 13:47:39 -0500 Subject: [PATCH 092/109] simplify --- src/main.cpp | 28 +++++++++++++++++----------- 1 file changed, 17 insertions(+), 11 deletions(-) diff --git a/src/main.cpp b/src/main.cpp index 746ccc41e9..e3e304a0d4 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -34,6 +34,13 @@ using namespace LAMMPS_NS; +// for convenience +static void finalize() +{ + lammps_kokkos_finalize(); + lammps_python_finalize(); +} + /* ---------------------------------------------------------------------- main program to drive LAMMPS ------------------------------------------------------------------------- */ @@ -41,7 +48,6 @@ using namespace LAMMPS_NS; int main(int argc, char **argv) { MPI_Init(&argc, &argv); - MPI_Comm lammps_comm = MPI_COMM_WORLD; #if defined(LMP_MDI) @@ -75,19 +81,21 @@ int main(int argc, char **argv) lammps->input->file(); delete lammps; } catch (LAMMPSAbortException &ae) { - lammps_kokkos_finalize(); - lammps_python_finalize(); + finalize(); MPI_Abort(ae.universe, 1); } catch (LAMMPSException &) { - lammps_kokkos_finalize(); - lammps_python_finalize(); + finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); exit(1); } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); - lammps_kokkos_finalize(); - lammps_python_finalize(); + finalize(); + MPI_Abort(MPI_COMM_WORLD, 1); + exit(1); + } catch (std::exception &e) { + fprintf(stderr, "Exception: %s\n", e.what()); + finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); } @@ -98,14 +106,12 @@ int main(int argc, char **argv) delete lammps; } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); - lammps_kokkos_finalize(); - lammps_python_finalize(); + finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); } #endif - lammps_kokkos_finalize(); - lammps_python_finalize(); + finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); } From 2aa0e76ad97409759cace54a604fb8450579e760 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Mar 2023 13:43:27 -0500 Subject: [PATCH 093/109] avoid linking errors due to nvcc wrapper warning silencing. --- cmake/CMakeLists.txt | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index a6956f5f5d..41229e9cd6 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -538,7 +538,10 @@ set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine separate_arguments(CMAKE_TUNE_FLAGS) foreach(_FLAG ${CMAKE_TUNE_FLAGS}) target_compile_options(lammps PRIVATE ${_FLAG}) - target_compile_options(lmp PRIVATE ${_FLAG}) + # skip these flags when linking the main executable + if(NOT (("${_FLAG}" STREQUAL "-Xcudafe") OR (("${_FLAG}" STREQUAL "--diag_suppress=unrecognized_pragma")))) + target_compile_options(lmp PRIVATE ${_FLAG}) + endif() endforeach() ######################################################################## # Basic system tests (standard libraries, headers, functions, types) # From b21d915a7ce5e1b55008383f3d38ec174c0abc0d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Mar 2023 13:47:39 -0500 Subject: [PATCH 094/109] simplify --- src/main.cpp | 28 +++++++++++++++++----------- 1 file changed, 17 insertions(+), 11 deletions(-) diff --git a/src/main.cpp b/src/main.cpp index 746ccc41e9..e3e304a0d4 100644 --- a/src/main.cpp +++ b/src/main.cpp @@ -34,6 +34,13 @@ using namespace LAMMPS_NS; +// for convenience +static void finalize() +{ + lammps_kokkos_finalize(); + lammps_python_finalize(); +} + /* ---------------------------------------------------------------------- main program to drive LAMMPS ------------------------------------------------------------------------- */ @@ -41,7 +48,6 @@ using namespace LAMMPS_NS; int main(int argc, char **argv) { MPI_Init(&argc, &argv); - MPI_Comm lammps_comm = MPI_COMM_WORLD; #if defined(LMP_MDI) @@ -75,19 +81,21 @@ int main(int argc, char **argv) lammps->input->file(); delete lammps; } catch (LAMMPSAbortException &ae) { - lammps_kokkos_finalize(); - lammps_python_finalize(); + finalize(); MPI_Abort(ae.universe, 1); } catch (LAMMPSException &) { - lammps_kokkos_finalize(); - lammps_python_finalize(); + finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); exit(1); } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); - lammps_kokkos_finalize(); - lammps_python_finalize(); + finalize(); + MPI_Abort(MPI_COMM_WORLD, 1); + exit(1); + } catch (std::exception &e) { + fprintf(stderr, "Exception: %s\n", e.what()); + finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); } @@ -98,14 +106,12 @@ int main(int argc, char **argv) delete lammps; } catch (fmt::format_error &fe) { fprintf(stderr, "fmt::format_error: %s\n", fe.what()); - lammps_kokkos_finalize(); - lammps_python_finalize(); + finalize(); MPI_Abort(MPI_COMM_WORLD, 1); exit(1); } #endif - lammps_kokkos_finalize(); - lammps_python_finalize(); + finalize(); MPI_Barrier(lammps_comm); MPI_Finalize(); } From c2d0734bc46439852fe5615d585d2aae3fd0f5ce Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Mar 2023 14:36:56 -0500 Subject: [PATCH 095/109] rerun updated examples and record log files --- examples/PACKAGES/dielectric/in.nopbc | 2 +- .../dielectric/log.07Mar23.confined.dof.g++.1 | 192 ++++++++++++++++++ .../dielectric/log.07Mar23.confined.dof.g++.4 | 192 ++++++++++++++++++ .../log.07Mar23.confined.gmres.g++.1 | 8 +- .../log.07Mar23.confined.gmres.g++.4 | 8 +- .../dielectric/log.07Mar23.confined.icc.g++.1 | 6 +- .../dielectric/log.07Mar23.confined.icc.g++.4 | 8 +- .../dielectric/log.07Mar23.nopbc.dof.g++.1 | 136 +++++++++++++ .../dielectric/log.07Mar23.nopbc.dof.g++.4 | 136 +++++++++++++ .../dielectric/log.07Mar23.nopbc.gmres.g++.1 | 26 +-- .../dielectric/log.07Mar23.nopbc.gmres.g++.4 | 30 +-- .../dielectric/log.07Mar23.nopbc.icc.g++.1 | 28 +-- .../dielectric/log.07Mar23.nopbc.icc.g++.4 | 30 +-- 13 files changed, 729 insertions(+), 73 deletions(-) create mode 100644 examples/PACKAGES/dielectric/log.07Mar23.confined.dof.g++.1 create mode 100644 examples/PACKAGES/dielectric/log.07Mar23.confined.dof.g++.4 create mode 100644 examples/PACKAGES/dielectric/log.07Mar23.nopbc.dof.g++.1 create mode 100644 examples/PACKAGES/dielectric/log.07Mar23.nopbc.dof.g++.4 diff --git a/examples/PACKAGES/dielectric/in.nopbc b/examples/PACKAGES/dielectric/in.nopbc index e6f63f3444..cbb0d45377 100644 --- a/examples/PACKAGES/dielectric/in.nopbc +++ b/examples/PACKAGES/dielectric/in.nopbc @@ -27,7 +27,7 @@ neigh_modify one 5000 #compute ef all efield/atom #dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] # -dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +#dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] #dump_modify 1 sort id fix 1 ions nve diff --git a/examples/PACKAGES/dielectric/log.07Mar23.confined.dof.g++.1 b/examples/PACKAGES/dielectric/log.07Mar23.confined.dof.g++.1 new file mode 100644 index 0000000000..2634bf3232 --- /dev/null +++ b/examples/PACKAGES/dielectric/log.07Mar23.confined.dof.g++.1 @@ -0,0 +1,192 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +# Two ions, a cation and an anion, confined between two interfaces: epsilon1 | epsilon2 | epsilon1 +# The interface normal vectors should be consistent with ed, pointing from region with epsilon1 to that with epsilon2 +# bottom interface: n = (0, 0, 1) +# top interface: n = (0, 0, -1) +# so that ed's are the same for both interfaces + +# Dielectric constants can be set to be different from the input data file + +variable epsilon1 index 20 +variable epsilon2 index 10 + +variable data index data.confined + +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary p p f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +# compute the relevant values for the interface particles + +variable ed equal "v_epsilon2 - v_epsilon1" +variable em equal "(v_epsilon2 + v_epsilon1)/2" +variable epsilon equal 1.0 # epsilon at the patch, not used for now +variable area equal 0.866 # patch area, same as in the data file + +read_data ${data} +read_data data.confined +Reading data file ... + orthogonal box = (0 0 0) to (40.000006 43.301277 40) + 1 by 1 by 1 MPI processor grid +WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) + reading atoms ... + 4002 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.013 seconds + +group interface type 1 +4000 atoms in group interface +group ions type 2 3 +2 atoms in group ions + +group cations type 2 +1 atoms in group cations +group anions type 3 +1 atoms in group anions + +# set the dielectric constant of the medium where the ions reside + +set group cations epsilon ${epsilon2} +set group cations epsilon 10 +Setting atom values ... + 1 settings made for epsilon +set group anions epsilon ${epsilon2} +set group anions epsilon 10 +Setting atom values ... + 1 settings made for epsilon + +pair_style lj/cut/coul/long/dielectric 1.122 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +kspace_style pppm/dielectric 0.0001 +kspace_modify slab 3.0 + +neigh_modify every 1 delay 0 check yes one 5000 + +#compute ef all efield/atom +#dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id + +#dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1] c_ef[2] c_ef[3] + +fix 1 ions nve + +# fix modify is used to set the properties of the interface particle group + +if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == dof" "fix 3 interface polarize/functional 1 0.0001" "fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" else "print 'Unsupported polarization solver' " +fix 3 interface polarize/functional 1 0.0001 +fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL +fix_modify 3 dielectrics -10 ${em} ${epsilon} ${area} NULL +fix_modify 3 dielectrics -10 15 ${epsilon} ${area} NULL +fix_modify 3 dielectrics -10 15 1 ${area} NULL +fix_modify 3 dielectrics -10 15 1 0.866 NULL + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair #f_3 +thermo_modify flush yes + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006 + +@Article{TrungCPC19, + author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica} + title = {Incorporating Surface Polarization Effects Into Large-Scale + Coarse-Grained Molecular Dynamics Simulation}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2019, + volume = 241, + pages = {80--91} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.24260797 + grid = 12 12 36 + stencil order = 5 + estimated absolute RMS force accuracy = 2.5219574e-07 + estimated relative force accuracy = 2.5219574e-07 + using double precision KISS FFT + 3d grid and FFT values/proc = 10982 5184 +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +Direct solver using a variational approach for 4000 induced charges +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 5000, page size: 100000 + master list distance cutoff = 10.3 + ghost atom cutoff = 10.3 + binsize = 5.15, bins = 8 9 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long/dielectric, perpetual + attributes: full, newton off + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) fix polarize/functional, perpetual, copy from (1) + attributes: full, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 753.9 | 753.9 | 753.9 Mbytes + Step E_vdwl E_coul E_long E_pair + 0 0 0 -1.8534698e-05 -1.8534698e-05 +Loop time of 1.622e-06 on 1 procs for 0 steps with 4002 atoms + +185.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.622e-06 | | |100.00 + +Nlocal: 4002 ave 4002 max 4002 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 4832 ave 4832 max 4832 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: 1.51316e+06 ave 1.51316e+06 max 1.51316e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1513160 +Ave neighs/atom = 378.10095 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + + + + +Total wall time: 0:00:05 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.confined.dof.g++.4 b/examples/PACKAGES/dielectric/log.07Mar23.confined.dof.g++.4 new file mode 100644 index 0000000000..7ece331863 --- /dev/null +++ b/examples/PACKAGES/dielectric/log.07Mar23.confined.dof.g++.4 @@ -0,0 +1,192 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +# Two ions, a cation and an anion, confined between two interfaces: epsilon1 | epsilon2 | epsilon1 +# The interface normal vectors should be consistent with ed, pointing from region with epsilon1 to that with epsilon2 +# bottom interface: n = (0, 0, 1) +# top interface: n = (0, 0, -1) +# so that ed's are the same for both interfaces + +# Dielectric constants can be set to be different from the input data file + +variable epsilon1 index 20 +variable epsilon2 index 10 + +variable data index data.confined + +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary p p f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +# compute the relevant values for the interface particles + +variable ed equal "v_epsilon2 - v_epsilon1" +variable em equal "(v_epsilon2 + v_epsilon1)/2" +variable epsilon equal 1.0 # epsilon at the patch, not used for now +variable area equal 0.866 # patch area, same as in the data file + +read_data ${data} +read_data data.confined +Reading data file ... + orthogonal box = (0 0 0) to (40.000006 43.301277 40) + 2 by 2 by 1 MPI processor grid +WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) + reading atoms ... + 4002 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.013 seconds + +group interface type 1 +4000 atoms in group interface +group ions type 2 3 +2 atoms in group ions + +group cations type 2 +1 atoms in group cations +group anions type 3 +1 atoms in group anions + +# set the dielectric constant of the medium where the ions reside + +set group cations epsilon ${epsilon2} +set group cations epsilon 10 +Setting atom values ... + 1 settings made for epsilon +set group anions epsilon ${epsilon2} +set group anions epsilon 10 +Setting atom values ... + 1 settings made for epsilon + +pair_style lj/cut/coul/long/dielectric 1.122 10.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +kspace_style pppm/dielectric 0.0001 +kspace_modify slab 3.0 + +neigh_modify every 1 delay 0 check yes one 5000 + +#compute ef all efield/atom +#dump 1 all custom 100 all.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump 2 interface custom 100 interface.dump id mol type q x y z #fx fy fz c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id + +#dump 3 ions custom 100 ions.dump id mol type q x y z fx fy fz #c_ef[1] c_ef[2] c_ef[3] + +fix 1 ions nve + +# fix modify is used to set the properties of the interface particle group + +if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" "fix_modify 3 itr_max 50 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" elif "${method} == dof" "fix 3 interface polarize/functional 1 0.0001" "fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL" else "print 'Unsupported polarization solver' " +fix 3 interface polarize/functional 1 0.0001 +fix_modify 3 dielectrics ${ed} ${em} ${epsilon} ${area} NULL +fix_modify 3 dielectrics -10 ${em} ${epsilon} ${area} NULL +fix_modify 3 dielectrics -10 15 ${epsilon} ${area} NULL +fix_modify 3 dielectrics -10 15 1 ${area} NULL +fix_modify 3 dielectrics -10 15 1 0.866 NULL + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair #f_3 +thermo_modify flush yes + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006 + +@Article{TrungCPC19, + author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica} + title = {Incorporating Surface Polarization Effects Into Large-Scale + Coarse-Grained Molecular Dynamics Simulation}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2019, + volume = 241, + pages = {80--91} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:342) + G vector (1/distance) = 0.24260797 + grid = 12 12 36 + stencil order = 5 + estimated absolute RMS force accuracy = 2.5219574e-07 + estimated relative force accuracy = 2.5219574e-07 + using double precision KISS FFT + 3d grid and FFT values/proc = 4598 1296 +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +Direct solver using a variational approach for 4000 induced charges +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 5000, page size: 100000 + master list distance cutoff = 10.3 + ghost atom cutoff = 10.3 + binsize = 5.15, bins = 8 9 8 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/long/dielectric, perpetual + attributes: full, newton off + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) fix polarize/functional, perpetual, copy from (1) + attributes: full, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 744 | 744 | 744 Mbytes + Step E_vdwl E_coul E_long E_pair + 0 0 0 -1.8534698e-05 -1.8534698e-05 +Loop time of 2.36225e-06 on 4 procs for 0 steps with 4002 atoms + +148.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Kspace | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.362e-06 | | |100.00 + +Nlocal: 1000.5 ave 1001 max 1000 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 2889.5 ave 2890 max 2889 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 378290 ave 378465 max 378117 min +Histogram: 2 0 0 0 0 0 0 0 0 2 + +Total # of neighbors = 1513160 +Ave neighs/atom = 378.10095 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + + + + +Total wall time: 0:00:02 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.1 b/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.1 index ca0c22e5d3..5b6461dcdb 100644 --- a/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.1 +++ b/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.1 @@ -47,7 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.001 seconds + special bonds CPU = 0.000 seconds read_data CPU = 0.013 seconds group interface type 1 @@ -149,9 +149,9 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 381.6 | 381.6 | 381.6 Mbytes Step E_vdwl E_coul E_long E_pair 0 0 -1.7228107e-08 -1.8534756e-05 -1.8551984e-05 -Loop time of 1.872e-06 on 1 procs for 0 steps with 4002 atoms +Loop time of 1.939e-06 on 1 procs for 0 steps with 4002 atoms -160.3% CPU use with 1 MPI tasks x 1 OpenMP threads +103.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -163,7 +163,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.872e-06 | | |100.00 +Other | | 1.939e-06 | | |100.00 Nlocal: 4002 ave 4002 max 4002 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.4 b/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.4 index f4e855ad42..fa59c736d4 100644 --- a/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.4 +++ b/examples/PACKAGES/dielectric/log.07Mar23.confined.gmres.g++.4 @@ -48,7 +48,7 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-4 neighbors 1 = max # of special neighbors special bonds CPU = 0.001 seconds - read_data CPU = 0.011 seconds + read_data CPU = 0.012 seconds group interface type 1 4000 atoms in group interface @@ -149,9 +149,9 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 376.2 | 376.2 | 376.2 Mbytes Step E_vdwl E_coul E_long E_pair 0 0 -1.7228107e-08 -1.8534756e-05 -1.8551984e-05 -Loop time of 1.49983e-05 on 4 procs for 0 steps with 4002 atoms +Loop time of 1.6531e-05 on 4 procs for 0 steps with 4002 atoms -85.0% CPU use with 4 MPI tasks x 1 OpenMP threads +102.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -163,7 +163,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.5e-05 | | |100.00 +Other | | 1.653e-05 | | |100.00 Nlocal: 1000.5 ave 1001 max 1000 min Histogram: 2 0 0 0 0 0 0 0 0 2 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.1 b/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.1 index 9c1ab22f90..d63235cff1 100644 --- a/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.1 +++ b/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.1 @@ -151,9 +151,9 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 14.99 | 14.99 | 14.99 Mbytes Step E_vdwl E_coul E_long E_pair 0 0 -1.7228514e-08 -1.8534756e-05 -1.8551985e-05 -Loop time of 1.573e-06 on 1 procs for 0 steps with 4002 atoms +Loop time of 1.823e-06 on 1 procs for 0 steps with 4002 atoms -190.7% CPU use with 1 MPI tasks x 1 OpenMP threads +109.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -165,7 +165,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.573e-06 | | |100.00 +Other | | 1.823e-06 | | |100.00 Nlocal: 4002 ave 4002 max 4002 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.4 b/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.4 index c60b803cd1..e908ce82f9 100644 --- a/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.4 +++ b/examples/PACKAGES/dielectric/log.07Mar23.confined.icc.g++.4 @@ -47,7 +47,7 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.001 seconds + special bonds CPU = 0.000 seconds read_data CPU = 0.012 seconds group interface type 1 @@ -151,9 +151,9 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 9.647 | 9.647 | 9.647 Mbytes Step E_vdwl E_coul E_long E_pair 0 0 -1.7228514e-08 -1.8534756e-05 -1.8551985e-05 -Loop time of 1.23127e-05 on 4 procs for 0 steps with 4002 atoms +Loop time of 2.29425e-06 on 4 procs for 0 steps with 4002 atoms -103.6% CPU use with 4 MPI tasks x 1 OpenMP threads +141.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -165,7 +165,7 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.231e-05 | | |100.00 +Other | | 2.294e-06 | | |100.00 Nlocal: 1000.5 ave 1001 max 1000 min Histogram: 2 0 0 0 0 0 0 0 0 2 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.dof.g++.1 b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.dof.g++.1 new file mode 100644 index 0000000000..f964d4d8f4 --- /dev/null +++ b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.dof.g++.1 @@ -0,0 +1,136 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +# Interface +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary f f f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +variable data index data.sphere + +read_data ${data} +read_data data.sphere +Reading data file ... + orthogonal box = (0 0 0) to (100 100 100) + 1 by 1 by 1 MPI processor grid +WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) + reading atoms ... + 643 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds + +group interface type 1 +642 atoms in group interface +group ions type 2 3 +1 atoms in group ions + +pair_style lj/cut/coul/cut/dielectric 1.122 20.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +neigh_modify one 5000 + +#compute ef all efield/atom +#dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +# +#dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id + +fix 1 ions nve + +if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" elif "${method} == dof" "fix 3 interface polarize/functional 1 1.0e-4" else "print 'Unsupported method for polarization' " +fix 3 interface polarize/functional 1 1.0e-4 + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair +thermo_modify flush yes + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006 + +@Article{TrungCPC19, + author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica} + title = {Incorporating Surface Polarization Effects Into Large-Scale + Coarse-Grained Molecular Dynamics Simulation}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2019, + volume = 241, + pages = {80--91} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +Direct solver using a variational approach for 642 induced charges +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 5000, page size: 100000 + master list distance cutoff = 20.3 + ghost atom cutoff = 20.3 + binsize = 10.15, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/cut/dielectric, perpetual + attributes: full, newton off + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) fix polarize/functional, perpetual, copy from (1) + attributes: full, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 29.83 | 29.83 | 29.83 Mbytes + Step E_vdwl E_coul E_long E_pair + 0 0 -0.011053355 0 -0.011053355 +Loop time of 1.691e-06 on 1 procs for 0 steps with 643 atoms + +177.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.691e-06 | | |100.00 + +Nlocal: 643 ave 643 max 643 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 0 ave 0 max 0 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: 412806 ave 412806 max 412806 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 412806 +Ave neighs/atom = 642 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + + +Total wall time: 0:00:02 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.dof.g++.4 b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.dof.g++.4 new file mode 100644 index 0000000000..f1848bd130 --- /dev/null +++ b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.dof.g++.4 @@ -0,0 +1,136 @@ +LAMMPS (8 Feb 2023) + using 1 OpenMP thread(s) per MPI task +# Interface +newton off +units lj +atom_style dielectric +atom_modify map array +dimension 3 +boundary f f f + +variable method index gmres # gmres = BEM/GMRES + # icc = BEM/ICC* + # dof = Direct optimization of the functional + # none + +variable data index data.sphere + +read_data ${data} +read_data data.sphere +Reading data file ... + orthogonal box = (0 0 0) to (100 100 100) + 1 by 2 by 2 MPI processor grid +WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) + reading atoms ... + 643 atoms +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 0 = max # of 1-2 neighbors + 0 = max # of 1-3 neighbors + 0 = max # of 1-4 neighbors + 1 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.004 seconds + +group interface type 1 +642 atoms in group interface +group ions type 2 3 +1 atoms in group ions + +pair_style lj/cut/coul/cut/dielectric 1.122 20.0 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.0 1.0 + +neigh_modify one 5000 + +#compute ef all efield/atom +#dump 1 all custom 100 all.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +# +#dump 2 interface custom 100 interface.dump id mol type q x y z #c_ef[1] c_ef[2] c_ef[3] +#dump_modify 1 sort id + +fix 1 ions nve + +if "${method} == gmres" then "fix 3 interface polarize/bem/gmres 1 1.0e-4" elif "${method} == icc" "fix 3 interface polarize/bem/icc 1 1.0e-4" elif "${method} == dof" "fix 3 interface polarize/functional 1 1.0e-4" else "print 'Unsupported method for polarization' " +fix 3 interface polarize/functional 1 1.0e-4 + +thermo 1000 +thermo_style custom step evdwl ecoul elong epair +thermo_modify flush yes + +run 0 + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Your simulation uses code contributions which should be cited: + +- DIELECTRIC package: doi:10.1016/j.cpc.2019.03.006 + +@Article{TrungCPC19, + author = {Trung Dac Nguyen and Honghao Li and Debarshee Bagchi and Francisco J. Solis and Olvera de la Cruz, Monica} + title = {Incorporating Surface Polarization Effects Into Large-Scale + Coarse-Grained Molecular Dynamics Simulation}, + journal = {Comput.\ Phys.\ Commun.}, + year = 2019, + volume = 241, + pages = {80--91} +} + +CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE + +Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule +Direct solver using a variational approach for 642 induced charges +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 5000, page size: 100000 + master list distance cutoff = 20.3 + ghost atom cutoff = 20.3 + binsize = 10.15, bins = 10 10 10 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair lj/cut/coul/cut/dielectric, perpetual + attributes: full, newton off + pair build: full/bin + stencil: full/bin/3d + bin: standard + (2) fix polarize/functional, perpetual, copy from (1) + attributes: full, newton off + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 26.9 | 27.48 | 27.67 Mbytes + Step E_vdwl E_coul E_long E_pair + 0 0 -0.011053355 0 -0.011053355 +Loop time of 2.96225e-06 on 4 procs for 0 steps with 643 atoms + +143.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Bond | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 2.962e-06 | | |100.00 + +Nlocal: 160.75 ave 178 max 145 min +Histogram: 1 0 0 0 2 0 0 0 0 1 +Nghost: 482.25 ave 498 max 465 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 103202 ave 114276 max 93090 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 412806 +Ave neighs/atom = 642 +Ave special neighs/atom = 0 +Neighbor list builds = 0 +Dangerous builds = 0 + + + +Total wall time: 0:00:01 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.1 b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.1 index 08cbbb2b7d..77e448b807 100644 --- a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.1 +++ b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.1 @@ -22,7 +22,7 @@ Reading data file ... 1 by 1 by 1 MPI processor grid WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) reading atoms ... - 2563 atoms + 643 atoms Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 @@ -31,10 +31,10 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-4 neighbors 1 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.011 seconds + read_data CPU = 0.004 seconds group interface type 1 -2562 atoms in group interface +642 atoms in group interface group ions type 2 3 1 atoms in group ions @@ -80,7 +80,7 @@ Your simulation uses code contributions which should be cited: CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule -BEM/GMRES solver for 2562 induced charges using maximum 2561 q-vectors +BEM/GMRES solver for 642 induced charges using maximum 641 q-vectors Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 5000, page size: 100000 @@ -93,12 +93,12 @@ Neighbor list info ... pair build: full/bin stencil: full/bin/3d bin: standard -Per MPI rank memory allocation (min/avg/max) = 183.5 | 183.5 | 183.5 Mbytes +Per MPI rank memory allocation (min/avg/max) = 18.6 | 18.6 | 18.6 Mbytes Step E_vdwl E_coul E_long E_pair - 0 0 2.1870454e-07 0 2.1870454e-07 -Loop time of 1.538e-06 on 1 procs for 0 steps with 2563 atoms + 0 0 -0.011226675 0 -0.011226675 +Loop time of 1.659e-06 on 1 procs for 0 steps with 643 atoms -195.1% CPU use with 1 MPI tasks x 1 OpenMP threads +120.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -109,19 +109,19 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.538e-06 | | |100.00 +Other | | 1.659e-06 | | |100.00 -Nlocal: 2563 ave 2563 max 2563 min +Nlocal: 643 ave 643 max 643 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 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: 6.56561e+06 ave 6.56561e+06 max 6.56561e+06 min +FullNghs: 412806 ave 412806 max 412806 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 6565612 -Ave neighs/atom = 2561.6902 +Total # of neighbors = 412806 +Ave neighs/atom = 642 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.4 b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.4 index 060c00a9be..2a7c703e1a 100644 --- a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.4 +++ b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.gmres.g++.4 @@ -22,7 +22,7 @@ Reading data file ... 1 by 2 by 2 MPI processor grid WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) reading atoms ... - 2563 atoms + 643 atoms Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 @@ -30,11 +30,11 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.001 seconds - read_data CPU = 0.009 seconds + special bonds CPU = 0.000 seconds + read_data CPU = 0.003 seconds group interface type 1 -2562 atoms in group interface +642 atoms in group interface group ions type 2 3 1 atoms in group ions @@ -80,7 +80,7 @@ Your simulation uses code contributions which should be cited: CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule -BEM/GMRES solver for 2562 induced charges using maximum 2561 q-vectors +BEM/GMRES solver for 642 induced charges using maximum 641 q-vectors Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 5000, page size: 100000 @@ -93,12 +93,12 @@ Neighbor list info ... pair build: full/bin stencil: full/bin/3d bin: standard -Per MPI rank memory allocation (min/avg/max) = 164.6 | 164.7 | 165 Mbytes +Per MPI rank memory allocation (min/avg/max) = 17.2 | 17.49 | 17.58 Mbytes Step E_vdwl E_coul E_long E_pair - 0 0 2.1870454e-07 0 2.1870454e-07 -Loop time of 2.4415e-06 on 4 procs for 0 steps with 2563 atoms + 0 0 -0.011226675 0 -0.011226675 +Loop time of 6.7975e-06 on 4 procs for 0 steps with 643 atoms -133.1% CPU use with 4 MPI tasks x 1 OpenMP threads +80.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -109,19 +109,19 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.442e-06 | | |100.00 +Other | | 6.797e-06 | | |100.00 -Nlocal: 640.75 ave 674 max 609 min +Nlocal: 160.75 ave 178 max 145 min Histogram: 1 0 0 0 2 0 0 0 0 1 -Nghost: 1922.25 ave 1954 max 1889 min +Nghost: 482.25 ave 498 max 465 min Histogram: 1 0 0 0 0 2 0 0 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 1.6414e+06 ave 1.72639e+06 max 1.56007e+06 min +FullNghs: 103202 ave 114276 max 93090 min Histogram: 1 0 0 0 2 0 0 0 0 1 -Total # of neighbors = 6565612 -Ave neighs/atom = 2561.6902 +Total # of neighbors = 412806 +Ave neighs/atom = 642 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.1 b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.1 index cdde6a228a..91e9ba130b 100644 --- a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.1 +++ b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.1 @@ -22,7 +22,7 @@ Reading data file ... 1 by 1 by 1 MPI processor grid WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) reading atoms ... - 2563 atoms + 643 atoms Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 @@ -31,10 +31,10 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-4 neighbors 1 = max # of special neighbors special bonds CPU = 0.000 seconds - read_data CPU = 0.011 seconds + read_data CPU = 0.004 seconds group interface type 1 -2562 atoms in group interface +642 atoms in group interface group ions type 2 3 1 atoms in group ions @@ -80,7 +80,7 @@ Your simulation uses code contributions which should be cited: CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule -BEM/ICC solver for 2562 induced charges +BEM/ICC solver for 642 induced charges using pair style lj/cut/coul/cut/dielectric Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -94,12 +94,12 @@ Neighbor list info ... pair build: full/bin stencil: full/bin/3d bin: standard -Per MPI rank memory allocation (min/avg/max) = 32.96 | 32.96 | 32.96 Mbytes +Per MPI rank memory allocation (min/avg/max) = 8.898 | 8.898 | 8.898 Mbytes Step E_vdwl E_coul E_long E_pair - 0 0 2.1870503e-07 0 2.1870503e-07 -Loop time of 1.536e-06 on 1 procs for 0 steps with 2563 atoms + 0 0 -0.011226707 0 -0.011226707 +Loop time of 1.532e-06 on 1 procs for 0 steps with 643 atoms -195.3% CPU use with 1 MPI tasks x 1 OpenMP threads +130.5% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -110,23 +110,23 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 1.536e-06 | | |100.00 +Other | | 1.532e-06 | | |100.00 -Nlocal: 2563 ave 2563 max 2563 min +Nlocal: 643 ave 643 max 643 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 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: 6.56561e+06 ave 6.56561e+06 max 6.56561e+06 min +FullNghs: 412806 ave 412806 max 412806 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 6565612 -Ave neighs/atom = 2561.6902 +Total # of neighbors = 412806 +Ave neighs/atom = 642 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 -Total wall time: 0:00:01 +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.4 b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.4 index e329d5c958..0d4eaf79ff 100644 --- a/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.4 +++ b/examples/PACKAGES/dielectric/log.07Mar23.nopbc.icc.g++.4 @@ -22,7 +22,7 @@ Reading data file ... 1 by 2 by 2 MPI processor grid WARNING: Atom style in data file differs from currently defined atom style (src/read_data.cpp:620) reading atoms ... - 2563 atoms + 643 atoms Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 @@ -30,11 +30,11 @@ Finding 1-2 1-3 1-4 neighbors ... 0 = max # of 1-3 neighbors 0 = max # of 1-4 neighbors 1 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.008 seconds + special bonds CPU = 0.001 seconds + read_data CPU = 0.004 seconds group interface type 1 -2562 atoms in group interface +642 atoms in group interface group ions type 2 3 1 atoms in group ions @@ -80,7 +80,7 @@ Your simulation uses code contributions which should be cited: CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule -BEM/ICC solver for 2562 induced charges +BEM/ICC solver for 642 induced charges using pair style lj/cut/coul/cut/dielectric Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes @@ -94,12 +94,12 @@ Neighbor list info ... pair build: full/bin stencil: full/bin/3d bin: standard -Per MPI rank memory allocation (min/avg/max) = 14.03 | 14.12 | 14.41 Mbytes +Per MPI rank memory allocation (min/avg/max) = 7.496 | 7.783 | 7.878 Mbytes Step E_vdwl E_coul E_long E_pair - 0 0 2.1870503e-07 0 2.1870503e-07 -Loop time of 2.408e-06 on 4 procs for 0 steps with 2563 atoms + 0 0 -0.011226707 0 -0.011226707 +Loop time of 6.43925e-06 on 4 procs for 0 steps with 643 atoms -135.0% CPU use with 4 MPI tasks x 1 OpenMP threads +93.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total @@ -110,19 +110,19 @@ Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 2.408e-06 | | |100.00 +Other | | 6.439e-06 | | |100.00 -Nlocal: 640.75 ave 674 max 609 min +Nlocal: 160.75 ave 178 max 145 min Histogram: 1 0 0 0 2 0 0 0 0 1 -Nghost: 1922.25 ave 1954 max 1889 min +Nghost: 482.25 ave 498 max 465 min Histogram: 1 0 0 0 0 2 0 0 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 1.6414e+06 ave 1.72639e+06 max 1.56007e+06 min +FullNghs: 103202 ave 114276 max 93090 min Histogram: 1 0 0 0 2 0 0 0 0 1 -Total # of neighbors = 6565612 -Ave neighs/atom = 2561.6902 +Total # of neighbors = 412806 +Ave neighs/atom = 642 Ave special neighs/atom = 0 Neighbor list builds = 0 Dangerous builds = 0 From 01c03bddf62ea0064b0df3ddce3fab9d43472cb9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Mar 2023 15:22:54 -0500 Subject: [PATCH 096/109] improve style mismatch warning messages in read_data --- src/read_data.cpp | 67 +++++++++++++++++++++++++++-------------------- 1 file changed, 38 insertions(+), 29 deletions(-) diff --git a/src/read_data.cpp b/src/read_data.cpp index 6785e51ecc..bf96fa362a 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -336,8 +336,8 @@ void ReadData::command(int narg, char **arg) error->all(FLERR, "Cannot run 2d simulation with nonperiodic Z dimension"); if ((domain->nonperiodic == 2) && utils::strmatch(force->kspace_style, "^msm")) error->all(FLERR, - "Reading a data file with shrinkwrap boundaries is " - "not compatible with a MSM KSpace style"); + "Reading a data file with shrinkwrap boundaries is not " + "compatible with a MSM KSpace style"); if (domain->box_exist && !addflag) error->all(FLERR, "Cannot use read_data without add keyword after simulation box is defined"); if (!domain->box_exist && addflag) @@ -561,8 +561,8 @@ void ReadData::command(int narg, char **arg) // only done if firstpass and not first data file if (firstpass && addflag != NONE) { - double oldboxlo[3] = { domain->boxlo[0], domain->boxlo[1] , domain->boxlo[2]}; - double oldboxhi[3] = { domain->boxhi[0], domain->boxhi[1] , domain->boxhi[2]}; + double oldboxlo[3] = {domain->boxlo[0], domain->boxlo[1], domain->boxlo[2]}; + double oldboxhi[3] = {domain->boxhi[0], domain->boxhi[1], domain->boxhi[2]}; domain->boxlo[0] = MIN(domain->boxlo[0], boxlo[0] + shift[0]); domain->boxhi[0] = MAX(domain->boxhi[0], boxhi[0] + shift[0]); domain->boxlo[1] = MIN(domain->boxlo[1], boxlo[1] + shift[1]); @@ -575,7 +575,7 @@ void ReadData::command(int narg, char **arg) (oldboxlo[2] != domain->boxlo[2]) || (oldboxhi[0] != domain->boxhi[0]) || (oldboxhi[1] != domain->boxhi[1]) || (oldboxhi[2] != domain->boxhi[2])) { int iflag = 1; - for (int i=0; i < atom->nlocal; ++i) { + for (int i = 0; i < atom->nlocal; ++i) { int xbox = (atom->image[i] & IMGMASK) - IMGMAX; int ybox = (atom->image[i] >> IMGBITS & IMGMASK) - IMGMAX; int zbox = (atom->image[i] >> IMG2BITS) - IMGMAX; @@ -584,9 +584,9 @@ void ReadData::command(int narg, char **arg) if (zbox != 0) iflag = 1; } int flag_all; - MPI_Allreduce(&iflag,&flag_all, 1, MPI_INT, MPI_SUM, world); + MPI_Allreduce(&iflag, &flag_all, 1, MPI_INT, MPI_SUM, world); if ((flag_all > 0) && (comm->me == 0)) - error->warning(FLERR,"Non-zero image flags with growing box leads to bad coordinates"); + error->warning(FLERR, "Non-zero image flags with growing box leads to bad coordinates"); } // NOTE: not sure what to do about tilt value in subsequent data files @@ -617,8 +617,9 @@ void ReadData::command(int narg, char **arg) atomflag = 1; if (firstpass) { if (me == 0 && !style_match(style, atom->atom_style)) - error->warning(FLERR, - "Atom style in data file differs from currently defined atom style"); + error->warning( + FLERR, "Atom style in data file {} differs from currently defined atom style {}", + style, atom->atom_style); atoms(); } else skip_lines(natoms); @@ -696,8 +697,9 @@ void ReadData::command(int narg, char **arg) if (force->pair == nullptr) error->all(FLERR, "Must define pair_style before Pair Coeffs"); if (firstpass) { if (me == 0 && !style_match(style, force->pair_style)) - error->warning(FLERR, - "Pair style in data file differs from currently defined pair style"); + error->warning( + FLERR, "Pair style {} in data file differs from currently defined pair style {}", + style, force->pair_style); paircoeffs(); } else skip_lines(ntypes); @@ -706,9 +708,9 @@ void ReadData::command(int narg, char **arg) error->all(FLERR, "Must define pair_style before PairIJ Coeffs"); if (firstpass) { if (me == 0 && !style_match(style, force->pair_style)) - error->warning(FLERR, - "Pair style in data file differs " - "from currently defined pair style"); + error->warning( + FLERR, "Pair style {} in data file differs from currently defined pair style {}", + style, force->pair_style); pairIJcoeffs(); } else skip_lines(ntypes * (ntypes + 1) / 2); @@ -718,8 +720,9 @@ void ReadData::command(int narg, char **arg) if (force->bond == nullptr) error->all(FLERR, "Must define bond_style before Bond Coeffs"); if (firstpass) { if (me == 0 && !style_match(style, force->bond_style)) - error->warning(FLERR, - "Bond style in data file differs from currently defined bond style"); + error->warning( + FLERR, "Bond style {} in data file differs from currently defined bond style {}", + style, force->bond_style); bondcoeffs(); } else skip_lines(nbondtypes); @@ -730,8 +733,9 @@ void ReadData::command(int narg, char **arg) error->all(FLERR, "Must define angle_style before Angle Coeffs"); if (firstpass) { if (me == 0 && !style_match(style, force->angle_style)) - error->warning(FLERR, - "Angle style in data file differs from currently defined angle style"); + error->warning( + FLERR, "Angle style {} in data file differs from currently defined angle style {}", + style, force->angle_style); anglecoeffs(0); } else skip_lines(nangletypes); @@ -742,9 +746,10 @@ void ReadData::command(int narg, char **arg) error->all(FLERR, "Must define dihedral_style before Dihedral Coeffs"); if (firstpass) { if (me == 0 && !style_match(style, force->dihedral_style)) - error->warning(FLERR, - "Dihedral style in data file differs " - "from currently defined dihedral style"); + error->warning( + FLERR, + "Dihedral style {} in data file differs from currently defined dihedral style {}", + style, force->dihedral_style); dihedralcoeffs(0); } else skip_lines(ndihedraltypes); @@ -755,9 +760,10 @@ void ReadData::command(int narg, char **arg) error->all(FLERR, "Must define improper_style before Improper Coeffs"); if (firstpass) { if (me == 0 && !style_match(style, force->improper_style)) - error->warning(FLERR, - "Improper style in data file differs " - "from currently defined improper style"); + error->warning( + FLERR, + "Improper style {} in data file differs from currently defined improper style {}", + style, force->improper_style); impropercoeffs(0); } else skip_lines(nimpropertypes); @@ -2018,8 +2024,10 @@ void ReadData::pairIJcoeffs() *next = '\0'; parse_coeffs(buf, nullptr, 0, 2, toffset, tlabelflag, lmap->lmap2lmap.atom); if (ncoeffarg == 0) - error->all(FLERR, "Unexpected empty line in PairIJCoeffs section. " - "Expected {} lines.", (ntypes-1)*ntypes); + error->all(FLERR, + "Unexpected empty line in PairIJCoeffs section. " + "Expected {} lines.", + (ntypes - 1) * ntypes); force->pair->coeff(ncoeffarg, coeffarg); buf = next + 1; } @@ -2049,7 +2057,8 @@ void ReadData::bondcoeffs() *next = '\0'; parse_coeffs(buf, nullptr, 0, 1, boffset, blabelflag, lmap->lmap2lmap.bond); if (ncoeffarg == 0) - error->all(FLERR, "Unexpected empty line in BondCoeffs section. Expected {} lines.", nbondtypes); + error->all(FLERR, "Unexpected empty line in BondCoeffs section. Expected {} lines.", + nbondtypes); force->bond->coeff(ncoeffarg, coeffarg); buf = next + 1; } @@ -2442,12 +2451,12 @@ void ReadData::parse_coeffs(char *line, const char *addstr, int dupflag, int nof int value = utils::inumeric(FLERR, coeffarg[0], false, lmp); if (labelmode) value = ilabel[value - 1]; argoffset1 = std::to_string(value + offset); - coeffarg[0] = (char *)argoffset1.c_str(); + coeffarg[0] = (char *) argoffset1.c_str(); if (noffset == 2) { value = utils::inumeric(FLERR, coeffarg[1], false, lmp); if (labelmode) value = ilabel[value - 1]; argoffset2 = std::to_string(value + offset); - coeffarg[1] = (char *)argoffset2.c_str(); + coeffarg[1] = (char *) argoffset2.c_str(); } } } From 381d0445ed6835aa8d9109c954cc358bfd658463 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 7 Mar 2023 19:41:50 -0500 Subject: [PATCH 097/109] fix spelling issues --- doc/src/Install_windows.rst | 2 +- doc/src/balance.rst | 2 +- doc/src/fix_balance.rst | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/src/Install_windows.rst b/doc/src/Install_windows.rst index f23092941a..fdfd406c8b 100644 --- a/doc/src/Install_windows.rst +++ b/doc/src/Install_windows.rst @@ -20,7 +20,7 @@ The LAMMPS binaries contain *all* :doc:`optional packages ` included in the source distribution except: ADIOS, H5MD, KIM, ML-PACE, ML-QUIP, MSCG, NETCDF, PLUMED, QMMM, SCAFACOS, and VTK. The serial version also does not include the MPIIO and LATBOLTZ packages. The -PYTHON package is only available in the Python installaers that bundle a +PYTHON package is only available in the Python installers that bundle a Python runtime. The GPU package is compiled for OpenCL with mixed precision kernels. diff --git a/doc/src/balance.rst b/doc/src/balance.rst index c30c133a8b..4eaa00ea84 100644 --- a/doc/src/balance.rst +++ b/doc/src/balance.rst @@ -498,7 +498,7 @@ data to other processors during load-balancing will be random or deterministic. Random is generally faster; deterministic will ensure the new ordering of atoms on each processor is the same each time the same simulation is run. This can be useful for debugging purposes. -Since the balance commmand is a one-time operation, the default is +Since the balance command is a one-time operation, the default is *yes* to perform sorting. The *out* keyword writes a text file to the specified *filename* with diff --git a/doc/src/fix_balance.rst b/doc/src/fix_balance.rst index 8c65e8341d..0672a05470 100644 --- a/doc/src/fix_balance.rst +++ b/doc/src/fix_balance.rst @@ -314,7 +314,7 @@ data to other processors during load-balancing will be random or deterministic. Random is generally faster; deterministic will ensure the new ordering of atoms on each processor is the same each time the same simulation is run. This can be useful for debugging purposes. -Since the fix balance commmand is performed during timestepping, the +Since the fix balance command is performed during timestepping, the default is *no* so that sorting is not performed. The *out* keyword writes text to the specified *filename* with the From 451f3f71b81867ca841d7e27765bc0cd64992f48 Mon Sep 17 00:00:00 2001 From: alanhsieh4444 <110726422+alanhsieh4444@users.noreply.github.com> Date: Wed, 8 Mar 2023 13:37:46 +0800 Subject: [PATCH 098/109] Update molecule.rst --- doc/src/molecule.rst | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst index 5dcd30f508..c3c578f5ec 100644 --- a/doc/src/molecule.rst +++ b/doc/src/molecule.rst @@ -121,6 +121,11 @@ molecule (header keyword = inertia). ensure space is allocated for storing topology info for molecules that are added later. +---------- + +Format of a molecule file +""""""""""""""""""""" + The format of an individual molecule file is similar but (not identical) to the data file read by the :doc:`read_data ` commands, and is as follows. From c3c99b701cb7b1087af2ff90fb528eaf1a85c036 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 8 Mar 2023 07:21:21 -0500 Subject: [PATCH 099/109] correct underline --- doc/src/molecule.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/molecule.rst b/doc/src/molecule.rst index c3c578f5ec..b42bece327 100644 --- a/doc/src/molecule.rst +++ b/doc/src/molecule.rst @@ -124,7 +124,7 @@ molecule (header keyword = inertia). ---------- Format of a molecule file -""""""""""""""""""""" +""""""""""""""""""""""""" The format of an individual molecule file is similar but (not identical) to the data file read by the :doc:`read_data ` From 189be4625e63c99b82160e8a28620d2a4701d29c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 8 Mar 2023 18:25:58 -0500 Subject: [PATCH 100/109] improve/correct error messages for fix efield --- src/fix_efield.cpp | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/src/fix_efield.cpp b/src/fix_efield.cpp index e1d70e832f..3514ad1c34 100644 --- a/src/fix_efield.cpp +++ b/src/fix_efield.cpp @@ -42,7 +42,7 @@ FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr), estr(nullptr), idregion(nullptr), region(nullptr), efield(nullptr) { - if (narg < 6) error->all(FLERR, "Illegal fix efield command"); + if (narg < 6) utils::missing_cmd_args(FLERR, "fix efield", error); dynamic_group_allow = 1; vector_flag = 1; @@ -85,20 +85,20 @@ FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) : int iarg = 6; while (iarg < narg) { if (strcmp(arg[iarg], "region") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix efield command"); + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix efield region", error); region = domain->get_region_by_id(arg[iarg + 1]); if (!region) error->all(FLERR, "Region {} for fix efield does not exist", arg[iarg + 1]); idregion = utils::strdup(arg[iarg + 1]); iarg += 2; } else if (strcmp(arg[iarg], "energy") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix efield command"); + if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix efield energy", error); if (utils::strmatch(arg[iarg + 1], "^v_")) { estr = utils::strdup(arg[iarg + 1] + 2); } else - error->all(FLERR, "Illegal fix efield command"); + error->all(FLERR, "Illegal fix efield energy value argument"); iarg += 2; } else - error->all(FLERR, "Illegal fix efield command"); + error->all(FLERR, "Unknown fix efield keyword: {}", arg[iarg]); } force_flag = 0; @@ -188,7 +188,7 @@ void FixEfield::init() if (idregion) { region = domain->get_region_by_id(idregion); - if (!region) error->all(FLERR, "Region {} for fix aveforce does not exist", idregion); + if (!region) error->all(FLERR, "Region {} for fix efield does not exist", idregion); } if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM) From 0088607bc71dc140374c77282b15d4d97d730f4c Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 9 Mar 2023 08:31:44 +0200 Subject: [PATCH 101/109] Include method declaration in pair_nm_cut_coul_cut.h --- src/EXTRA-PAIR/pair_nm_cut_coul_cut.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/EXTRA-PAIR/pair_nm_cut_coul_cut.h b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.h index ff51920c63..f2254f7fd3 100644 --- a/src/EXTRA-PAIR/pair_nm_cut_coul_cut.h +++ b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.h @@ -41,6 +41,7 @@ class PairNMCutCoulCut : public Pair { void write_data(FILE *) override; void write_data_all(FILE *) override; double single(int, int, int, int, double, double, double, double &) override; + void born_matrix(int, int, int, int, double, double, double, double &, double &) override; void *extract(const char *, int &) override; protected: From 7da2f62bf6b3285bd0acfe04999b1bcf0fdc11f2 Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 9 Mar 2023 08:33:57 +0200 Subject: [PATCH 102/109] Implement born_matrix in pair_nm_cut_coul_cut.cpp --- src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp | 33 +++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp index adc6d5a058..531f0e615f 100644 --- a/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp +++ b/src/EXTRA-PAIR/pair_nm_cut_coul_cut.cpp @@ -37,6 +37,7 @@ using namespace MathConst; PairNMCutCoulCut::PairNMCutCoulCut(LAMMPS *lmp) : Pair(lmp) { + born_matrix_enable = 1; writedata = 1; } @@ -481,6 +482,38 @@ double PairNMCutCoulCut::single(int i, int j, int itype, int jtype, /* ---------------------------------------------------------------------- */ +void PairNMCutCoulCut::born_matrix(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, double &dupair, + double &du2pair) +{ + double r, rinv, r2inv, r3inv; + double du_lj, du2_lj, du_coul, du2_coul; + + double *q = atom->q; + double qqrd2e = force->qqrd2e; + + r2inv = 1.0 / rsq; + rinv = sqrt(r2inv); + r3inv = r2inv * rinv; + r = sqrt(rsq); + + double prefactor = e0nm[itype][jtype]*nm[itype][jtype]; + + du_lj = prefactor * + (r0m[itype][jtype]/pow(r,mm[itype][jtype]) - r0n[itype][jtype]/pow(r,nn[itype][jtype])) / r; + du2_lj = prefactor * + (r0n[itype][jtype]*(nn[itype][jtype] + 1.0) / pow(r,nn[itype][jtype]) - + r0m[itype][jtype]*(mm[itype][jtype] + 1.0) / pow(r,mm[itype][jtype])) / rsq; + + du_coul = -qqrd2e * q[i] * q[j] * r2inv; + du2_coul = 2.0 * qqrd2e * q[i] * q[j] * r3inv; + + dupair = factor_lj * du_lj + factor_coul * du_coul; + du2pair = factor_lj * du2_lj + factor_coul * du2_coul; +} + +/* ---------------------------------------------------------------------- */ + void *PairNMCutCoulCut::extract(const char *str, int &dim) { dim = 2; From 544a4e3d7f2582b4a44020657bbfb686d06db71b Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 9 Mar 2023 10:03:57 +0200 Subject: [PATCH 103/109] Include method declaration in pair_lj_cut_coul_cut.h --- src/pair_lj_cut_coul_cut.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/pair_lj_cut_coul_cut.h b/src/pair_lj_cut_coul_cut.h index b4e1bfb5c9..fdf54d9340 100644 --- a/src/pair_lj_cut_coul_cut.h +++ b/src/pair_lj_cut_coul_cut.h @@ -40,6 +40,7 @@ class PairLJCutCoulCut : public Pair { void write_data(FILE *) override; void write_data_all(FILE *) override; double single(int, int, int, int, double, double, double, double &) override; + void born_matrix(int, int, int, int, double, double, double, double &, double &) override; void *extract(const char *, int &) override; protected: From d5f6c7e0be742ad19d34cf4e0e8754d029e5197c Mon Sep 17 00:00:00 2001 From: Evangelos Voyiatzis Date: Thu, 9 Mar 2023 10:06:04 +0200 Subject: [PATCH 104/109] Implement born_matrix in pair_lj_cut_coul_cut.cpp --- src/pair_lj_cut_coul_cut.cpp | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/src/pair_lj_cut_coul_cut.cpp b/src/pair_lj_cut_coul_cut.cpp index bc5f5ed93e..5438e82377 100644 --- a/src/pair_lj_cut_coul_cut.cpp +++ b/src/pair_lj_cut_coul_cut.cpp @@ -32,6 +32,7 @@ using namespace MathConst; PairLJCutCoulCut::PairLJCutCoulCut(LAMMPS *lmp) : Pair(lmp) { + born_matrix_enable = 1; writedata = 1; } @@ -460,6 +461,35 @@ double PairLJCutCoulCut::single(int i, int j, int itype, int jtype, double rsq, /* ---------------------------------------------------------------------- */ +void PairLJCutCoulCut::born_matrix(int i, int j, int itype, int jtype, double rsq, + double factor_coul, double factor_lj, double &dupair, + double &du2pair) +{ + double rinv, r2inv, r3inv, r6inv, du, du2; + double du_lj, du2_lj, du_coul, du2_coul; + + double *q = atom->q; + double qqrd2e = force->qqrd2e; + + r2inv = 1.0 / rsq; + rinv = sqrt(r2inv); + r3inv = r2inv * rinv; + r6inv = r2inv * r2inv * r2inv; + + // Reminder: lj1 = 48*e*s^12, lj2 = 24*e*s^6 + + du_lj = r6inv * rinv * (lj2[itype][jtype] - lj1[itype][jtype] * r6inv); + du2_lj = r6inv * r2inv * (13 * lj1[itype][jtype] * r6inv - 7 * lj2[itype][jtype]); + + du_coul = -qqrd2e * q[i] * q[j] * r2inv; + du2_coul = 2.0 * qqrd2e * q[i] * q[j] * r3inv; + + dupair = factor_lj * du_lj + factor_coul * du_coul; + du2pair = factor_lj * du2_lj + factor_coul * du2_coul; +} + +/* ---------------------------------------------------------------------- */ + void *PairLJCutCoulCut::extract(const char *str, int &dim) { dim = 2; From e8871d990ac87f3bb8d59763286268af40d2c42e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 10 Mar 2023 09:16:00 -0500 Subject: [PATCH 105/109] clarify --- doc/src/fix_shake.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_shake.rst b/doc/src/fix_shake.rst index 4688fcbf2a..2483b9431a 100644 --- a/doc/src/fix_shake.rst +++ b/doc/src/fix_shake.rst @@ -63,7 +63,7 @@ however, can *only* be applied during molecular dynamics runs. .. versionchanged:: 15Sep2022 -These fixes may still be used during minimization. In that case the +These fixes may now also be used during minimization. In that case the constraints are *approximated* by strong harmonic restraints. **SHAKE vs RATTLE:** From 233c55337c0a2a6f959bf3ae2665566d84a461e1 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 10 Mar 2023 12:35:17 -0500 Subject: [PATCH 106/109] fix typo --- doc/src/Howto_tip4p.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/Howto_tip4p.rst b/doc/src/Howto_tip4p.rst index 7912557e61..0a263499cc 100644 --- a/doc/src/Howto_tip4p.rst +++ b/doc/src/Howto_tip4p.rst @@ -239,7 +239,7 @@ rigid/nvt/small can identify rigid bodies by their molecule ID: 1 0.00000 -0.06556 0.00000 2 0.75695 0.52032 0.00000 - 2 -0.75695 0.52032 0.00000 + 3 -0.75695 0.52032 0.00000 4 0.00000 0.08444 0.00000 Types From 2dad2586f149b1b2972bc8991f8adc5a1a501a75 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 10 Mar 2023 20:16:39 -0500 Subject: [PATCH 107/109] update help message --- tools/msi2lmp/src/msi2lmp.c | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/msi2lmp/src/msi2lmp.c b/tools/msi2lmp/src/msi2lmp.c index 3136678023..0d9623e322 100644 --- a/tools/msi2lmp/src/msi2lmp.c +++ b/tools/msi2lmp/src/msi2lmp.c @@ -239,7 +239,7 @@ int main (int argc, char *argv[]) frc_dir_name = getenv("MSI2LMP_LIBRARY"); if (argc < 2) { - printf("usage: %s [-class ] [-frc ] [-print #] [-ignore] [-nocenter] [-oldstyle]\n",argv[0]); + printf("usage: %s [-class ] [-frc ] [-print #] [-ignore] [-nocenter] [-oldstyle]\n",argv[0]); return 1; } else { /* rootname was supplied as first argument, copy to rootname */ int len = strlen(argv[1]) + 1; From 80233f353f7966bf6eda1c4c8c335a024abf0651 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 10 Mar 2023 20:56:55 -0500 Subject: [PATCH 108/109] port UTF-8 to ASCII substitution to msi2lmp and apply to reading .frc files --- tools/msi2lmp/src/SearchAndFill.c | 11 +++- tools/msi2lmp/src/msi2lmp.c | 98 +++++++++++++++++++++++++++++++ tools/msi2lmp/src/msi2lmp.h | 3 + 3 files changed, 110 insertions(+), 2 deletions(-) diff --git a/tools/msi2lmp/src/SearchAndFill.c b/tools/msi2lmp/src/SearchAndFill.c index ff05ff13d0..f195e739c9 100644 --- a/tools/msi2lmp/src/SearchAndFill.c +++ b/tools/msi2lmp/src/SearchAndFill.c @@ -48,6 +48,7 @@ const char *SearchAndCheck(const char *keyword) fprintf(stderr," Exiting....\n"); exit(1); } + if (has_utf8(line)) utf8_subst(line); if (line[0] == '@') { if (string_match(strtok(line+1," '\t\n\r\f("),keyword)) { got_it = 1; @@ -82,6 +83,7 @@ void SearchAndFill(struct FrcFieldItem *item) fprintf(stderr," Exiting....\n"); exit(1); } + if (has_utf8(line)) utf8_subst(line); if (line[0] == '#') { if (string_match(strtok(line," '\t\r\n("),item->keyword)) got_it = 1; } @@ -116,13 +118,16 @@ void SearchAndFill(struct FrcFieldItem *item) ctr = 0; while ( strncmp(line,"!---", 4) != 0 ) { fgets(line, MAX_LINE_LENGTH, FrcF); + if (has_utf8(line)) utf8_subst(line); } /* Get first line of data that isn't commented out */ fgets(line, MAX_LINE_LENGTH, FrcF); + if (has_utf8(line)) utf8_subst(line); while (strncmp(line,"!",1) == 0) { fgets( line, MAX_LINE_LENGTH, FrcF); + if (has_utf8(line)) utf8_subst(line); } /* Read data into structure */ @@ -225,11 +230,13 @@ void SearchAndFill(struct FrcFieldItem *item) ctr++; } fgets( line, MAX_LINE_LENGTH, FrcF); + if (has_utf8(line)) utf8_subst(line); + /*if blank line encountered, get next */ - while((blank_line(line)) || - (strncmp(line,"!",1) == 0)) { + while((blank_line(line)) || (strncmp(line,"!",1) == 0)) { status = fgets( line, MAX_LINE_LENGTH, FrcF); if (status == NULL) break; + if (has_utf8(line)) utf8_subst(line); } } item->entries = ctr; diff --git a/tools/msi2lmp/src/msi2lmp.c b/tools/msi2lmp/src/msi2lmp.c index 0d9623e322..2eb05fd5c5 100644 --- a/tools/msi2lmp/src/msi2lmp.c +++ b/tools/msi2lmp/src/msi2lmp.c @@ -444,3 +444,101 @@ int main (int argc, char *argv[]) printf("\nNormal program termination\n"); return 0; } + +/* detect if a line has UTF-8 characters */ + +int has_utf8(const char *line) +{ + const unsigned char *c = (const unsigned char *)line; + + while (*c != '\0') { + if (*c & 0x80U) return 1; + ++c; + } + return 0; +} + +/* replace UTF-8 characters with ASCII counterparts where known and possible */ + +void utf8_subst(char *line) +{ + unsigned char *buf, *in, *out; + int i, len; + + in = (unsigned char *)line; + len = strlen(line); + buf = (unsigned char *)malloc(len+1); + out = buf; + + for (i = 0; i < len; ++i) { + + /* UTF-8 2-byte character */ + if ((in[i] & 0xe0U) == 0xc0U) { + if ((i + 1) < len) { + /* NON-BREAKING SPACE (U+00A0) */ + if ((in[i] == 0xc2U) && (in[i + 1] == 0xa0U)) *out++ = ' ', ++i; + /* MODIFIER LETTER PLUS SIGN (U+02D6) */ + if ((in[i] == 0xcbU) && (in[i + 1] == 0x96U)) *out++ = '+', ++i; + /* MODIFIER LETTER MINUS SIGN (U+02D7) */ + if ((in[i] == 0xcbU) && (in[i + 1] == 0x97U)) *out++ = '-', ++i; + } + /* UTF-8 3-byte character */ + } else if ((in[i] & 0xf0U) == 0xe0U) { + if ((i + 2) < len) { + /* EN QUAD (U+2000) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x80U)) *out++ = ' ', i += 2; + /* EM QUAD (U+2001) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x81U)) *out++ = ' ', i += 2; + /* EN SPACE (U+2002) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x82U)) *out++ = ' ', i += 2; + /* EM SPACE (U+2003) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x83U)) *out++ = ' ', i += 2; + /* THREE-PER-EM SPACE (U+2004) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x84U)) *out++ = ' ', i += 2; + /* FOUR-PER-EM SPACE (U+2005) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x85U)) *out++ = ' ', i += 2; + /* SIX-PER-EM SPACE (U+2006) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x86U)) *out++ = ' ', i += 2; + /* FIGURE SPACE (U+2007) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x87U)) *out++ = ' ', i += 2; + /* PUNCTUATION SPACE (U+2008) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x88U)) *out++ = ' ', i += 2; + /* THIN SPACE (U+2009) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x89U)) *out++ = ' ', i += 2; + /* HAIR SPACE (U+200A) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x8aU)) *out++ = ' ', i += 2; + /* ZERO WIDTH SPACE (U+200B) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x8bU)) *out++ = ' ', i += 2; + /* LEFT SINGLE QUOTATION MARK (U+2018) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x98U)) *out++ = '\'', i += 2; + /* RIGHT SINGLE QUOTATION MARK (U+2019) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x99U)) *out++ = '\'', i += 2; + /* LEFT DOUBLE QUOTATION MARK (U+201C) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x9cU)) *out++ = '"', i += 2; + /* RIGHT DOUBLE QUOTATION MARK (U+201D) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x9dU)) *out++ = '"', i += 2; + /* NARROW NO-BREAK SPACE (U+202F) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0xafU)) *out++ = ' ', i += 2; + /* WORD JOINER (U+2060) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x81U) && (in[i + 2] == 0xa0U)) *out++ = ' ', i += 2; + /* INVISIBLE SEPARATOR (U+2063) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x81U) && (in[i + 2] == 0xa3U)) *out++ = ' ', i += 2; + /* INVISIBLE PLUS (U+2064) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x81U) && (in[i + 2] == 0xa4U)) *out++ = '+', i += 2; + /* MINUS SIGN (U+2212) */ + if ((in[i] == 0xe2U) && (in[i + 1] == 0x88U) && (in[i + 2] == 0x92U)) *out++ = '-', i += 2; + /* ZERO WIDTH NO-BREAK SPACE (U+FEFF) */ + if ((in[i] == 0xefU) && (in[i + 1] == 0xbbU) && (in[i + 2] == 0xbfU)) *out++ = ' ', i += 2; + } + /* UTF-8 4-byte character */ + } else if ((in[i] & 0xf8U) == 0xf0U) { + if ((i + 3) < len) { ; } + } else { + *out++ = in[i]; + } + } + + *out = '\0'; + strncpy(line, (char *)buf, len); + free(buf); +} diff --git a/tools/msi2lmp/src/msi2lmp.h b/tools/msi2lmp/src/msi2lmp.h index af7978d181..b64c6fd834 100644 --- a/tools/msi2lmp/src/msi2lmp.h +++ b/tools/msi2lmp/src/msi2lmp.h @@ -226,3 +226,6 @@ extern void lamda2x(double *lamda, double *x, double *h, double *boxlo); extern void x2lamda(double *x, double *lamda, double *h_inv, double *boxlo); extern void condexit(int); + +extern int has_utf8(const char *line); +extern void utf8_subst(char *line); From 2b6c2e07a4ece5619711b53f732d491b64a1e805 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 10 Mar 2023 21:26:40 -0500 Subject: [PATCH 109/109] add -help flag and help message output. step version number. update docs. --- doc/msi2lmp.1 | 7 ++- tools/msi2lmp/README | 19 ++++++-- tools/msi2lmp/src/msi2lmp.c | 93 +++++++++++++++++++++++++++++++------ tools/msi2lmp/src/msi2lmp.h | 2 +- 4 files changed, 101 insertions(+), 20 deletions(-) diff --git a/doc/msi2lmp.1 b/doc/msi2lmp.1 index f088603483..5cb0754e4f 100644 --- a/doc/msi2lmp.1 +++ b/doc/msi2lmp.1 @@ -1,11 +1,11 @@ -.TH MSI2LMP "1" "v3.9.9" "2018-11-05" +.TH MSI2LMP "1" "v3.9.10" "2023-03-10" .SH NAME .B MSI2LMP \- Converter for Materials Studio files to LAMMPS .SH SYNOPSIS .B msi2lmp - [-class ] [-frc ] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift ] +[-help] [-class ] [-frc ] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift ] .SH DESCRIPTION .PP @@ -22,6 +22,9 @@ needed between .frc and .car/.mdf files are the atom types. .SH OPTIONS .TP +\fB\-h\fR, \fB\-help\fR, +Print detailed help message to the screen and stop. +.TP \fB\\fR This has to be the first argument and is a .B mandatory diff --git a/tools/msi2lmp/README b/tools/msi2lmp/README index 401ec536fd..9c9706fc97 100644 --- a/tools/msi2lmp/README +++ b/tools/msi2lmp/README @@ -76,10 +76,14 @@ This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT The program is started by supplying information at the command prompt according to the usage described below. - USAGE: msi2lmp.exe {-print #} {-class #} {-frc FRC_FILE} - {-ignore} {-nocenter} {-shift # # #} + USAGE: msi2lmp.exe [-help] [-print #] [-class #] [-frc FRC_FILE] + [-ignore] [-nocenter] [-shift # # #] -- msi2lmp.exe is the name of the executable + + -- -help (or -h) + Print detailed this help message and exit. + -- is the base name of the .car and .mdf files -- -print (or -p) @@ -148,6 +152,15 @@ msi2lmp has the following known limitations: CHANGELOG +10 Mar 2023 Axel Kohlmeyer + +Substitute UTF-8 characters in .frc files with known ASCII equivalents +and add help message output + +05 Nov 2018 Axel Kohlmeyer + +Teach msi2lmp to not generate dihedrals with identical 1-4 atoms + 06 Oct 2016 Axel Kohlmeyer Improved whitespace handling in parsing topology and force field @@ -239,5 +252,5 @@ for number_of_dihedrals, etc. could be unpredictable in these systems. ----------------------------- - msi2lmp v3.9.8 6/10/2016 + msi2lmp v3.9.10 3/10/2023 diff --git a/tools/msi2lmp/src/msi2lmp.c b/tools/msi2lmp/src/msi2lmp.c index 2eb05fd5c5..68aaf566b2 100644 --- a/tools/msi2lmp/src/msi2lmp.c +++ b/tools/msi2lmp/src/msi2lmp.c @@ -2,26 +2,29 @@ * * msi2lmp.exe * -* v3.9.9 AK- Teach msi2lmp to not generate dihedrals with identical 1-4 atoms +* v3.9.10 AK - Substitute UTF-8 characters in .frc files with known ASCII equivalents +* - add help message output * -* v3.9.8 AK- Improved whitespace handling in parsing topology and force -* field files to avoid bogus warnings about type name truncation +* v3.9.9 AK - Teach msi2lmp to not generate dihedrals with identical 1-4 atoms * -* v3.9.7 AK- Add check to enforce that Class1/OPLS-AA use A-B parameter -* conventions in force field file and Class2 us r-eps conventions +* v3.9.8 AK - Improved whitespace handling in parsing topology and force +* field files to avoid bogus warnings about type name truncation * -* v3.9.6 AK- Refactoring of MDF file parser with more consistent -* handling of compile time constants MAX_NAME and MAX_STRING +* v3.9.7 AK - Add check to enforce that Class1/OPLS-AA use A-B parameter +* conventions in force field file and Class2 us r-eps conventions * -* v3.9.5 AK- Add TopoTools style force field parameter type hints +* v3.9.6 AK - Refactoring of MDF file parser with more consistent +* handling of compile time constants MAX_NAME and MAX_STRING * -* v3.9.4 AK- Make force field style hints optional with a flag +* v3.9.5 AK - Add TopoTools style force field parameter type hints * -* v3.9.3 AK- Bugfix for triclinic cells. +* v3.9.4 AK - Make force field style hints optional with a flag * -* v3.9.2 AK- Support for writing out force field style hints +* v3.9.3 AK - Bugfix for triclinic cells. * -* v3.9.1 AK- Bugfix for Class2. Free allocated memory. Print version number. +* v3.9.2 AK - Support for writing out force field style hints +* +* v3.9.1 AK - Bugfix for Class2. Free allocated memory. Print version number. * * v3.9 AK - Rudimentary support for OPLS-AA * @@ -156,6 +159,59 @@ #include #endif +const char helpmesg[] = + " USAGE: msi2lmp [-help] ROOTNAME [-print #] [-class #] [-frc FRC_FILE] [-ignore] [-nocenter] [-oldstyle]\n" + "\n" + " -- msi2lmp is the name of the executable\n" + "\n" + " -- -help or -h triggers printing this message and exits\n" + "\n" + " -- ROOTNAME is the base name of the .car and .mdf files\n" + " -- all opther flags are optional and can be abbreviated (e.g. -p instead of -print)\n" + "\n" + " -- -print\n" + " # is the print level: 0 - silent except for errors\n" + " 1 - minimal (default)\n" + " 2 - more verbose\n" + " 3 - even more verbose\n" + " -- -class\n" + " # is the class of forcefield to use (I or 1 = Class I e.g., CVFF, clayff)\n" + " (II or 2 = Class II e.g., CFFx, COMPASS)\n" + " (O or 0 = OPLS-AA)\n" + " default is -class I\n" + "\n" + " -- -ignore - tells msi2lmp to ignore warnings and errors and keep going\n" + "\n" + " -- -nocenter - tells msi2lmp to not center the box around the (geometrical)\n" + " center of the atoms, but around the origin\n" + "\n" + " -- -oldstyle - tells msi2lmp to write out a data file without style hints\n" + " (to be compatible with older LAMMPS versions)\n" + "\n" + " -- -shift - tells msi2lmp to shift the entire system (box and coordinates)\n" + " by a vector (default: 0.0 0.0 0.0)\n" + "\n" + " -- -frc - specifies name of the forcefield file (e.g., cff91)\n" + "\n" + " If the name includes a hard wired directory (i.e., if the name\n" + " starts with . or /), then the name is used alone. Otherwise,\n" + " the program looks for the forcefield file in $MSI2LMP_LIBRARY.\n" + " If $MSI2LMP_LIBRARY is not set, then the current directory is\n" + " used.\n" + "\n" + " If the file name does not include a dot after the first\n" + " character, then .frc is appended to the name.\n" + "\n" + " For example, -frc cvff (assumes cvff.frc is in $MSI2LMP_LIBRARY or .)\n" + "\n" + " -frc cff/cff91 (assumes cff91.frc is in $MSI2LMP_LIBRARY/cff or ./cff)\n" + "\n" + " -frc /usr/local/forcefields/cff95 (absolute location)\n" + "\n" + " By default, the program uses $MSI2LMP_LIBRARY/cvff.frc\n" + "\n" + " -- output is written to a file called ROOTNAME.data\n"; + /* global variables */ char *rootname; @@ -239,9 +295,14 @@ int main (int argc, char *argv[]) frc_dir_name = getenv("MSI2LMP_LIBRARY"); if (argc < 2) { - printf("usage: %s [-class ] [-frc ] [-print #] [-ignore] [-nocenter] [-oldstyle]\n",argv[0]); + printf("usage: %s [-help|-h] [-class ] [-frc ] [-print #] [-ignore] [-nocenter] [-oldstyle]\n",argv[0]); return 1; - } else { /* rootname was supplied as first argument, copy to rootname */ + } else { + if ((strcmp(argv[1],"-help") == 0) || (strcmp(argv[1],"-h") == 0)) { + puts(helpmesg); + return 1; + } + /* rootname was supplied as first argument, copy to rootname */ int len = strlen(argv[1]) + 1; rootname = (char *)malloc(len); strcpy(rootname,argv[1]); @@ -249,6 +310,10 @@ int main (int argc, char *argv[]) n = 2; while (n < argc) { + if ((strcmp(argv[n],"-help") == 0) || (strcmp(argv[1],"-h") == 0)) { + puts(helpmesg); + return 1; + } if (strncmp(argv[n],"-c",2) == 0) { n++; if (check_arg(argv,"-class",n,argc)) diff --git a/tools/msi2lmp/src/msi2lmp.h b/tools/msi2lmp/src/msi2lmp.h index b64c6fd834..3e1de85cbe 100644 --- a/tools/msi2lmp/src/msi2lmp.h +++ b/tools/msi2lmp/src/msi2lmp.h @@ -36,7 +36,7 @@ #include /* IWYU pragma: export */ -#define MSI2LMP_VERSION "v3.9.9 / 05 Nov 2018" +#define MSI2LMP_VERSION "v3.9.10 / 10 Mar 2023" #define PI_180 0.01745329251994329576