forked from lijiext/lammps
Switch shear strain fields to symmetric
This commit is contained in:
Aidan Thompson
parent
f205567fa6
commit
67ffef094d
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@ -1,4 +1,4 @@
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LAMMPS (7 Jan 2022)
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LAMMPS (17 Feb 2022)
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# Numerical difference calculation
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# of error in forces, virial stress, and Born matrix
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@ -117,71 +117,71 @@ Neighbor list info ...
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 6.823 | 6.823 | 6.823 Mbytes
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Step Temp PotEng TotEng Press v_frelerr v_vrelerr v_brelerr
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0 10 -6.6101864 -6.471878 947.70558 5.7012262e-09 1.4849734e-08 9.072204e-09
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10 9.9357441 -6.6092976 -6.471878 949.3486 1.3828998e-08 1.9248385e-09 3.0140952e-09
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20 9.7444561 -6.6066519 -6.4718779 954.23637 1.385204e-08 1.7476399e-09 2.8104946e-09
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30 9.4311148 -6.6023181 -6.4718779 962.23331 1.4147226e-08 1.7647816e-09 3.038408e-09
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40 9.0043293 -6.5964152 -6.4718778 973.10762 1.4128155e-08 1.6390138e-09 3.1677083e-09
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50 8.4762135 -6.5891108 -6.4718777 986.53572 1.4168048e-08 2.3910821e-09 3.2880496e-09
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60 7.8621735 -6.5806179 -6.4718775 1002.1092 1.411958e-08 2.0683414e-09 2.650625e-09
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70 7.1805874 -6.5711908 -6.4718773 1019.3448 1.4139911e-08 1.6084571e-09 2.7690475e-09
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80 6.4523557 -6.5611186 -6.4718771 1037.6974 1.4105096e-08 1.9929271e-09 3.7464396e-09
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90 5.7003071 -6.5507169 -6.4718769 1056.5767 1.4084183e-08 1.750579e-09 4.1502319e-09
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100 4.9484503 -6.5403179 -6.4718767 1075.3674 1.4063796e-08 1.0250271e-09 3.0940885e-09
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110 4.221081 -6.5302576 -6.4718765 1093.4526 1.400901e-08 1.389277e-09 3.3111451e-09
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120 3.5417733 -6.520862 -6.4718763 1110.2388 1.4038158e-08 8.6231891e-10 2.6872042e-09
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130 2.9323072 -6.5124324 -6.4718762 1125.183 1.4048645e-08 7.0840985e-10 2.5616823e-09
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140 2.411607 -6.5052306 -6.471876 1137.8182 1.3968429e-08 1.8508015e-09 3.984183e-09
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150 1.9947801 -6.4994654 -6.4718759 1147.7764 1.395965e-08 1.9484728e-09 3.8459442e-09
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160 1.6923481 -6.4952825 -6.4718759 1154.8063 1.3948606e-08 1.5275137e-09 3.4566825e-09
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170 1.5097515 -6.492757 -6.4718759 1158.7853 1.3845523e-08 1.5455e-09 2.4291888e-09
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180 1.4471795 -6.4918916 -6.4718759 1159.7221 1.3788451e-08 1.578099e-09 2.2452653e-09
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190 1.4997431 -6.4926187 -6.471876 1157.7529 1.374841e-08 2.142073e-09 2.3614867e-09
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200 1.6579637 -6.4948072 -6.4718761 1153.1286 1.3674788e-08 2.111894e-09 3.4774073e-09
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210 1.908522 -6.4982727 -6.4718763 1146.1965 1.3639408e-08 1.2386489e-09 2.1550029e-09
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220 2.23518 -6.5027908 -6.4718764 1137.3775 1.3524209e-08 1.7016573e-09 3.3806952e-09
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230 2.6197892 -6.5081105 -6.4718766 1127.1415 1.3344007e-08 1.5843477e-09 2.9517742e-09
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240 3.043298 -6.5139681 -6.4718768 1115.9815 1.3245227e-08 1.5502368e-09 3.7751316e-09
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250 3.4866901 -6.5201007 -6.4718769 1104.3906 1.3080142e-08 1.369987e-09 3.1015926e-09
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260 3.9318061 -6.5262572 -6.4718771 1092.84 1.2885339e-08 1.0743728e-09 3.2781775e-09
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270 4.3620216 -6.5322076 -6.4718772 1081.7617 1.2705966e-08 1.3618619e-09 3.2074528e-09
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280 4.7627723 -6.5377504 -6.4718773 1071.5341 1.2480463e-08 1.4346869e-09 2.6014531e-09
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290 5.1219322 -6.542718 -6.4718774 1062.4716 1.2434727e-08 2.1935942e-09 2.8738025e-09
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300 5.4300557 -6.5469796 -6.4718774 1054.8177 1.2321314e-08 8.2365886e-10 3.0321861e-09
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310 5.6804997 -6.5504435 -6.4718774 1048.7409 1.2300884e-08 1.4855741e-09 3.0631008e-09
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320 5.8694423 -6.5530567 -6.4718774 1044.3341 1.2483087e-08 1.8711589e-09 3.9505726e-09
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330 5.9958115 -6.5548045 -6.4718774 1041.6165 1.2627617e-08 1.9256986e-09 2.0214697e-09
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340 6.0611353 -6.555708 -6.4718774 1040.5369 1.2935701e-08 1.6609255e-09 3.0860271e-09
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350 6.0693222 -6.5558211 -6.4718773 1040.9803 1.3218179e-08 1.985355e-09 2.8012116e-09
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360 6.0263776 -6.5552271 -6.4718773 1042.7755 1.3471701e-08 1.5125203e-09 2.8686484e-09
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370 5.9400629 -6.5540332 -6.4718772 1045.7049 1.3676495e-08 1.7364093e-09 2.578312e-09
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380 5.8195019 -6.5523657 -6.4718771 1049.515 1.3859995e-08 1.6834835e-09 2.9599336e-09
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390 5.6747442 -6.5503635 -6.471877 1053.9288 1.3987553e-08 1.7893896e-09 2.5163687e-09
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400 5.5162948 -6.5481719 -6.4718769 1058.6583 1.4091878e-08 1.4468098e-09 2.1565248e-09
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410 5.3546269 -6.5459358 -6.4718768 1063.4182 1.4188438e-08 1.7231047e-09 2.8650537e-09
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420 5.1996958 -6.5437929 -6.4718768 1067.9384 1.4205207e-08 1.3551982e-09 4.5778887e-09
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430 5.0604771 -6.5418673 -6.4718767 1071.9767 1.4267199e-08 1.361845e-09 3.0381078e-09
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440 4.9445529 -6.5402639 -6.4718766 1075.3292 1.4253464e-08 1.3945282e-09 2.820632e-09
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450 4.8577717 -6.5390637 -6.4718766 1077.8394 1.4240998e-08 1.8767323e-09 3.4379833e-09
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460 4.8040023 -6.53832 -6.4718766 1079.4048 1.4242259e-08 1.4785379e-09 4.399133e-09
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470 4.7849977 -6.5380571 -6.4718766 1079.9795 1.4227939e-08 1.8623848e-09 3.0102588e-09
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480 4.8003794 -6.5382699 -6.4718766 1079.5756 1.4215836e-08 1.2821795e-09 3.0643976e-09
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490 4.8477405 -6.538925 -6.4718767 1078.2596 1.4186541e-08 2.47604e-09 3.3809071e-09
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500 4.9228588 -6.539964 -6.4718767 1076.1469 1.4099819e-08 1.6653302e-09 3.4324143e-09
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Loop time of 0.476785 on 1 procs for 500 steps with 108 atoms
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0 10 -6.6101864 -6.471878 947.70558 5.7012262e-09 1.4849734e-08 9.036398e-09
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10 9.9357441 -6.6092976 -6.471878 949.3486 1.3828998e-08 1.9248385e-09 4.0233493e-09
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20 9.7444561 -6.6066519 -6.4718779 954.23637 1.385204e-08 1.7476399e-09 4.0061081e-09
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30 9.4311148 -6.6023181 -6.4718779 962.23331 1.4147226e-08 1.7647816e-09 3.3866543e-09
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40 9.0043293 -6.5964152 -6.4718778 973.10762 1.4128155e-08 1.6390138e-09 3.2652821e-09
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50 8.4762135 -6.5891108 -6.4718777 986.53572 1.4168048e-08 2.3910821e-09 4.7266627e-09
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60 7.8621735 -6.5806179 -6.4718775 1002.1092 1.411958e-08 2.0683414e-09 2.6951001e-09
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70 7.1805874 -6.5711908 -6.4718773 1019.3448 1.4139911e-08 1.6084571e-09 3.1477301e-09
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80 6.4523557 -6.5611186 -6.4718771 1037.6974 1.4105096e-08 1.9929271e-09 3.4733802e-09
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90 5.7003071 -6.5507169 -6.4718769 1056.5767 1.4084183e-08 1.750579e-09 4.310104e-09
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100 4.9484503 -6.5403179 -6.4718767 1075.3674 1.4063796e-08 1.0250271e-09 2.9213594e-09
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110 4.221081 -6.5302576 -6.4718765 1093.4526 1.400901e-08 1.389277e-09 4.3909721e-09
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120 3.5417733 -6.520862 -6.4718763 1110.2388 1.4038158e-08 8.6231891e-10 2.5890696e-09
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130 2.9323072 -6.5124324 -6.4718762 1125.183 1.4048645e-08 7.0840985e-10 3.388192e-09
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140 2.411607 -6.5052306 -6.471876 1137.8182 1.3968429e-08 1.8508015e-09 3.2976031e-09
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150 1.9947801 -6.4994654 -6.4718759 1147.7764 1.395965e-08 1.9484728e-09 4.2924605e-09
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160 1.6923481 -6.4952825 -6.4718759 1154.8063 1.3948606e-08 1.5275137e-09 4.0204309e-09
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170 1.5097515 -6.492757 -6.4718759 1158.7853 1.3845523e-08 1.5455e-09 4.8781309e-09
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180 1.4471795 -6.4918916 -6.4718759 1159.7221 1.3788451e-08 1.578099e-09 3.0795316e-09
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190 1.4997431 -6.4926187 -6.471876 1157.7529 1.374841e-08 2.142073e-09 2.4376961e-09
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200 1.6579637 -6.4948072 -6.4718761 1153.1286 1.3674788e-08 2.111894e-09 3.7055708e-09
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210 1.908522 -6.4982727 -6.4718763 1146.1965 1.3639408e-08 1.2386489e-09 3.160881e-09
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220 2.23518 -6.5027908 -6.4718764 1137.3775 1.3524209e-08 1.7016573e-09 3.6982265e-09
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230 2.6197892 -6.5081105 -6.4718766 1127.1415 1.3344007e-08 1.5843477e-09 3.7272821e-09
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240 3.043298 -6.5139681 -6.4718768 1115.9815 1.3245227e-08 1.5502368e-09 3.898015e-09
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250 3.4866901 -6.5201007 -6.4718769 1104.3906 1.3080142e-08 1.369987e-09 4.9133863e-09
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260 3.9318061 -6.5262572 -6.4718771 1092.84 1.2885339e-08 1.0743728e-09 5.7271364e-09
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270 4.3620216 -6.5322076 -6.4718772 1081.7617 1.2705966e-08 1.3618619e-09 2.3225062e-09
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280 4.7627723 -6.5377504 -6.4718773 1071.5341 1.2480463e-08 1.4346869e-09 3.281167e-09
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290 5.1219322 -6.542718 -6.4718774 1062.4716 1.2434727e-08 2.1935942e-09 2.8198924e-09
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300 5.4300557 -6.5469796 -6.4718774 1054.8177 1.2321314e-08 8.2365886e-10 3.2731015e-09
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310 5.6804997 -6.5504435 -6.4718774 1048.7409 1.2300884e-08 1.4855741e-09 4.1031988e-09
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320 5.8694423 -6.5530567 -6.4718774 1044.3341 1.2483087e-08 1.8711589e-09 3.9368436e-09
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330 5.9958115 -6.5548045 -6.4718774 1041.6165 1.2627617e-08 1.9256986e-09 4.3283764e-09
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340 6.0611353 -6.555708 -6.4718774 1040.5369 1.2935701e-08 1.6609255e-09 3.8728039e-09
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350 6.0693222 -6.5558211 -6.4718773 1040.9803 1.3218179e-08 1.985355e-09 2.618577e-09
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360 6.0263776 -6.5552271 -6.4718773 1042.7755 1.3471701e-08 1.5125203e-09 2.936238e-09
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370 5.9400629 -6.5540332 -6.4718772 1045.7049 1.3676495e-08 1.7364093e-09 2.9097362e-09
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380 5.8195019 -6.5523657 -6.4718771 1049.515 1.3859995e-08 1.6834835e-09 2.7416302e-09
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390 5.6747442 -6.5503635 -6.471877 1053.9288 1.3987553e-08 1.7893896e-09 2.8552537e-09
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400 5.5162948 -6.5481719 -6.4718769 1058.6583 1.4091878e-08 1.4468098e-09 3.2733654e-09
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410 5.3546269 -6.5459358 -6.4718768 1063.4182 1.4188438e-08 1.7231047e-09 3.3165187e-09
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420 5.1996958 -6.5437929 -6.4718768 1067.9384 1.4205207e-08 1.3551982e-09 3.8687611e-09
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430 5.0604771 -6.5418673 -6.4718767 1071.9767 1.4267199e-08 1.361845e-09 3.1210672e-09
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440 4.9445529 -6.5402639 -6.4718766 1075.3292 1.4253464e-08 1.3945282e-09 2.6483572e-09
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450 4.8577717 -6.5390637 -6.4718766 1077.8394 1.4240998e-08 1.8767323e-09 3.2040422e-09
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460 4.8040023 -6.53832 -6.4718766 1079.4048 1.4242259e-08 1.4785379e-09 3.4402279e-09
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470 4.7849977 -6.5380571 -6.4718766 1079.9795 1.4227939e-08 1.8623848e-09 4.3634918e-09
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480 4.8003794 -6.5382699 -6.4718766 1079.5756 1.4215836e-08 1.2821795e-09 2.6846581e-09
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490 4.8477405 -6.538925 -6.4718767 1078.2596 1.4186541e-08 2.47604e-09 3.2044632e-09
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500 4.9228588 -6.539964 -6.4718767 1076.1469 1.4099819e-08 1.6653302e-09 3.267113e-09
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Loop time of 0.458483 on 1 procs for 500 steps with 108 atoms
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Performance: 90.607 ns/day, 0.265 hours/ns, 1048.692 timesteps/s
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99.6% CPU use with 1 MPI tasks x no OpenMP threads
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Performance: 94.224 ns/day, 0.255 hours/ns, 1090.552 timesteps/s
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99.7% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0043699 | 0.0043699 | 0.0043699 | 0.0 | 0.92
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Neigh | 0.026529 | 0.026529 | 0.026529 | 0.0 | 5.56
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Comm | 0.0026272 | 0.0026272 | 0.0026272 | 0.0 | 0.55
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Output | 0.014971 | 0.014971 | 0.014971 | 0.0 | 3.14
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Modify | 0.42777 | 0.42777 | 0.42777 | 0.0 | 89.72
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Other | | 0.0005208 | | | 0.11
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Pair | 0.0042278 | 0.0042278 | 0.0042278 | 0.0 | 0.92
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Neigh | 0.02481 | 0.02481 | 0.02481 | 0.0 | 5.41
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Comm | 0.002944 | 0.002944 | 0.002944 | 0.0 | 0.64
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Output | 0.014731 | 0.014731 | 0.014731 | 0.0 | 3.21
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Modify | 0.41122 | 0.41122 | 0.41122 | 0.0 | 89.69
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Other | | 0.0005545 | | | 0.12
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Nlocal: 108 ave 108 max 108 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -1,4 +1,4 @@
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LAMMPS (7 Jan 2022)
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LAMMPS (17 Feb 2022)
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# Numerical difference calculation
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# of error in forces, virial stress, and Born matrix
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@ -117,71 +117,71 @@ Neighbor list info ...
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 6.816 | 6.816 | 6.816 Mbytes
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Step Temp PotEng TotEng Press v_frelerr v_vrelerr v_brelerr
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0 10 -6.6101864 -6.471878 947.70558 1.9110624e-09 9.4407596e-10 3.6112548e-09
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10 9.9369961 -6.6093149 -6.471878 949.31222 1.3055176e-08 4.996456e-10 1.8135199e-09
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20 9.7500224 -6.6067289 -6.4718779 954.07898 1.3721178e-08 5.6039795e-10 1.6247414e-09
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30 9.4448115 -6.6025075 -6.4718779 961.85502 1.3813156e-08 6.8451692e-10 1.3087974e-09
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40 9.0305392 -6.5967776 -6.4718777 972.39819 1.3961749e-08 3.1134064e-10 2.0036072e-09
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50 8.5196068 -6.5897109 -6.4718776 985.38158 1.3996941e-08 7.0149406e-10 1.6670043e-09
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60 7.9273388 -6.5815192 -6.4718775 1000.4024 1.4000005e-08 3.5766629e-10 2.53484e-09
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70 7.2715879 -6.5724494 -6.4718773 1016.9932 1.3996503e-08 6.2731503e-10 1.9890841e-09
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80 6.5722375 -6.5627766 -6.4718771 1034.6361 1.3973603e-08 3.1142917e-10 1.3798878e-09
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90 5.8505991 -6.5527956 -6.4718769 1052.7794 1.3983301e-08 3.9931135e-10 2.7529755e-09
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100 5.128708 -6.542811 -6.4718767 1070.8561 1.395586e-08 2.3152413e-10 2.0674207e-09
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110 4.4285344 -6.5331269 -6.4718766 1088.305 1.3938374e-08 4.2173005e-10 1.5662067e-09
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120 3.7711361 -6.5240343 -6.4718764 1104.5919 1.3915264e-08 2.5458038e-10 1.5849397e-09
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130 3.1757964 -6.5158002 -6.4718762 1119.2319 1.3858843e-08 5.7490448e-10 3.0296967e-09
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140 2.6591997 -6.5086551 -6.4718761 1131.8095 1.3814891e-08 3.5434633e-10 1.6789888e-09
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150 2.2347034 -6.5027839 -6.471876 1141.9961 1.3781115e-08 5.0639594e-10 2.9776968e-09
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160 1.9117661 -6.4983173 -6.471876 1149.564 1.3734288e-08 3.1954962e-10 1.3139064e-09
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170 1.6955808 -6.4953273 -6.471876 1154.3946 1.3682252e-08 3.5426781e-10 2.5537158e-09
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180 1.586949 -6.4938249 -6.471876 1156.4812 1.363e-08 4.0804881e-10 1.5958563e-09
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190 1.5824056 -6.4937621 -6.4718761 1155.925 1.3532637e-08 4.0767685e-10 2.3016751e-09
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200 1.6745831 -6.4950371 -6.4718762 1152.926 1.3455927e-08 2.953369e-10 2.1101198e-09
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210 1.8527803 -6.4975018 -6.4718763 1147.7684 1.335224e-08 3.5042319e-10 1.7878344e-09
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220 2.1036825 -6.5009721 -6.4718764 1140.8026 1.3239176e-08 3.5988448e-10 1.9695755e-09
|
||||
230 2.4121721 -6.5052389 -6.4718766 1132.4243 1.3090019e-08 3.5004036e-10 1.5993755e-09
|
||||
240 2.7621668 -6.5100798 -6.4718767 1123.0538 1.2946525e-08 4.1216361e-10 2.1544908e-09
|
||||
250 3.1374274 -6.5152701 -6.4718768 1113.1152 1.277789e-08 5.9848318e-10 2.5891141e-09
|
||||
260 3.5222906 -6.5205932 -6.471877 1103.0171 1.2591089e-08 2.0080182e-10 1.9280289e-09
|
||||
270 3.9022942 -6.5258491 -6.4718771 1093.1369 1.2432232e-08 4.2494727e-10 2.2260348e-09
|
||||
280 4.2646753 -6.5308612 -6.4718772 1083.8072 1.2268238e-08 6.1239266e-10 1.7606971e-09
|
||||
290 4.598736 -6.5354816 -6.4718772 1075.306 1.2181179e-08 4.9338341e-10 1.5542041e-09
|
||||
300 4.896078 -6.5395941 -6.4718773 1067.85 1.2098274e-08 3.4564838e-10 1.9030041e-09
|
||||
310 5.150715 -6.543116 -6.4718773 1061.5918 1.2184958e-08 4.2383299e-10 1.6691938e-09
|
||||
320 5.3590742 -6.5459978 -6.4718773 1056.6189 1.2312948e-08 3.5194185e-10 1.340539e-09
|
||||
330 5.5199009 -6.5482222 -6.4718773 1052.9565 1.2573918e-08 4.2401322e-10 1.6425443e-09
|
||||
340 5.6340787 -6.5498013 -6.4718773 1050.5719 1.2821551e-08 5.8802825e-10 1.9791699e-09
|
||||
350 5.7043792 -6.5507736 -6.4718772 1049.3813 1.3067314e-08 4.0014945e-10 1.0305017e-09
|
||||
360 5.7351548 -6.5511992 -6.4718772 1049.2581 1.331283e-08 4.1684815e-10 1.3051661e-09
|
||||
370 5.7319891 -6.5511553 -6.4718771 1050.042 1.354018e-08 3.8495426e-10 1.5606716e-09
|
||||
380 5.7013193 -6.5507311 -6.4718771 1051.5496 1.3734888e-08 3.5333605e-10 1.6933716e-09
|
||||
390 5.6500487 -6.5500219 -6.471877 1053.5847 1.3892287e-08 3.8154957e-10 1.5483204e-09
|
||||
400 5.5851679 -6.5491245 -6.471877 1055.9489 1.3988171e-08 5.8769536e-10 1.860034e-09
|
||||
410 5.5134009 -6.5481319 -6.4718769 1058.4508 1.4088779e-08 3.6754739e-10 3.0708184e-09
|
||||
420 5.4408957 -6.547129 -6.4718769 1060.9152 1.4139924e-08 4.9030281e-10 2.8908455e-09
|
||||
430 5.3729707 -6.5461895 -6.4718768 1063.1898 1.4173041e-08 5.2345074e-10 1.9816809e-09
|
||||
440 5.3139284 -6.5453729 -6.4718768 1065.1506 1.4191516e-08 5.9481094e-10 1.6654998e-09
|
||||
450 5.2669383 -6.5447229 -6.4718768 1066.7054 1.4168424e-08 3.0799668e-10 2.0838273e-09
|
||||
460 5.2339881 -6.5442672 -6.4718768 1067.7958 1.4163444e-08 6.3927736e-10 2.7292416e-09
|
||||
470 5.2158979 -6.544017 -6.4718768 1068.3968 1.413819e-08 5.5108262e-10 1.3969622e-09
|
||||
480 5.2123873 -6.5439685 -6.4718768 1068.5155 1.4083227e-08 3.9249548e-10 1.6717922e-09
|
||||
490 5.2221849 -6.544104 -6.4718768 1068.188 1.4035287e-08 2.1988631e-10 1.75155e-09
|
||||
500 5.2431716 -6.5443943 -6.4718768 1067.4759 1.3968666e-08 3.9100701e-10 1.9215444e-09
|
||||
Loop time of 0.169723 on 4 procs for 500 steps with 108 atoms
|
||||
0 10 -6.6101864 -6.471878 947.70558 1.9110624e-09 9.4407596e-10 3.1867416e-09
|
||||
10 9.9369961 -6.6093149 -6.471878 949.31222 1.3055176e-08 4.996456e-10 2.7421655e-09
|
||||
20 9.7500224 -6.6067289 -6.4718779 954.07898 1.3721178e-08 5.6039795e-10 2.3689718e-09
|
||||
30 9.4448115 -6.6025075 -6.4718779 961.85502 1.3813156e-08 6.8451692e-10 1.9844663e-09
|
||||
40 9.0305392 -6.5967776 -6.4718777 972.39819 1.3961749e-08 3.1134064e-10 1.7915052e-09
|
||||
50 8.5196068 -6.5897109 -6.4718776 985.38158 1.3996941e-08 7.0149406e-10 2.002272e-09
|
||||
60 7.9273388 -6.5815192 -6.4718775 1000.4024 1.4000005e-08 3.5766629e-10 2.4944703e-09
|
||||
70 7.2715879 -6.5724494 -6.4718773 1016.9932 1.3996503e-08 6.2731503e-10 1.7010533e-09
|
||||
80 6.5722375 -6.5627766 -6.4718771 1034.6361 1.3973603e-08 3.1142917e-10 2.808524e-09
|
||||
90 5.8505991 -6.5527956 -6.4718769 1052.7794 1.3983301e-08 3.9931135e-10 2.6118214e-09
|
||||
100 5.128708 -6.542811 -6.4718767 1070.8561 1.395586e-08 2.3152413e-10 2.8742755e-09
|
||||
110 4.4285344 -6.5331269 -6.4718766 1088.305 1.3938374e-08 4.2173005e-10 2.3059886e-09
|
||||
120 3.7711361 -6.5240343 -6.4718764 1104.5919 1.3915264e-08 2.5458038e-10 1.4864012e-09
|
||||
130 3.1757964 -6.5158002 -6.4718762 1119.2319 1.3858843e-08 5.7490448e-10 2.6191823e-09
|
||||
140 2.6591997 -6.5086551 -6.4718761 1131.8095 1.3814891e-08 3.5434633e-10 2.2009364e-09
|
||||
150 2.2347034 -6.5027839 -6.471876 1141.9961 1.3781115e-08 5.0639594e-10 2.9032558e-09
|
||||
160 1.9117661 -6.4983173 -6.471876 1149.564 1.3734288e-08 3.1954962e-10 2.6097446e-09
|
||||
170 1.6955808 -6.4953273 -6.471876 1154.3946 1.3682252e-08 3.5426781e-10 2.9605676e-09
|
||||
180 1.586949 -6.4938249 -6.471876 1156.4812 1.363e-08 4.0804881e-10 2.1707904e-09
|
||||
190 1.5824056 -6.4937621 -6.4718761 1155.925 1.3532637e-08 4.0767685e-10 3.0091462e-09
|
||||
200 1.6745831 -6.4950371 -6.4718762 1152.926 1.3455927e-08 2.953369e-10 2.5029298e-09
|
||||
210 1.8527803 -6.4975018 -6.4718763 1147.7684 1.335224e-08 3.5042319e-10 3.0550064e-09
|
||||
220 2.1036825 -6.5009721 -6.4718764 1140.8026 1.3239176e-08 3.5988448e-10 2.6852683e-09
|
||||
230 2.4121721 -6.5052389 -6.4718766 1132.4243 1.3090019e-08 3.5004036e-10 2.8838602e-09
|
||||
240 2.7621668 -6.5100798 -6.4718767 1123.0538 1.2946525e-08 4.1216361e-10 2.1105916e-09
|
||||
250 3.1374274 -6.5152701 -6.4718768 1113.1152 1.277789e-08 5.9848318e-10 2.3087106e-09
|
||||
260 3.5222906 -6.5205932 -6.471877 1103.0171 1.2591089e-08 2.0080182e-10 1.6969069e-09
|
||||
270 3.9022942 -6.5258491 -6.4718771 1093.1369 1.2432232e-08 4.2494727e-10 1.7375594e-09
|
||||
280 4.2646753 -6.5308612 -6.4718772 1083.8072 1.2268238e-08 6.1239266e-10 1.7005135e-09
|
||||
290 4.598736 -6.5354816 -6.4718772 1075.306 1.2181179e-08 4.9338341e-10 2.1326848e-09
|
||||
300 4.896078 -6.5395941 -6.4718773 1067.85 1.2098274e-08 3.4564838e-10 2.4199891e-09
|
||||
310 5.150715 -6.543116 -6.4718773 1061.5918 1.2184958e-08 4.2383299e-10 2.2243759e-09
|
||||
320 5.3590742 -6.5459978 -6.4718773 1056.6189 1.2312948e-08 3.5194185e-10 1.3856935e-09
|
||||
330 5.5199009 -6.5482222 -6.4718773 1052.9565 1.2573918e-08 4.2401322e-10 2.9882e-09
|
||||
340 5.6340787 -6.5498013 -6.4718773 1050.5719 1.2821551e-08 5.8802825e-10 2.7333289e-09
|
||||
350 5.7043792 -6.5507736 -6.4718772 1049.3813 1.3067314e-08 4.0014945e-10 2.3564728e-09
|
||||
360 5.7351548 -6.5511992 -6.4718772 1049.2581 1.331283e-08 4.1684815e-10 1.735621e-09
|
||||
370 5.7319891 -6.5511553 -6.4718771 1050.042 1.354018e-08 3.8495426e-10 2.4460056e-09
|
||||
380 5.7013193 -6.5507311 -6.4718771 1051.5496 1.3734888e-08 3.5333605e-10 2.5174342e-09
|
||||
390 5.6500487 -6.5500219 -6.471877 1053.5847 1.3892287e-08 3.8154957e-10 1.77358e-09
|
||||
400 5.5851679 -6.5491245 -6.471877 1055.9489 1.3988171e-08 5.8769536e-10 1.9262201e-09
|
||||
410 5.5134009 -6.5481319 -6.4718769 1058.4508 1.4088779e-08 3.6754739e-10 2.7586362e-09
|
||||
420 5.4408957 -6.547129 -6.4718769 1060.9152 1.4139924e-08 4.9030281e-10 3.2871245e-09
|
||||
430 5.3729707 -6.5461895 -6.4718768 1063.1898 1.4173041e-08 5.2345074e-10 3.5995984e-09
|
||||
440 5.3139284 -6.5453729 -6.4718768 1065.1506 1.4191516e-08 5.9481094e-10 2.5005297e-09
|
||||
450 5.2669383 -6.5447229 -6.4718768 1066.7054 1.4168424e-08 3.0799668e-10 2.0864191e-09
|
||||
460 5.2339881 -6.5442672 -6.4718768 1067.7958 1.4163444e-08 6.3927736e-10 2.2872669e-09
|
||||
470 5.2158979 -6.544017 -6.4718768 1068.3968 1.413819e-08 5.5108262e-10 4.4334972e-09
|
||||
480 5.2123873 -6.5439685 -6.4718768 1068.5155 1.4083227e-08 3.9249548e-10 2.5568235e-09
|
||||
490 5.2221849 -6.544104 -6.4718768 1068.188 1.4035287e-08 2.1988631e-10 2.1264034e-09
|
||||
500 5.2431716 -6.5443943 -6.4718768 1067.4759 1.3968666e-08 3.9100701e-10 3.290368e-09
|
||||
Loop time of 0.170182 on 4 procs for 500 steps with 108 atoms
|
||||
|
||||
Performance: 254.532 ns/day, 0.094 hours/ns, 2945.973 timesteps/s
|
||||
Performance: 253.846 ns/day, 0.095 hours/ns, 2938.035 timesteps/s
|
||||
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0012438 | 0.0014032 | 0.0015571 | 0.4 | 0.83
|
||||
Neigh | 0.0048166 | 0.0051267 | 0.0054319 | 0.4 | 3.02
|
||||
Comm | 0.0075482 | 0.0081723 | 0.0087409 | 0.6 | 4.82
|
||||
Output | 0.0081869 | 0.0082763 | 0.0085015 | 0.1 | 4.88
|
||||
Modify | 0.14635 | 0.14641 | 0.14646 | 0.0 | 86.26
|
||||
Other | | 0.0003391 | | | 0.20
|
||||
Pair | 0.0012069 | 0.0012994 | 0.0013512 | 0.2 | 0.76
|
||||
Neigh | 0.0048233 | 0.0050244 | 0.0053881 | 0.3 | 2.95
|
||||
Comm | 0.0072462 | 0.0078013 | 0.008175 | 0.4 | 4.58
|
||||
Output | 0.0080632 | 0.0081244 | 0.0082899 | 0.1 | 4.77
|
||||
Modify | 0.1476 | 0.14764 | 0.14768 | 0.0 | 86.75
|
||||
Other | | 0.0002961 | | | 0.17
|
||||
|
||||
Nlocal: 27 ave 31 max 24 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
|
|
|
|||
|
|
@ -372,6 +372,7 @@ void ComputeBornMatrix::compute_vector()
|
|||
}
|
||||
|
||||
for (int m = 0; m < nvalues; m++) vector[m] = values_global[m];
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -528,7 +529,8 @@ void ComputeBornMatrix::compute_numdiff()
|
|||
// apply derivative factor
|
||||
|
||||
double denominator = -0.5 / numdelta;
|
||||
for (int m = 0; m < nvalues; m++) values_global[m] *= denominator;
|
||||
for (int m = 0; m < nvalues; m++)
|
||||
values_global[m] *= denominator;
|
||||
|
||||
// recompute virial so all virial and energy contributions are as before
|
||||
// also needed for virial stress addon contributions to Born matrix
|
||||
|
|
@ -553,13 +555,25 @@ void ComputeBornMatrix::displace_atoms(int nall, int idir, double magnitude)
|
|||
{
|
||||
double **x = atom->x;
|
||||
|
||||
// NOTE: transposing k and l would seem to be equivalent but it is not
|
||||
// only this version matches analytic results for lj/cut
|
||||
// NOTE: virial_addon() expressions predicated on
|
||||
// shear strain fields (l != k) being symmetric here
|
||||
|
||||
int k = dirlist[idir][0];
|
||||
int l = dirlist[idir][1];
|
||||
for (int i = 0; i < nall; i++)
|
||||
x[i][k] = temp_x[i][k] + numdelta * magnitude * (temp_x[i][l] - fixedpoint[l]);
|
||||
|
||||
// axial strain
|
||||
|
||||
if (l == k)
|
||||
for (int i = 0; i < nall; i++)
|
||||
x[i][k] = temp_x[i][k] + numdelta * magnitude * (temp_x[i][l] - fixedpoint[l]);
|
||||
|
||||
// symmetric shear strain
|
||||
|
||||
else
|
||||
for (int i = 0; i < nall; i++) {
|
||||
x[i][k] = temp_x[i][k] + 0.5 * numdelta * magnitude * (temp_x[i][l] - fixedpoint[l]);
|
||||
x[i][l] = temp_x[i][l] + 0.5 * numdelta * magnitude * (temp_x[i][k] - fixedpoint[k]);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -572,8 +586,15 @@ void ComputeBornMatrix::restore_atoms(int nall, int idir)
|
|||
// reset only idir coord
|
||||
|
||||
int k = dirlist[idir][0];
|
||||
int l = dirlist[idir][1];
|
||||
double **x = atom->x;
|
||||
for (int i = 0; i < nall; i++) x[i][k] = temp_x[i][k];
|
||||
if (l == k)
|
||||
for (int i = 0; i < nall; i++) x[i][k] = temp_x[i][k];
|
||||
else
|
||||
for (int i = 0; i < nall; i++) {
|
||||
x[i][l] = temp_x[i][l];
|
||||
x[i][k] = temp_x[i][k];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
@ -619,7 +640,6 @@ void ComputeBornMatrix::virial_addon()
|
|||
int m;
|
||||
|
||||
double *sigv = compute_virial->vector;
|
||||
double modefactor[6] = {1.0, 1.0, 1.0, 0.5, 0.5, 0.5};
|
||||
|
||||
// you can compute these factor by looking at
|
||||
// every Dijkl terms and adding the proper virials
|
||||
|
|
@ -628,30 +648,35 @@ void ComputeBornMatrix::virial_addon()
|
|||
// but D3232=D2323
|
||||
// and Cijkl = (Bijkl+Bjikl+Bijlk+Bjilk)/4. = (Bijkl+Bjilk)/2.
|
||||
|
||||
// these values have been verified correct to about 1e-9
|
||||
// against the analytic expressions for lj/cut
|
||||
|
||||
// these expressions have been verified
|
||||
// correct to about 1e-7 compared
|
||||
// to the analytic expressions for lj/cut,
|
||||
// predicated on shear strain fields being
|
||||
// symmetric in displace_atoms()
|
||||
|
||||
values_global[0] += 2.0 * sigv[0];
|
||||
values_global[1] += 2.0 * sigv[1];
|
||||
values_global[2] += 2.0 * sigv[2];
|
||||
values_global[3] += sigv[2];
|
||||
values_global[4] += sigv[2];
|
||||
values_global[5] += sigv[1];
|
||||
|
||||
values_global[3] += 0.5 * (sigv[1] + sigv[2]);
|
||||
values_global[4] += 0.5 * (sigv[0] + sigv[2]);
|
||||
values_global[5] += 0.5 * (sigv[0] + sigv[1]);
|
||||
values_global[6] += 0.0;
|
||||
values_global[7] += 0.0;
|
||||
values_global[8] += 0.0;
|
||||
values_global[9] += 2.0 * sigv[4];
|
||||
values_global[10] += 2.0 * sigv[3];
|
||||
values_global[9] += sigv[4];
|
||||
values_global[10] += sigv[3];
|
||||
values_global[11] += 0.0;
|
||||
values_global[12] += 2.0 * sigv[5];
|
||||
values_global[12] += sigv[5];
|
||||
values_global[13] += 0.0;
|
||||
values_global[14] += 0.0;
|
||||
values_global[15] += 0.0;
|
||||
values_global[16] += 0.0;
|
||||
values_global[14] += sigv[3];
|
||||
values_global[15] += sigv[5];
|
||||
values_global[16] += sigv[4];
|
||||
values_global[17] += 0.0;
|
||||
values_global[18] += 0.0;
|
||||
values_global[19] += 0.0;
|
||||
values_global[20] += sigv[5];
|
||||
values_global[18] += 0.5 * sigv[3];
|
||||
values_global[19] += 0.5 * sigv[4];
|
||||
values_global[20] += 0.5 * sigv[5];
|
||||
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
|
|
|||
Loading…
Reference in New Issue