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1. better GPU total energy calculation
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   1.0 VDW, Real, and Fourier (Ewald summation)
   1.1 added GPU DRIFT at the end of the file
   1.2 works for multiple framework components (for example, extra-framework molecules)
2. Fixed Widom Insertion (and henry's constant). More testing/bug-fix going on.
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@Zhaoli2042
Zhaoli2042 committed Aug 4, 2024
1 parent 7a7b8d3 commit 00504f7
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Showing 22 changed files with 1,879 additions and 650 deletions.
251 changes: 197 additions & 54 deletions Examples/Bae-Mixture/output.txt
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205 changes: 109 additions & 96 deletions Examples/CO2-MFI/output.txt
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150 changes: 126 additions & 24 deletions Examples/Methane-TMMC/output.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
/home/z/Desktop/gRASPA_fork/src_clean/nvc_main.xChecking if all inputs are defined
True path of exe is /home/z/Desktop/gRASPA_fork/src_clean/
/home/z/Desktop/gRASPA_versions/080424-code/gRASPA_fork/src_clean/nvc_main.xChecking if all inputs are defined
True path of exe is /home/z/Desktop/gRASPA_versions/080424-code/gRASPA_fork/src_clean/
There are 1 simulations
running only one simulation
------------------PARSING FORCE FIELD MIXING RULES----------------
Expand Down Expand Up @@ -403,6 +403,7 @@ Parsing [1] Component
Component 0 starts at line number 37
-------------- READING AdsorbateComponent 0 (methane) --------------
Adsorbate Component is rigid
CH4_sp3, type: 13, Acharge = 0.00000
Bonds not implemented. Break
Atom [0]: Type [13], Name: CH4_sp3, Mass: 16.000000, position: 0.00000 0.00000 0.00000
Adsorbate Type[13], Name: CH4_sp3, #: 1
Expand Down Expand Up @@ -447,24 +448,39 @@ Box Temperature: 95.00000
Host-Host VDW: 0.00000; Real: 0.00000
Host-Guest VDW: 0.00000; Real: 0.00000
Guest-Guest VDW: 0.00000; Real: 0.00000
Ewald Summation (total energy) on the CPU took 0.00000 secs
Ewald Summation (total energy) on the GPU took 0.00000 secs
********** PRINTING COMPONENT ENERGIES**********
Compoent [0-0], VDW: 0.00000, Real: 0.00000
Compoent [0-1], VDW: 0.00000, Real: 0.00000
Compoent [1-1], VDW: 0.00000, Real: 0.00000
THERE IS MORE THAN 1 FRAMEWORK COMPONENTS
Framework Comp Zero Atoms: 207, Other Comp Atoms: 0
NFrameworkZero_ExtraFramework interactions: 0, NExtraFrameworkAtoms * (NExtraFrameworkAtoms - 1) / 2: 0
VDW + Real on the GPU took 0.00001 secs
Total GPU Energy:
HHVDW: 0.00000, HHReal: 0.00000, HGVDW: 0.00000, HGReal: 0.00000, GGVDW: 0.00000, GGReal: 0.00000, HHEwaldE: 0.00000, HGEwaldE: 0.00000, GGEwaldE: 0.00000, TailE: 0.00000, DNN_E: 0.00000
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
====================== DONE CALCULATING INITIAL STAGE ENERGY ======================
Component 1, Need to create 0 full molecule
======================== CALCULATING CREATE_MOLECULE STAGE ENERGY ========================
****** Calculating VDW + Real Energy (CPU) ******
Host-Host VDW: 0.00000; Real: 0.00000
Host-Guest VDW: 0.00000; Real: 0.00000
Guest-Guest VDW: 0.00000; Real: 0.00000
Ewald Summation (total energy) on the CPU took 0.00000 secs
Ewald Summation (total energy) on the GPU took 0.00000 secs
********** PRINTING COMPONENT ENERGIES**********
Compoent [0-0], VDW: 0.00000, Real: 0.00000
Compoent [0-1], VDW: 0.00000, Real: 0.00000
Compoent [1-1], VDW: 0.00000, Real: 0.00000
THERE IS MORE THAN 1 FRAMEWORK COMPONENTS
Framework Comp Zero Atoms: 207, Other Comp Atoms: 0
NFrameworkZero_ExtraFramework interactions: 0, NExtraFrameworkAtoms * (NExtraFrameworkAtoms - 1) / 2: 0
VDW + Real on the GPU took 0.00000 secs
Total GPU Energy:
HHVDW: 0.00000, HHReal: 0.00000, HGVDW: 0.00000, HGReal: 0.00000, GGVDW: 0.00000, GGReal: 0.00000, HHEwaldE: 0.00000, HGEwaldE: 0.00000, GGEwaldE: 0.00000, TailE: 0.00000, DNN_E: 0.00000
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
====================== DONE CALCULATING CREATE_MOLECULE STAGE ENERGY ======================
Running Simulation Boxes in SERIAL, currently [0] box; pres: 0.00041, temp: 95.00000
Number of Frameworks: 1
INITIALIZATION Cycle: 0, 0 Adsorbate Molecules, Total Energy: 0.00000 || Component 0 [667.cif], 1 Molecules || Component 1 [methane], 0 Molecules ||
Cycle [4], Printing DeltaE
HHVDW: 0.00000, HHReal: 0.00000, HGVDW: 0.00000, HGReal: 0.00000, GGVDW: 0.00000, GGReal: 0.00000, HHEwaldE: 0.00000, HGEwaldE: 0.00000, GGEwaldE: 0.00000, TailE: 0.00000, DNN_E: 0.00000
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
======================== MOVE STATISTICS FOR COMPONENT [1] (methane) ========================
=====================SWAP MOVES=====================
Insertion Performed: 1678
Expand All @@ -480,9 +496,6 @@ Reinsertion Accepted: 389
Running Simulation Boxes in SERIAL, currently [0] box; pres: 0.00041, temp: 95.00000
Number of Frameworks: 1
EQUILIBRATION Cycle: 0, 59 Adsorbate Molecules, Total Energy: -48094.15797 || Component 0 [667.cif], 1 Molecules || Component 1 [methane], 59 Molecules ||
Cycle [4], Printing DeltaE
HHVDW: 0.00000, HHReal: 0.00000, HGVDW: 0.00000, HGReal: 0.00000, GGVDW: 0.00000, GGReal: 0.00000, HHEwaldE: 0.00000, HGEwaldE: 0.00000, GGEwaldE: 0.00000, TailE: 0.00000, DNN_E: 0.00000
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
EQUILIBRATION Cycle: 10000, 62 Adsorbate Molecules, Total Energy: -52121.68757 || Component 0 [667.cif], 1 Molecules || Component 1 [methane], 62 Molecules ||
EQUILIBRATION Cycle: 20000, 56 Adsorbate Molecules, Total Energy: -45419.04810 || Component 0 [667.cif], 1 Molecules || Component 1 [methane], 56 Molecules ||
EQUILIBRATION Cycle: 30000, 58 Adsorbate Molecules, Total Energy: -48166.04905 || Component 0 [667.cif], 1 Molecules || Component 1 [methane], 58 Molecules ||
Expand All @@ -507,9 +520,6 @@ Printing: Component: 0 [ 667.cif ], NumMol: 1, Molsize: 207
Printing: Component: 1 [ methane ], NumMol: 60, Molsize: 1
Component 0, Molsize: 207
Component 1, Molsize: 1
Cycle [4], Printing DeltaE
HHVDW: 0.00000, HHReal: 0.00000, HGVDW: -87.54050, HGReal: 0.00000, GGVDW: -42.40380, GGReal: 0.00000, HHEwaldE: 0.00000, HGEwaldE: 0.00000, GGEwaldE: 0.00000, TailE: 0.00000, DNN_E: 0.00000
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
PRODUCTION Cycle: 10000, 62 Adsorbate Molecules, Total Energy: -48220.01615 || Component 0 [667.cif], 1 Molecules || Component 1 [methane], 62 Molecules ||
Printing: Component: 0 [ 667.cif ], NumMol: 1, Molsize: 207
Printing: Component: 1 [ methane ], NumMol: 62, Molsize: 1
Expand Down Expand Up @@ -632,11 +642,73 @@ BLOCK [4], Blocksize: 10000, Average: 12.41149, ErrorBar: 9.85773
Overall: Average: 34.71939, ErrorBar: 28.98501
----------------------------------------------------------
==============================================================
=====================Rosenbluth Summary=====================
There are 5 blocks
=====BLOCK 0=====
Widom Performed: 3369.0
Framework Density: 116.33074 [kg/m^3]
(Total) Averaged Rosenbluth Weight: 795.7580576518
(Total) Averaged Excess Mu: -634.2347235877
(Total) Averaged Henry Coefficient: 0.0086602168
(Total) Converted to Fugacity: 344.8401406044 [Pascal], Temp: 95.00000 [K]
Framework Density: 116.33074 [kg/m^3]
(Insertion) Averaged Rosenbluth Weight: 795.7580576518
(Insertion) Averaged Excess Mu: -634.2347235877
(Insertion) Converted to Fugacity: 344.8401406044 [Pascal], Temp: 95.00000 [K]
=====BLOCK 1=====
Widom Performed: 3286.0
Framework Density: 116.33074 [kg/m^3]
(Total) Averaged Rosenbluth Weight: 655.3110108386
(Total) Averaged Excess Mu: -615.7957984343
(Total) Averaged Henry Coefficient: 0.0071317348
(Total) Converted to Fugacity: 418.7466957660 [Pascal], Temp: 95.00000 [K]
Framework Density: 116.33074 [kg/m^3]
(Insertion) Averaged Rosenbluth Weight: 655.3110108386
(Insertion) Averaged Excess Mu: -615.7957984343
(Insertion) Converted to Fugacity: 418.7466957660 [Pascal], Temp: 95.00000 [K]
=====BLOCK 2=====
Widom Performed: 3349.0
Framework Density: 116.33074 [kg/m^3]
(Total) Averaged Rosenbluth Weight: 685.9186917949
(Total) Averaged Excess Mu: -620.1304285532
(Total) Averaged Henry Coefficient: 0.0074648375
(Total) Converted to Fugacity: 400.0610039794 [Pascal], Temp: 95.00000 [K]
Framework Density: 116.33074 [kg/m^3]
(Insertion) Averaged Rosenbluth Weight: 685.9186917949
(Insertion) Averaged Excess Mu: -620.1304285532
(Insertion) Converted to Fugacity: 400.0610039794 [Pascal], Temp: 95.00000 [K]
=====BLOCK 3=====
Widom Performed: 3289.0
Framework Density: 116.33074 [kg/m^3]
(Total) Averaged Rosenbluth Weight: 448.0360138531
(Total) Averaged Excess Mu: -579.6903295768
(Total) Averaged Henry Coefficient: 0.0048759657
(Total) Converted to Fugacity: 612.4715692558 [Pascal], Temp: 95.00000 [K]
Framework Density: 116.33074 [kg/m^3]
(Insertion) Averaged Rosenbluth Weight: 448.0360138531
(Insertion) Averaged Excess Mu: -579.6903295768
(Insertion) Converted to Fugacity: 612.4715692558 [Pascal], Temp: 95.00000 [K]
=====BLOCK 4=====
Widom Performed: 3325.0
Framework Density: 116.33074 [kg/m^3]
(Total) Averaged Rosenbluth Weight: 556.6735704443
(Total) Averaged Excess Mu: -600.3056460581
(Total) Averaged Henry Coefficient: 0.0060582658
(Total) Converted to Fugacity: 492.9447616288 [Pascal], Temp: 95.00000 [K]
Framework Density: 116.33074 [kg/m^3]
(Insertion) Averaged Rosenbluth Weight: 556.6735704443
(Insertion) Averaged Excess Mu: -600.3056460581
(Insertion) Converted to Fugacity: 492.9447616288 [Pascal], Temp: 95.00000 [K]
=========================AVERAGE========================
Averaged Rosenbluth Weight: 628.3394689165 +/- 236.1646065721
Averaged Excess Chemical Potential: -610.0313852420 +/- 37.2686504599
Averaged Henry Coefficient [mol/kg/Pa]: 0.006838204138 +/- 0.002570174038
Averaged Fugacity: 453.8128342469 +/- 184.8195730328
Printing: Component: 0 [ 667.cif ], NumMol: 1, Molsize: 207
Printing: Component: 1 [ methane ], NumMol: 6, Molsize: 1
Component 0, Molsize: 207
Component 1, Molsize: 1
Work took 3.235230 seconds
Work took 3.160120 seconds
======================================
CHECKING FINAL ENERGY FOR SYSTEM [0]
======================================
Expand All @@ -645,8 +717,23 @@ CHECKING FINAL ENERGY FOR SYSTEM [0]
Host-Host VDW: 0.00000; Real: 0.00000
Host-Guest VDW: -4894.72762; Real: 0.00000
Guest-Guest VDW: -51.91054; Real: 0.00000
Ewald Summation (total energy) on the CPU took 0.00000 secs
Ewald Summation (total energy) on the GPU took 0.00000 secs
********** PRINTING COMPONENT ENERGIES**********
Compoent [0-0], VDW: 0.00000, Real: 0.00000
Compoent [0-1], VDW: -4894.72762, Real: 0.00000
Compoent [1-1], VDW: -51.91054, Real: 0.00000
THERE IS MORE THAN 1 FRAMEWORK COMPONENTS
Framework Comp Zero Atoms: 207, Other Comp Atoms: 0
NFrameworkZero_ExtraFramework interactions: 0, NExtraFrameworkAtoms * (NExtraFrameworkAtoms - 1) / 2: 0
Atoms: 207 6
Interactions: 0 1242 15
Nblock 2, blocks: 0 1 1, threads needed: 0 13 1, Nthread: 128
GPU VDW REAL ENERGY:
HHVDW: 0.00000, HHReal: 0.00000, HGVDW: -4894.72762, HGReal: 0.00000, GGVDW: -51.91054, GGReal: 0.00000, HHEwaldE: 0.00000, HGEwaldE: 0.00000, GGEwaldE: 0.00000, TailE: 0.00000, DNN_E: 0.00000
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
VDW + Real on the GPU took 0.00018 secs
Total GPU Energy:
HHVDW: 0.00000, HHReal: 0.00000, HGVDW: -4894.72762, HGReal: 0.00000, GGVDW: -51.91054, GGReal: 0.00000, HHEwaldE: 0.00000, HGEwaldE: 0.00000, GGEwaldE: 0.00000, TailE: 0.00000, DNN_E: 0.00000
Stored HGVDW: 0.00000, Stored HGReal: 0.00000, Stored HGEwaldE: 0.00000
====================== DONE CALCULATING FINAL STAGE ENERGY ======================
======================================
======================== ENERGY SUMMARY (Simulation 0) =========================
Expand Down Expand Up @@ -740,7 +827,7 @@ DNN Energy: 0.00000 (0.00000 [K])
Tail Correction Energy: 0.00000 (0.00000 [K])
Total Energy: -4946.63815 (-5949.44183 [K])
========================================================================
*** CHECK DELTA_E (FINAL - CREATE MOLECULE) ***
*** CHECK DELTA_E (RUNNING FINAL - CREATE MOLECULE) ***
========================================================================
VDW [Host-Host]: 0.00000 (0.00000 [K])
VDW [Host-Guest]: -4894.72762 (-5887.00777 [K])
Expand All @@ -755,7 +842,22 @@ DNN Energy: 0.00000 (0.00000 [K])
Tail Correction Energy: 0.00000 (0.00000 [K])
Total Energy: -4946.63815 (-5949.44183 [K])
========================================================================
*** ENERGY DRIFT ***
*** ENERGY DRIFT (CPU FINAL - RUNNING FINAL) ***
========================================================================
VDW [Host-Host]: 0.00000 (0.00000 [K])
VDW [Host-Guest]: -0.00000 (-0.00000 [K])
VDW [Guest-Guest]: 0.00000 (0.00000 [K])
Real Coulomb [Host-Host]: 0.00000 (0.00000 [K])
Real Coulomb [Host-Guest]: 0.00000 (0.00000 [K])
Real Coulomb [Guest-Guest]: 0.00000 (0.00000 [K])
Ewald [Host-Host]: 0.00000 (0.00000 [K])
Ewald [Host-Guest]: 0.00000 (0.00000 [K])
Ewald [Guest-Guest]: 0.00000 (0.00000 [K])
DNN Energy: 0.00000 (0.00000 [K])
Tail Correction Energy: 0.00000 (0.00000 [K])
Total Energy: -0.00000 (-0.00000 [K])
========================================================================
*** GPU DRIFT (GPU FINAL - CPU FINAL) ***
========================================================================
VDW [Host-Host]: 0.00000 (0.00000 [K])
VDW [Host-Guest]: -0.00000 (-0.00000 [K])
Expand Down Expand Up @@ -833,8 +935,8 @@ PseudoAtom Type: Hw[10], #: 0
PseudoAtom Type: Ow[11], #: 0
PseudoAtom Type: CH3_sp3[12], #: 0
PseudoAtom Type: CH4_sp3[13], #: 6
Total Program Size: 5577 MB
Resident Set Size: 115 MB
Shared Pages: 94 MB
Total Program Size: 5578 MB
Resident Set Size: 116 MB
Shared Pages: 95 MB
Text (code): 0 MB
Data + Stack: 67 MB
Data + Stack: 68 MB
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