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10 Commits

Author SHA1 Message Date
chn
e441395c36 fix build 2024-09-14 22:42:26 +08:00
chn
35856d9293 Merge branch 'debug' into production 2024-09-14 22:30:31 +08:00
chn
36190b5e93 flake: 整理 srv1 2024-09-14 22:30:15 +08:00
chn
14c86412a1 modules.packages.desktop: remove etcher 2024-09-14 22:19:46 +08:00
chn
8d3e516c62 modules.user.chn: fix 2024-09-14 22:16:38 +08:00
chn
e3fe00a53d modules.users.chn: 使用来自 home-manager 的 impermanence 2024-09-14 19:12:22 +08:00
chn
feb5a5b952 split flake 2024-09-14 18:49:12 +08:00
chn
59c3b98223 packages.ufo: fix 2024-09-14 18:01:29 +08:00
chn
14fdf5a1f6 packages.ufo: fix 2024-09-14 13:16:44 +08:00
chn
1a7137fda7 packages.ufo: fix 2024-09-14 12:15:39 +08:00
41 changed files with 535 additions and 661 deletions

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@ -41,7 +41,7 @@ inputs:
initrd.sshd.enable = true;
nixpkgs.march = "silvermont";
nix.substituters = [ "https://nix-store.chn.moe?priority=100" ];
networking = { hostname = "nas"; networkd = {}; };
networking.networkd = {};
};
hardware = { cpus = [ "intel" ]; gpu.type = "intel"; };
services =

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@ -53,7 +53,6 @@ inputs:
modules.modprobeConfig =
[ "options iwlwifi power_save=0" "options iwlmvm power_scheme=1" "options iwlwifi uapsd_disable=1" ];
};
networking.hostname = "pc";
sysctl.laptop-mode = 5;
gui.enable = true;
};

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@ -18,7 +18,7 @@ inputs:
swap = [ "/nix/swap/swap" ];
rollingRootfs = {};
};
networking = { hostname = "pi3b"; networkd = {}; };
networking.networkd = {};
nixpkgs.arch = "aarch64";
kernel.variant = "nixos";
};

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@ -1,50 +0,0 @@
inputs:
{
config =
{
nixos =
{
system =
{
fileSystems =
{
mount =
{
vfat."/dev/disk/by-uuid/7A60-4232" = "/boot";
btrfs."/dev/mapper/root1" = { "/nix" = "/nix"; "/nix/rootfs/current" = "/"; };
};
swap = [ "/dev/mapper/swap" ];
rollingRootfs = {};
};
nixpkgs.march = "cascadelake";
kernel.variant = "xanmod-lts";
networking.hostname = "srv1-node0";
gui.enable = true;
};
packages.vasp = null;
hardware.cpus = [ "intel" ];
services =
{
snapper.enable = true;
sshd = {};
xray.client.enable = true;
smartd.enable = true;
beesd.instances.root = { device = "/"; hashTableSizeMB = 4096; threads = 4; };
wireguard =
{
enable = true;
peers = [ "vps6" ];
publicKey = "l1gFSDCeBxyf/BipXNvoEvVvLqPgdil84nmr5q6+EEw=";
wireguardIp = "192.168.83.3";
};
slurm =
{
enable = true;
cpu = { cores = 16; threads = 2; mpiThreads = 2; openmpThreads = 4; };
memoryMB = 90112;
};
};
user.users = [ "chn" ];
};
};
}

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@ -1,50 +0,0 @@
inputs:
{
config =
{
nixos =
{
system =
{
fileSystems =
{
mount =
{
vfat."/dev/disk/by-uuid/7A60-4232" = "/boot";
btrfs."/dev/mapper/root1" = { "/nix" = "/nix"; "/nix/rootfs/current" = "/"; };
};
swap = [ "/dev/mapper/swap" ];
rollingRootfs = {};
};
nixpkgs.march = "broadwell";
kernel.variant = "xanmod-lts";
networking.hostname = "srv1-node3";
gui.enable = true;
};
packages.vasp = null;
hardware.cpus = [ "intel" ];
services =
{
snapper.enable = true;
sshd = {};
xray.client.enable = true;
smartd.enable = true;
beesd.instances.root = { device = "/"; hashTableSizeMB = 4096; threads = 4; };
wireguard =
{
enable = true;
peers = [ "vps6" ];
publicKey = "l1gFSDCeBxyf/BipXNvoEvVvLqPgdil84nmr5q6+EEw=";
wireguardIp = "192.168.83.3";
};
slurm =
{
enable = true;
cpu = { cores = 16; threads = 2; mpiThreads = 2; openmpThreads = 4; };
memoryMB = 90112;
};
};
user.users = [ "chn" ];
};
};
}

29
devices/srv1/default.nix Normal file
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@ -0,0 +1,29 @@
inputs:
{
config =
{
nixos =
{
system =
{
fileSystems = { swap = [ "/dev/mapper/swap" ]; rollingRootfs = {}; };
kernel.variant = "xanmod-lts";
gui.enable = true;
};
hardware.cpus = [ "intel" ];
services =
{
snapper.enable = true;
sshd = {};
smartd.enable = true;
slurm =
{
enable = true;
cpu = { cores = 16; threads = 2; mpiThreads = 2; openmpThreads = 4; };
memoryMB = 90112;
};
};
user.users = [ "chn" ];
};
};
}

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@ -0,0 +1,31 @@
inputs:
{
config =
{
nixos =
{
system =
{
fileSystems.mount =
{
vfat."/dev/disk/by-uuid/7A60-4232" = "/boot";
btrfs."/dev/mapper/root1" = { "/nix" = "/nix"; "/nix/rootfs/current" = "/"; };
};
nixpkgs.march = "cascadelake";
};
packages.vasp = null;
services =
{
xray.client.enable = true;
beesd.instances.root = { device = "/"; hashTableSizeMB = 4096; threads = 4; };
wireguard =
{
enable = true;
peers = [ "vps6" ];
publicKey = "l1gFSDCeBxyf/BipXNvoEvVvLqPgdil84nmr5q6+EEw=";
wireguardIp = "192.168.83.3";
};
};
};
};
}

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@ -0,0 +1,31 @@
inputs:
{
config =
{
nixos =
{
system =
{
fileSystems.mount =
{
vfat."/dev/disk/by-uuid/7A60-4232" = "/boot";
btrfs."/dev/mapper/root1" = { "/nix" = "/nix"; "/nix/rootfs/current" = "/"; };
};
nixpkgs.march = "broadwell";
};
packages.vasp = null;
services =
{
xray.client.enable = true;
beesd.instances.root = { device = "/"; hashTableSizeMB = 4096; threads = 4; };
wireguard =
{
enable = true;
peers = [ "vps6" ];
publicKey = "l1gFSDCeBxyf/BipXNvoEvVvLqPgdil84nmr5q6+EEw=";
wireguardIp = "192.168.83.3";
};
};
};
};
}

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@ -26,7 +26,6 @@ inputs:
nixpkgs.march = "skylake";
nix = { substituters = [ "https://nix-store.chn.moe?priority=100" ]; githubToken.enable = true; };
kernel = { variant = "xanmod-lts"; patches = [ "surface" "hibernate-progress" ]; };
networking.hostname = "surface";
gui.enable = true;
};
hardware = { cpus = [ "intel" ]; gpu.type = "intel"; };

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@ -29,7 +29,7 @@ inputs:
nixpkgs.march = "znver2";
nix.substituters = [ "https://nix-store.chn.moe?priority=100" ];
initrd.sshd.enable = true;
networking = { hostname = "vps4"; networkd = {}; };
networking.networkd = {};
kernel.variant = "xanmod-latest";
nix-ld = null;
binfmt = null;

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@ -29,7 +29,7 @@ inputs:
nixpkgs.march = "sandybridge";
nix.substituters = [ "https://nix-store.chn.moe?priority=100" ];
initrd.sshd.enable = true;
networking = { hostname = "vps6"; networkd = {}; };
networking.networkd = {};
# do not use cachyos kernel, beesd + cachyos kernel + heavy io = system freeze, not sure why
};
services =

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@ -29,7 +29,7 @@ inputs:
nixpkgs.march = "znver2";
nix.substituters = [ "https://nix-store.chn.moe?priority=100" ];
initrd.sshd.enable = true;
networking = { hostname = "vps7"; networkd = {}; };
networking.networkd = {};
kernel.variant = "xanmod-lts";
};
services =

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@ -48,7 +48,6 @@ inputs:
};
};
gui = { enable = true; preferred = false; autoStart = true; };
networking.hostname = "xmupc1";
nix.remote.slave.enable = true;
};
hardware = { cpus = [ "amd" ]; gpu.type = "nvidia"; };

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@ -41,7 +41,6 @@ inputs:
};
};
gui = { enable = true; preferred = false; autoStart = true; };
networking.hostname = "xmupc2";
nix =
{
marches =

150
flake.nix
View File

@ -76,144 +76,14 @@
# nixos-wallpaper = { url = "git+https://git.chn.moe/chn/nixos-wallpaper.git"; flake = false; };
};
outputs = inputs:
let
localLib = import ./lib.nix inputs.nixpkgs.lib;
devices = builtins.filter (dir: (builtins.readDir ./devices/${dir})."default.nix" or null == "regular" )
(builtins.attrNames (builtins.readDir ./devices));
in
{
packages.x86_64-linux = rec
{
pkgs = (import inputs.nixpkgs
{
system = "x86_64-linux";
config.allowUnfree = true;
overlays = [ inputs.self.overlays.default ];
});
default = inputs.nixpkgs.legacyPackages.x86_64-linux.writeText "systems"
(builtins.concatStringsSep "\n" (builtins.map
(system: builtins.toString inputs.self.outputs.nixosConfigurations.${system}.config.system.build.toplevel)
devices));
hpcstat =
let
openssh = (pkgs.pkgsStatic.openssh.override { withLdns = false; etcDir = null; }).overrideAttrs
(prev: { doCheck = false; patches = prev.patches ++ [ ./packages/hpcstat/openssh.patch ];});
duc = pkgs.pkgsStatic.duc.override { enableCairo = false; cairo = null; pango = null; };
in pkgs.pkgsStatic.localPackages.hpcstat.override
{ inherit openssh duc; standalone = true; version = inputs.self.rev or "dirty"; };
ufo =
let
range-v3 = pkgs.pkgsStatic.range-v3.overrideAttrs (prev:
{
cmakeFlags = prev.cmakeFlags or []
++ [ "-DRANGE_V3_DOCS=OFF" "-DRANGE_V3_TESTS=OFF" "-DRANGE_V3_EXAMPLES=OFF" ];
doCheck = false;
});
tbb = pkgs.pkgsStatic.tbb_2021_11.overrideAttrs (prev: { cmakeFlags = prev.cmakeFlags or [] ++
[ "-DTBB_TEST=OFF" ]; });
biu = pkgs.pkgsStatic.localPackages.biu.override { inherit range-v3; };
matplotplusplus = pkgs.pkgsStatic.localPackages.matplotplusplus.override { libtiff = null; };
in pkgs.pkgsStatic.localPackages.ufo.override { inherit biu tbb matplotplusplus; };
chn-bsub = pkgs.pkgsStatic.localPackages.chn-bsub;
blog = pkgs.callPackage ./blog { inherit (inputs) hextra; };
}
// (builtins.listToAttrs (builtins.map
(system:
{
name = system;
value = inputs.self.outputs.nixosConfigurations.${system}.config.system.build.toplevel;
})
devices)
);
nixosConfigurations =
(
(builtins.listToAttrs (builtins.map
(system:
{
name = system;
value = inputs.nixpkgs.lib.nixosSystem
{
system = "x86_64-linux";
specialArgs = { topInputs = inputs; inherit localLib; };
modules = localLib.mkModules
[
(moduleInputs: { config.nixpkgs.overlays = [(prev: final:
# replace pkgs with final to avoid infinite recursion
{ localPackages = import ./packages (moduleInputs // { pkgs = final; }); })]; })
./modules
./devices/${system}
];
};
})
devices))
// {
pi3b = inputs.nixpkgs.lib.nixosSystem
{
system = "aarch64-linux";
specialArgs = { topInputs = inputs; inherit localLib; };
modules = localLib.mkModules
[
(moduleInputs: { config.nixpkgs.overlays = [(prev: final:
# replace pkgs with final to avoid infinite recursion
{ localPackages = import ./packages (moduleInputs // { pkgs = final; }); })]; })
./modules
./devices/pi3b
];
};
}
);
overlays.default = final: prev:
{ localPackages = (import ./packages { inherit (inputs) lib; pkgs = final; topInputs = inputs; }); };
config = { archive = false; branch = "production"; };
devShells.x86_64-linux = let inherit (inputs.self.nixosConfigurations.pc) pkgs; in
{
biu = pkgs.mkShell.override { stdenv = pkgs.clang18Stdenv; }
{
inputsFrom = [ pkgs.localPackages.biu ];
packages = [ pkgs.clang-tools_18 ];
CMAKE_EXPORT_COMPILE_COMMANDS = "1";
};
hpcstat = pkgs.mkShell.override { stdenv = pkgs.clang18Stdenv; }
{
inputsFrom = [ (pkgs.localPackages.hpcstat.override { version = null; }) ];
CMAKE_EXPORT_COMPILE_COMMANDS = "1";
};
sbatch-tui = pkgs.mkShell.override { stdenv = pkgs.clang18Stdenv; }
{
inputsFrom = [ pkgs.localPackages.sbatch-tui ];
CMAKE_EXPORT_COMPILE_COMMANDS = "1";
};
ufo = pkgs.mkShell.override { stdenv = pkgs.clang18Stdenv; }
{
inputsFrom = [ pkgs.localPackages.ufo ];
packages = [ pkgs.clang-tools_18 ];
CMAKE_EXPORT_COMPILE_COMMANDS = "1";
};
chn-bsub = pkgs.mkShell
{
inputsFrom = [ pkgs.localPackages.chn-bsub ];
packages = [ pkgs.clang-tools_18 ];
CMAKE_EXPORT_COMPILE_COMMANDS = "1";
};
winjob =
let inherit (pkgs) clang-tools_18; in let inherit (inputs.self.packages.x86_64-w64-mingw32) pkgs winjob;
in pkgs.mkShell.override { stdenv = pkgs.gcc14Stdenv; }
{
inputsFrom = [ winjob ];
packages = [ clang-tools_18 ];
CMAKE_EXPORT_COMPILE_COMMANDS = "1";
};
};
src = let inherit (inputs.self.packages.x86_64-linux) pkgs; in
{
nixos-wallpaper = pkgs.fetchgit
{
url = "https://git.chn.moe/chn/nixos-wallpaper.git";
rev = "1ad78b20b21c9f4f7ba5f4c897f74276763317eb";
sha256 = "0faahbzsr44bjmwr6508wi5hg59dfb57fzh5x6jh7zwmv4pzhqlb";
fetchLFS = true;
};
};
};
outputs = inputs: let localLib = import ./flake/lib.nix inputs.nixpkgs.lib; in
{
packages.x86_64-linux = import ./flake/packages.nix { inherit inputs localLib; };
nixosConfigurations = import ./flake/nixos.nix { inherit inputs localLib; };
overlays.default = final: prev:
{ localPackages = (import ./packages { inherit localLib; pkgs = final; topInputs = inputs; }); };
config = { archive = false; branch = "production"; };
devShells.x86_64-linux = import ./flake/dev.nix { inherit inputs; };
src = import ./flake/src.nix { inherit inputs; };
};
}

39
flake/dev.nix Normal file
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@ -0,0 +1,39 @@
{ inputs }: let inherit (inputs.self.nixosConfigurations.pc) pkgs; in
{
biu = pkgs.mkShell.override { stdenv = pkgs.clang18Stdenv; }
{
inputsFrom = [ pkgs.localPackages.biu ];
packages = [ pkgs.clang-tools_18 ];
CMAKE_EXPORT_COMPILE_COMMANDS = "1";
};
hpcstat = pkgs.mkShell.override { stdenv = pkgs.clang18Stdenv; }
{
inputsFrom = [ (pkgs.localPackages.hpcstat.override { version = null; }) ];
CMAKE_EXPORT_COMPILE_COMMANDS = "1";
};
sbatch-tui = pkgs.mkShell.override { stdenv = pkgs.clang18Stdenv; }
{
inputsFrom = [ pkgs.localPackages.sbatch-tui ];
CMAKE_EXPORT_COMPILE_COMMANDS = "1";
};
ufo = pkgs.mkShell.override { stdenv = pkgs.clang18Stdenv; }
{
inputsFrom = [ pkgs.localPackages.ufo ];
packages = [ pkgs.clang-tools_18 ];
CMAKE_EXPORT_COMPILE_COMMANDS = "1";
};
chn-bsub = pkgs.mkShell
{
inputsFrom = [ pkgs.localPackages.chn-bsub ];
packages = [ pkgs.clang-tools_18 ];
CMAKE_EXPORT_COMPILE_COMMANDS = "1";
};
winjob =
let inherit (pkgs) clang-tools_18; in let inherit (inputs.self.packages.x86_64-w64-mingw32) pkgs winjob;
in pkgs.mkShell.override { stdenv = pkgs.gcc14Stdenv; }
{
inputsFrom = [ winjob ];
packages = [ clang-tools_18 ];
CMAKE_EXPORT_COMPILE_COMMANDS = "1";
};
}

51
flake/nixos.nix Normal file
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@ -0,0 +1,51 @@
{ inputs, localLib }:
builtins.listToAttrs
(
(builtins.map
(system:
{
name = system;
value = inputs.nixpkgs.lib.nixosSystem
{
system = let arch.pi3b = "aarch64-linux"; in arch.${system} or "x86_64-linux";
specialArgs = { topInputs = inputs; inherit localLib; };
modules = localLib.mkModules
[
{
config =
{
nixpkgs.overlays = [ inputs.self.overlays.default ];
nixos.system.networking.hostname = system;
};
}
../modules
../devices/${system}
];
};
})
[ "nas" "pc" "pi3b" "surface" "vps4" "vps6" "vps7" "xmupc1" "xmupc2" ])
++ (builtins.map
(node:
{
name = "srv1-${node}";
value = inputs.nixpkgs.lib.nixosSystem
{
system = "x86_64-linux";
specialArgs = { topInputs = inputs; inherit localLib; };
modules = localLib.mkModules
[
{
config =
{
nixpkgs.overlays = [ inputs.self.overlays.default ];
nixos.system.cluster = { clusterName = "srv1"; nodeName = node; };
};
}
../modules
../devices/srv1
../devices/srv1/${node}
];
};
})
[ "node0" "node3" ])
)

21
flake/packages.nix Normal file
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@ -0,0 +1,21 @@
{ inputs, localLib }: rec
{
pkgs = (import inputs.nixpkgs
{
system = "x86_64-linux";
config.allowUnfree = true;
overlays = [ inputs.self.overlays.default ];
});
hpcstat =
let
openssh = (pkgs.pkgsStatic.openssh.override { withLdns = false; etcDir = null; }).overrideAttrs
(prev: { doCheck = false; patches = prev.patches ++ [ ../packages/hpcstat/openssh.patch ];});
duc = pkgs.pkgsStatic.duc.override { enableCairo = false; cairo = null; pango = null; };
in pkgs.pkgsStatic.localPackages.hpcstat.override
{ inherit openssh duc; standalone = true; version = inputs.self.rev or "dirty"; };
chn-bsub = pkgs.pkgsStatic.localPackages.chn-bsub;
blog = pkgs.callPackage ../blog { inherit (inputs) hextra; };
}
// (builtins.listToAttrs (builtins.map
(system: { inherit (system) name; value = system.value.config.system.build.toplevel; })
(localLib.attrsToList inputs.self.outputs.nixosConfigurations)))

10
flake/src.nix Normal file
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@ -0,0 +1,10 @@
{ inputs }: let inherit (inputs.self.packages.x86_64-linux) pkgs; in
{
nixos-wallpaper = pkgs.fetchgit
{
url = "https://git.chn.moe/chn/nixos-wallpaper.git";
rev = "1ad78b20b21c9f4f7ba5f4c897f74276763317eb";
sha256 = "0faahbzsr44bjmwr6508wi5hg59dfb57fzh5x6jh7zwmv4pzhqlb";
fetchLFS = true;
};
}

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@ -16,7 +16,7 @@ inputs:
# system management
# TODO: module should add yubikey-touch-detector into path
gparted wayland-utils clinfo glxinfo vulkan-tools dracut yubikey-touch-detector btrfs-assistant snapper-gui
kdePackages.qtstyleplugin-kvantum ventoy-full cpu-x inputs.pkgs."pkgs-23.11".etcher wl-mirror
kdePackages.qtstyleplugin-kvantum ventoy-full cpu-x wl-mirror # inputs.pkgs."pkgs-23.11".etcher
(
writeShellScriptBin "xclip"
''

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@ -0,0 +1,21 @@
inputs:
{
options.nixos.system.cluster = let inherit (inputs.lib) mkOption types; in mkOption
{
type = types.nullOr (types.submodule { options =
{
clusterName = mkOption { type = types.nonEmptyStr; };
nodeName = mkOption { type = types.nonEmptyStr; };
nodeType = mkOption { type = types.enum [ "master" "worker" ]; default = "worker"; };
};});
default = null;
};
config = let inherit (inputs.config.nixos.system) cluster; in inputs.lib.mkIf (cluster != null)
{
nixos.system.networking.hostname = "${cluster.clusterName}-${cluster.nodeName}";
# 作为从机时home-manager 需要被禁用
systemd.services = inputs.lib.mkIf (cluster.nodeType == "worker") (builtins.listToAttrs (builtins.map
(user: { name = "home-manager-${user}"; value.enable = false; })
inputs.config.nixos.user.users));
};
}

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@ -5,28 +5,26 @@ inputs:
enable = mkOption { type = types.bool; default = true; };
keyPathPrefix = mkOption { type = types.str; default = "/nix/persistent"; };
};
config =
let
inherit (inputs.lib) mkIf;
inherit (inputs.config.nixos.system) sops;
in mkIf sops.enable
config = let inherit (inputs.config.nixos.system) sops; in inputs.lib.mkIf sops.enable
{
sops =
{
sops =
{
defaultSopsFile =
let deviceDir = "${inputs.topInputs.self}/devices/${inputs.config.nixos.system.networking.hostname}";
in mkIf
(
builtins.pathExists "${deviceDir}/secrets.yaml"
|| builtins.pathExists "${deviceDir}/secrets/default.yaml"
)
(
if builtins.pathExists "${deviceDir}/secrets.yaml" then "${deviceDir}/secrets.yaml"
else "${deviceDir}/secrets/default.yaml"
);
# sops start before impermanence, so we need to use the absolute path
age.sshKeyPaths = [ "${sops.keyPathPrefix}/etc/ssh/ssh_host_ed25519_key" ];
gnupg.sshKeyPaths = [ "${sops.keyPathPrefix}/etc/ssh/ssh_host_rsa_key" ];
};
defaultSopsFile =
let deviceDir =
if (inputs.config.nixos.system.cluster == null) then
"${inputs.topInputs.self}/devices/${inputs.config.nixos.system.networking.hostname}"
else
"${inputs.topInputs.self}/devices/${inputs.config.nixos.system.cluster.clusterName}"
+ "/${inputs.config.nixos.system.cluster.nodeName}";
in inputs.lib.mkMerge
[
(inputs.lib.mkIf (builtins.pathExists "${deviceDir}/secrets.yaml") "${deviceDir}/secrets.yaml")
(inputs.lib.mkIf (builtins.pathExists "${deviceDir}/secrets/default.yaml")
"${deviceDir}/secrets/default.yaml")
];
# sops start before impermanence, so we need to use the absolute path
age.sshKeyPaths = [ "${sops.keyPathPrefix}/etc/ssh/ssh_host_ed25519_key" ];
gnupg.sshKeyPaths = [ "${sops.keyPathPrefix}/etc/ssh/ssh_host_rsa_key" ];
};
};
}

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@ -14,6 +14,7 @@ inputs:
};
home-manager.users.chn =
{
imports = [ "${inputs.topInputs.impermanence}/home-manager.nix" ];
config =
{
programs =
@ -81,39 +82,65 @@ inputs:
))
)
];
persistence =
{
"/nix/persistent/home/chn" =
{
directories =
[
# common things
"bin" "Desktop" "Documents" "Downloads" "Music" "Pictures" "repo" "share" "Public" "Videos"
".config" ".local/share"
# xmuvpn
".ecdata"
# firefox
".mozilla/firefox/default"
# ssh
".ssh"
# steam
".steam" # ".local/share/Steam"
# vscode
".vscode" # ".config/Code" ".config/grammarly-languageserver"
# zotero
".zotero" "Zotero"
];
allowOther = true;
};
"/nix/rootfs/current/home/chn".allowOther = true;
};
};
pam.yubico.authorizedYubiKeys.ids = [ "cccccbgrhnub" ];
};
};
environment.persistence =
let inherit (inputs.config.nixos.system) impermanence; in inputs.lib.mkIf impermanence.enable
{
# TODO: make copy or soft link of files
"${impermanence.persistence}".users.chn =
{
directories = builtins.map
(dir: { directory = dir.dir or dir; user = "chn"; group = "chn"; mode = dir.mode or "0755"; })
[
# common things
"bin" "Desktop" "Documents" "Downloads" "Music" "Pictures" "repo" "share" "Public" "Videos"
".config" ".local/share"
# # gnome
# { dir = ".config/dconf"; mode = "0700"; } ".config/gtk-2.0" ".config/gtk-3.0" ".config/gtk-4.0"
# ".config/libaccounts-glib"
# # android
# { dir = ".android"; mode = "0750";}
# xmuvpn
".ecdata"
# firefox
{ dir = ".mozilla/firefox/default"; mode = "0700"; }
# ssh
{ dir = ".ssh"; mode = "0700"; }
# steam
".steam" # ".local/share/Steam"
# vscode
".vscode" # ".config/Code" ".config/grammarly-languageserver"
# zotero
".zotero" "Zotero"
# environment.persistence =
# let inherit (inputs.config.nixos.system) impermanence; in inputs.lib.mkIf impermanence.enable
# {
# # TODO: make copy or soft link of files
# "${impermanence.persistence}".users.chn =
# {
# directories = builtins.map
# (dir: { directory = dir.dir or dir; user = "chn"; group = "chn"; mode = dir.mode or "0755"; })
# [
# # common things
# "bin" "Desktop" "Documents" "Downloads" "Music" "Pictures" "repo" "share" "Public" "Videos"
# ".config" ".local/share"
# # # gnome
# # { dir = ".config/dconf"; mode = "0700"; } ".config/gtk-2.0" ".config/gtk-3.0" ".config/gtk-4.0"
# # ".config/libaccounts-glib"
# # # android
# # { dir = ".android"; mode = "0750";}
# # xmuvpn
# ".ecdata"
# # firefox
# { dir = ".mozilla/firefox/default"; mode = "0700"; }
# # ssh
# { dir = ".ssh"; mode = "0700"; }
# # steam
# ".steam" # ".local/share/Steam"
# # vscode
# ".vscode" # ".config/Code" ".config/grammarly-languageserver"
# # zotero
# ".zotero" "Zotero"
# 百度网盘
# ".config/BaiduPCS-Go"
# # bitwarden
@ -196,7 +223,7 @@ inputs:
# ".local/share/waydroid"
# # zsh
# ".local/share/zsh"
];
# ];
# TODO: create file if not exist
# files = builtins.map
# (file: { inherit file; parentDirectory = { user = "chn"; group = "chn"; mode = "0755"; }; })
@ -212,7 +239,5 @@ inputs:
# # age TODO: use sops to storage
# ".config/sops/age/keys.txt"
# ];
};
};
};
}

View File

@ -2,74 +2,72 @@ inputs:
{
config = inputs.lib.mkIf inputs.config.nixos.system.gui.enable
{
home-manager.users.chn.config.home.file =
let
programs =
{
nheko = rec
home-manager.users.chn.config.home =
{
file =
let
programs =
{
fileName = "nheko.desktop";
path = "${inputs.pkgs.nheko}/share/applications/${fileName}";
nheko = rec
{
fileName = "nheko.desktop";
path = "${inputs.pkgs.nheko}/share/applications/${fileName}";
};
kclockd = rec
{
fileName = "org.kde.kclockd-autostart.desktop";
path = "${inputs.pkgs.kdePackages.kdeGear.kclock}/etc/xdg/autostart/${fileName}";
};
yakuake = rec
{
fileName = "org.kde.yakuake.desktop";
path = "${inputs.pkgs.yakuake}/share/applications/${fileName}";
};
telegram = rec
{
fileName = "org.telegram.desktop.desktop";
path = inputs.pkgs.writeText fileName (builtins.replaceStrings
[ "Exec=telegram-desktop -- %u" ] [ "Exec=telegram-desktop -autostart" ]
(builtins.readFile "${inputs.pkgs.telegram-desktop}/share/applications/${fileName}"));
};
element = rec
{
fileName = "element-desktop.desktop";
path = inputs.pkgs.writeText fileName (builtins.replaceStrings
[ "Exec=element-desktop %u" ] [ "Exec=element-desktop --hidden" ]
(builtins.readFile "${inputs.pkgs.element-desktop.desktopItem}/share/applications/${fileName}"));
};
kmail = rec
{
fileName = "org.kde.kmail2.desktop";
path = "${inputs.pkgs.kmail}/share/applications/${fileName}";
};
discord = rec
{
fileName = "discord.desktop";
path = inputs.pkgs.writeText fileName (builtins.replaceStrings
[ "Exec=Discord" ] [ "Exec=Discord --start-minimized" ]
(builtins.readFile "${inputs.pkgs.discord.desktopItem}/share/applications/${fileName}"));
};
crow-translate = rec
{
fileName = "io.crow_translate.CrowTranslate.desktop";
path = "${inputs.pkgs.crow-translate}/share/applications/${fileName}";
};
};
kclockd = rec
devices =
{
fileName = "org.kde.kclockd-autostart.desktop";
path = "${inputs.pkgs.kdePackages.kdeGear.kclock}/etc/xdg/autostart/${fileName}";
pc = [ "nheko" "kclockd" "yakuake" "telegram" "element" "kmail" "discord" "crow-translate" ];
surface = [ "kclockd" "yakuake" "telegram" "element" "crow-translate" ];
};
yakuake = rec
{
fileName = "org.kde.yakuake.desktop";
path = "${inputs.pkgs.yakuake}/share/applications/${fileName}";
};
telegram = rec
{
fileName = "org.telegram.desktop.desktop";
path = inputs.pkgs.writeText fileName (builtins.replaceStrings
[ "Exec=telegram-desktop -- %u" ] [ "Exec=telegram-desktop -autostart" ]
(builtins.readFile "${inputs.pkgs.telegram-desktop}/share/applications/${fileName}"));
};
element = rec
{
fileName = "element-desktop.desktop";
path = inputs.pkgs.writeText fileName (builtins.replaceStrings
[ "Exec=element-desktop %u" ] [ "Exec=element-desktop --hidden" ]
(builtins.readFile "${inputs.pkgs.element-desktop.desktopItem}/share/applications/${fileName}"));
};
kmail = rec
{
fileName = "org.kde.kmail2.desktop";
path = "${inputs.pkgs.kmail}/share/applications/${fileName}";
};
discord = rec
{
fileName = "discord.desktop";
path = inputs.pkgs.writeText fileName (builtins.replaceStrings
[ "Exec=Discord" ] [ "Exec=Discord --start-minimized" ]
(builtins.readFile "${inputs.pkgs.discord.desktopItem}/share/applications/${fileName}"));
};
crow-translate = rec
{
fileName = "io.crow_translate.CrowTranslate.desktop";
path = "${inputs.pkgs.crow-translate}/share/applications/${fileName}";
};
};
devices =
{
pc = [ "nheko" "kclockd" "yakuake" "telegram" "element" "kmail" "discord" "crow-translate" ];
surface = [ "kclockd" "yakuake" "telegram" "element" "crow-translate" ];
};
in builtins.listToAttrs (builtins.map
in builtins.listToAttrs (builtins.map
(file:
{
name = ".config/autostart/${programs.${file}.fileName}";
value.source = programs.${file}.path;
})
(devices.${inputs.config.nixos.system.networking.hostname} or []));
environment.persistence =
let impermanence = inputs.config.nixos.system.impermanence;
in inputs.lib.mkIf impermanence.enable
{
"${impermanence.root}".users.chn.directories = [ ".config/autostart" ];
};
persistence."/nix/rootfs/current/home/chn".directories = [ ".config/autostart" ];
};
};
}

View File

@ -63,12 +63,13 @@ inputs:
"Terminal Features".BlinkingCursorEnabled.value = true;
};
};
home.file.".local/share/konsole/Breeze.colorscheme".text = builtins.replaceStrings
[ "Opacity=1" ] [ "Opacity=0.9\nBlur=true" ]
(builtins.readFile "${inputs.pkgs.konsole}/share/konsole/Breeze.colorscheme");
home =
{
file.".local/share/konsole/Breeze.colorscheme".text = builtins.replaceStrings
[ "Opacity=1" ] [ "Opacity=0.9\nBlur=true" ]
(builtins.readFile "${inputs.pkgs.konsole}/share/konsole/Breeze.colorscheme");
persistence."/nix/rootfs/current/home/chn".directories = [ ".local/share/konsole" ".local/share/yakuake" ];
};
};
environment.persistence =
let impermanence = inputs.config.nixos.system.impermanence; in inputs.lib.mkIf impermanence.enable
{ "${impermanence.root}".users.chn.directories = [ ".local/share/konsole" ".local/share/yakuake" ]; };
};
}

View File

@ -84,9 +84,10 @@ inputs:
home-manager.users = builtins.listToAttrs (builtins.map
(name: { inherit name; value.imports = user.sharedModules; })
user.users);
environment.persistence."${inputs.config.nixos.system.impermanence.persistence}".directories = builtins.map
(user: { directory = "/home/${user}"; inherit user; group = user; mode = "0700"; })
(builtins.filter (user: user != "chn") user.users);
environment.persistence."${inputs.config.nixos.system.impermanence.persistence}".directories =
inputs.lib.mkIf (inputs.config.nixos.system.cluster.nodeType or null != "worker") (builtins.map
(user: { directory = "/home/${user}"; inherit user; group = user; mode = "0700"; })
(builtins.filter (user: user != "chn") user.users));
}
# set hashedPassword if it exist in secrets
(

View File

@ -2,7 +2,6 @@
# include <fmt/core.h>
# include <fmt/ranges.h>
# include <fmt/std.h>
# include <fmt/ostream.h>
# include <fmt/chrono.h>
# include <fmt/xchar.h>
# include <nameof.hpp>

View File

@ -7,6 +7,16 @@
namespace biu
{
// This should be defined in header
inline Atomic<Logger::LoggerConfigType_> Logger::LoggerConfig_ = Logger::LoggerConfigType_
{
std::experimental::make_observer(&std::clog), nullptr,
# ifdef NDEBUG
Logger::Level::Info
# else
Logger::Level::Debug
# endif
};
template <typename T> Logger::ObjectMonitor<T>::ObjectMonitor()
: CreateTime_{std::chrono::steady_clock::now()}
{

View File

@ -3,15 +3,6 @@
namespace biu
{
Atomic<Logger::LoggerConfigType_> Logger::LoggerConfig_ = Logger::LoggerConfigType_
{
std::experimental::make_observer(&std::clog), nullptr,
# ifdef NDEBUG
Logger::Level::Info
# else
Logger::Level::Debug
# endif
};
void Logger::init(std::experimental::observer_ptr<std::ostream> stream, Level level)
{ LoggerConfig_ = LoggerConfigType_{stream, nullptr, level}; }
void Logger::init(std::shared_ptr<std::ostream> stream, Level level)

View File

@ -28,6 +28,4 @@ message("List of compile features: ${CMAKE_CXX_COMPILE_FEATURES}")
include(CTest)
add_test(NAME fold COMMAND ufo fold ${PROJECT_SOURCE_DIR}/test/fold/config.yaml)
add_test(NAME fold-compare COMMAND ${CMAKE_COMMAND} -E compare_files fold-output.yaml
${PROJECT_SOURCE_DIR}/test/fold/output.yaml)
set_tests_properties(fold-compare PROPERTIES DEPENDS fold)

View File

@ -9,6 +9,7 @@ namespace ufo
// 也就是说, 正格子与倒格子的转置相乘, 得到单位矩阵.
using namespace biu::literals;
using namespace biu::stream_operators;
void fold(std::string config_file);
void unfold(std::string config_file);

View File

@ -4,7 +4,8 @@ void ufo::fold(std::string config_file)
{
struct Input
{
Eigen::Matrix<int, 3, 3> SuperCellTransformation;
Eigen::Matrix3d SuperCellDeformation;
Eigen::Vector3i SuperCellMultiplier;
std::vector<Eigen::Vector3d> Qpoints;
std::optional<std::string> OutputFile;
};
@ -15,7 +16,7 @@ void ufo::fold(std::string config_file)
auto fold = []
(
Eigen::Vector3d qpoint_in_reciprocal_primitive_cell_by_reciprocal_primitive_cell,
Eigen::Matrix<int, 3, 3> super_cell_transformation
Eigen::Matrix3d super_cell_transformation
) -> Eigen::Vector3d
{
/*
@ -35,8 +36,7 @@ void ufo::fold(std::string config_file)
*/
auto qpoint_by_reciprocal_super_cell =
(
super_cell_transformation.cast<double>()
* qpoint_in_reciprocal_primitive_cell_by_reciprocal_primitive_cell
super_cell_transformation * qpoint_in_reciprocal_primitive_cell_by_reciprocal_primitive_cell
).eval();
/*
q ReciprocalSuperCell
@ -49,7 +49,7 @@ void ufo::fold(std::string config_file)
output.Qpoints = input.Qpoints
| ranges::views::transform([&](auto& qpoint)
{
return fold(qpoint, input.SuperCellTransformation);
return fold(qpoint, input.SuperCellDeformation * input.SuperCellMultiplier.cast<double>().asDiagonal());
})
| ranges::to_vector;

View File

@ -11,9 +11,14 @@ void ufo::plot_band(std::string config_file)
// 内层表示一个路径上的 q 点,外层表示不同的路径
// 单位为倒格矢
std::vector<std::vector<Eigen::Vector3d>> Qpoints;
struct { std::size_t X, Y; } Resolution;
// 插值时使用的分辨率(不影响画出来图片的分辨率和横纵比)
std::array<std::size_t, 2> InterpolationResolution;
// 画图区域的y轴和x轴的比例。如果不指定则由matplot++自动调整(通常调整为正方形,即 1
std::optional<double> AspectRatio;
// 整张图片的分辨率
std::optional<std::array<std::size_t, 2>> PictureResolution;
// 画图的频率范围
struct { double Min, Max; } FrequencyRange;
std::array<double, 2> FrequencyRange;
// 搜索 q 点时的阈值,单位为埃^-1
std::optional<double> ThresholdWhenSearchingQpoints;
// 是否要在 y 轴上作一些标记
@ -81,8 +86,8 @@ void ufo::plot_band(std::string config_file)
// 所有 q 点的数据(需要用到它的频率和权重)
const std::vector<UnfoldOutput::QpointDataType>& qpoints,
// 用于插值的分辨率和范围
const std::pair<unsigned, unsigned>& resolution,
const std::pair<double, double>& frequency_range,
const std::array<std::size_t, 2>& resolution,
const std::array<double, 2>& frequency_range,
// 路径的总长度
double total_distance
)
@ -96,7 +101,7 @@ void ufo::plot_band(std::string config_file)
bool continuous,
// 第一个点占的比例
double ratio,
unsigned resolution, std::pair<double, double> frequency_range
std::size_t resolution, std::array<double, 2> frequency_range
) -> std::vector<double>
{
// 混合得到的频率和权重
@ -105,7 +110,7 @@ void ufo::plot_band(std::string config_file)
if (continuous)
{
assert(qpoints[a].ModeData.size() == qpoints[b].ModeData.size());
for (unsigned i = 0; i < qpoints[a].ModeData.size(); i++)
for (std::size_t i = 0; i < qpoints[a].ModeData.size(); i++)
{
frequency.push_back
(qpoints[a].ModeData[i].Frequency * ratio + qpoints[b].ModeData[i].Frequency * (1 - ratio));
@ -115,44 +120,44 @@ void ufo::plot_band(std::string config_file)
// 如果是不连续路径,将每个模式的权重乘以比例,最后相加
else
{
for (unsigned i = 0; i < qpoints[a].ModeData.size(); i++)
for (std::size_t i = 0; i < qpoints[a].ModeData.size(); i++)
{
frequency.push_back(qpoints[a].ModeData[i].Frequency);
weight.push_back(qpoints[a].ModeData[i].Weight * ratio);
}
for (unsigned i = 0; i < qpoints[b].ModeData.size(); i++)
for (std::size_t i = 0; i < qpoints[b].ModeData.size(); i++)
{
frequency.push_back(qpoints[b].ModeData[i].Frequency);
weight.push_back(qpoints[b].ModeData[i].Weight * (1 - ratio));
}
}
std::vector<double> result(resolution);
for (unsigned i = 0; i < frequency.size(); i++)
for (std::size_t i = 0; i < frequency.size(); i++)
{
int index = (frequency[i] - frequency_range.first) / (frequency_range.second - frequency_range.first)
std::ptrdiff_t index = (frequency[i] - frequency_range[0]) / (frequency_range[1] - frequency_range[0])
* resolution;
if (index >= 0 && index < static_cast<int>(resolution)) result[index] += weight[i];
if (index >= 0 && index < static_cast<std::ptrdiff_t>(resolution)) result[index] += weight[i];
}
return result;
};
std::vector<std::vector<double>> values;
for (unsigned i = 0; i < resolution.first; i++)
for (std::size_t i = 0; i < resolution[0]; i++)
{
auto current_distance = total_distance * i / resolution.first;
auto current_distance = total_distance * i / resolution[0];
auto it = path.lower_bound(current_distance);
if (it == path.begin()) values.push_back(blend
(it->second, it->second, true, 1, resolution.second, frequency_range));
(it->second, it->second, true, 1, resolution[1], frequency_range));
else if (it == path.end()) values.push_back(blend
(
std::prev(it)->second, std::prev(it)->second, true, 1,
resolution.second, frequency_range
resolution[1], frequency_range
));
else values.push_back(blend
(
std::prev(it)->second, it->second, !path_begin.contains(it->second),
(it->first - current_distance) / (it->first - std::prev(it)->first),
resolution.second, frequency_range
resolution[1], frequency_range
));
}
return values;
@ -164,7 +169,9 @@ void ufo::plot_band(std::string config_file)
const std::vector<std::vector<double>>& values,
const std::string& filename,
const std::vector<double>& x_ticks, const std::vector<double>& y_ticks,
const std::vector<std::string>& y_ticklabels
const std::vector<std::string>& y_ticklabels,
const std::optional<double>& aspect_ratio,
const std::optional<std::array<std::size_t, 2>>& resolution
)
{
std::vector<std::vector<double>>
@ -172,8 +179,8 @@ void ufo::plot_band(std::string config_file)
g(values[0].size(), std::vector<double>(values.size(), 0)),
b(values[0].size(), std::vector<double>(values.size(), 0)),
a(values[0].size(), std::vector<double>(values.size(), 0));
for (unsigned i = 0; i < values[0].size(); i++)
for (unsigned j = 0; j < values.size(); j++)
for (std::size_t i = 0; i < values[0].size(); i++)
for (std::size_t j = 0; j < values.size(); j++)
{
auto v = values[j][i];
if (v < 0.05) v = 0;
@ -196,6 +203,16 @@ void ufo::plot_band(std::string config_file)
ax->y_axis().tick_values(y_ticks);
ax->y_axis().tick_length(1);
ax->y_axis().ticklabels(y_ticklabels);
if (aspect_ratio)
{
ax->axes_aspect_ratio_auto(false);
ax->axes_aspect_ratio(*aspect_ratio);
}
if (resolution)
{
f->width((*resolution)[0]);
f->height((*resolution)[1]);
}
f->save(filename, "png");
};
@ -241,30 +258,34 @@ void ufo::plot_band(std::string config_file)
// 计算画图的数据
auto values = calculate_values
(
path, path_begin, unfolded_data.QpointData, {input.Resolution.X, input.Resolution.Y},
{input.FrequencyRange.Min, input.FrequencyRange.Max}, total_distance
path, path_begin, unfolded_data.QpointData, input.InterpolationResolution,
input.FrequencyRange, total_distance
);
auto x_ticks = x_ticks_index | ranges::views::transform([&](auto i)
{ return path.nth(i)->first / total_distance * input.Resolution.X; }) | ranges::to<std::vector>;
{ return path.nth(i)->first / total_distance * input.InterpolationResolution[0]; }) | ranges::to<std::vector>;
auto y_ticks = input.YTicks.value_or(std::vector<std::pair<double, std::string>>{})
| biu::toLvalue | ranges::views::keys
| ranges::views::transform([&](auto i)
{
return (i - input.FrequencyRange.Min) / (input.FrequencyRange.Max - input.FrequencyRange.Min)
* input.Resolution.Y;
return (i - input.FrequencyRange[0]) / (input.FrequencyRange[1] - input.FrequencyRange[0])
* input.InterpolationResolution[1];
})
| ranges::to_vector;
auto y_ticklabels = input.YTicks.value_or(std::vector<std::pair<double, std::string>>{})
| biu::toLvalue | ranges::views::values | ranges::to_vector;
if (input.OutputPictureFile) plot(values, input.OutputPictureFile.value(), x_ticks, y_ticks, y_ticklabels);
if (input.OutputPictureFile) plot
(
values, input.OutputPictureFile.value(),
x_ticks, y_ticks, y_ticklabels, input.AspectRatio, input.PictureResolution
);
if (input.OutputDataFile)
biu::Hdf5file(input.OutputDataFile.value(), true)
.write("Values", values)
.write("XTicks", x_ticks)
.write("YTicks", y_ticks)
.write("YTickLabels", y_ticklabels)
.write("Resolution", std::vector{input.Resolution.X, input.Resolution.Y})
.write("Range", std::vector{input.FrequencyRange.Min, input.FrequencyRange.Max});
.write("InterpolationResolution", input.InterpolationResolution)
.write("FrequencyRange", input.FrequencyRange);
}
void ufo::plot_point(std::string config_file)
@ -274,10 +295,12 @@ void ufo::plot_point(std::string config_file)
std::string UnfoldedDataFile;
// 要画图的 q 点
Eigen::Vector3d Qpoint;
// x 方向为频率y 方向没有用
struct { std::size_t X, Y; } Resolution;
// 插值的分辨率
std::size_t InterpolationResolution;
std::optional<double> AspectRatio;
std::optional<std::array<std::size_t, 2>> PictureResolution;
// 画图的频率范围
struct { double Min, Max; } FrequencyRange;
std::array<double, 2> FrequencyRange;
// 搜索 q 点时的阈值,单位为埃^-1
std::optional<double> ThresholdWhenSearchingQpoints;
// 是否要在 z 轴上作一些标记
@ -315,17 +338,17 @@ void ufo::plot_point(std::string config_file)
// q 点的数据(需要用到它的频率和权重)
const UnfoldOutput::QpointDataType& qpoint,
// 用于插值的分辨率和范围
unsigned resolution,
const std::pair<double, double>& frequency_range
std::size_t resolution,
const std::array<double, 2>& frequency_range
)
{
biu::Logger::Guard log;
std::vector<double> result(resolution);
for (auto& mode : qpoint.ModeData)
{
int index = (mode.Frequency - frequency_range.first) / (frequency_range.second - frequency_range.first)
std::ptrdiff_t index = (mode.Frequency - frequency_range[0]) / (frequency_range[1] - frequency_range[0])
* resolution;
if (index >= 0 && index < static_cast<int>(resolution)) result[index] += mode.Weight;
if (index >= 0 && index < static_cast<std::ptrdiff_t>(resolution)) result[index] += mode.Weight;
}
return log.rtn(result);
};
@ -334,7 +357,8 @@ void ufo::plot_point(std::string config_file)
auto plot = []
(
const std::vector<double>& values, const std::string& filename,
const std::vector<double>& x_ticks, const std::vector<std::string>& x_ticklabels, unsigned y_resolution
const std::vector<double>& x_ticks, const std::vector<std::string>& x_ticklabels, std::size_t y_resolution,
const std::optional<double>& aspect_ratio, const std::optional<std::array<std::size_t, 2>>& resolution
)
{
biu::Logger::Guard log;
@ -343,7 +367,7 @@ void ufo::plot_point(std::string config_file)
g(y_resolution, std::vector<double>(values.size(), 0)),
b(y_resolution, std::vector<double>(values.size(), 0)),
a(y_resolution, std::vector<double>(values.size(), 0));
for (unsigned i = 0; i < y_resolution; i++) for (unsigned j = 0; j < values.size(); j++)
for (std::size_t i = 0; i < y_resolution; i++) for (std::size_t j = 0; j < values.size(); j++)
{
auto v = values[j];
if (v < 0.05) v = 0;
@ -364,6 +388,16 @@ void ufo::plot_point(std::string config_file)
ax->x_axis().tick_length(1);
ax->x_axis().ticklabels(x_ticklabels);
ax->y_axis().tick_values({});
if (aspect_ratio)
{
ax->axes_aspect_ratio_auto(false);
ax->axes_aspect_ratio(*aspect_ratio);
}
if (resolution)
{
f->width((*resolution)[0]);
f->height((*resolution)[1]);
}
f->save(filename, "png");
};
@ -383,25 +417,28 @@ void ufo::plot_point(std::string config_file)
auto values = calculate_values
(
unfolded_data.QpointData[qpoint_index],
input.Resolution.X, {input.FrequencyRange.Min, input.FrequencyRange.Max}
input.InterpolationResolution, input.FrequencyRange
);
auto x_ticks = input.XTicks.value_or(std::vector<std::pair<double, std::string>>{})
| biu::toLvalue | ranges::views::keys
| ranges::views::transform([&](auto i)
{
return (i - input.FrequencyRange.Min) / (input.FrequencyRange.Max - input.FrequencyRange.Min)
* input.Resolution.X;
return (i - input.FrequencyRange[0]) / (input.FrequencyRange[1] - input.FrequencyRange[0])
* input.InterpolationResolution;
})
| ranges::to_vector;
auto x_ticklabels = input.XTicks.value_or(std::vector<std::pair<double, std::string>>{})
| biu::toLvalue | ranges::views::values | ranges::to_vector;
if (input.OutputPictureFile)
plot(values, input.OutputPictureFile.value(), x_ticks, x_ticklabels, input.Resolution.Y);
if (input.OutputPictureFile) plot
(
values, input.OutputPictureFile.value(),
x_ticks, x_ticklabels, 10, input.AspectRatio, input.PictureResolution
);
if (input.OutputDataFile)
biu::Hdf5file(input.OutputDataFile.value(), true)
.write("Values", values)
.write("XTicks", x_ticks)
.write("XTickLabels", x_ticklabels)
.write("Resolution", std::vector{input.Resolution.X, input.Resolution.Y})
.write("Range", std::vector{input.FrequencyRange.Min, input.FrequencyRange.Max});
.write("InterpolationResolution", input.InterpolationResolution)
.write("FrequencyRange", input.FrequencyRange);
}

View File

@ -29,10 +29,11 @@ void ufo::unfold(std::string config_file)
// PositionToSuperCell(line vector) * SuperCell = PositionToPrimativeCell(line vector) * PrimativeCell
// ReciprocalPositionToSuperCell(line vector) * ReciprocalSuperCell
// = ReciprocalPositionToPrimativeCell(line vector) * ReciprocalPrimativeCell
Eigen::Matrix3i SuperCellTransformation;
Eigen::Matrix3d SuperCellDeformation;
Eigen::Vector3i SuperCellMultiplier;
// 在单胞内取几个平面波的基矢
Eigen::Vector<unsigned, 3> PrimativeCellBasisNumber;
Eigen::Vector<std::size_t, 3> PrimativeCellBasisNumber;
// 超胞中原子的坐标,每行表示一个原子的坐标,单位为超胞的格矢
Eigen::MatrixX3d AtomPositionBySuperCell;
@ -89,17 +90,18 @@ void ufo::unfold(std::string config_file)
// 整理得到结果
auto number_of_qpoints = frequency.size(), num_of_modes = frequency[0].size();
std::vector<UnfoldOutput::MetaQpointDataType> qpoint_data(number_of_qpoints);
for (unsigned i = 0; i < number_of_qpoints; i++)
for (std::size_t i = 0; i < number_of_qpoints; i++)
{
qpoint_data[i].Qpoint = qpoint[i] | biu::toEigen<>;
qpoint_data[i].ModeData.resize(num_of_modes);
for (unsigned j = 0; j < num_of_modes; j++)
for (std::size_t j = 0; j < num_of_modes; j++)
{
qpoint_data[i].ModeData[j].Frequency = frequency[i][j];
auto n_modes = eigenvector_vector[i].size() / 3;
Eigen::MatrixX3cd eigenvectors(n_modes, 3);
for (unsigned k = 0; k < n_modes; k++) for (unsigned l = 0; l < 3; l++) eigenvectors(k, l)
= eigenvector_vector[i][k * 3 + l][j].r + eigenvector_vector[i][k * 3 + l][j].i * 1i;
auto number_of_atoms = eigenvector_vector[i].size() / 3;
Eigen::MatrixX3cd eigenvectors(number_of_atoms, 3);
for (std::size_t k = 0; k < number_of_atoms; k++) for (std::size_t l = 0; l < 3; l++)
eigenvectors(k, l)
= eigenvector_vector[i][k * 3 + l][j].r + eigenvector_vector[i][k * 3 + l][j].i * 1i;
// 原则上讲,需要对读入的原子运动状态作相位转换, 使得它们与我们的约定一致(对超胞周期性重复),但这个转换 phonopy 已经做了
// 这里还要需要做归一化处理 (指将数据简单地作为向量处理的归一化)
qpoint_data[i].ModeData[j].AtomMovement = eigenvectors / eigenvectors.norm();
@ -108,135 +110,6 @@ void ufo::unfold(std::string config_file)
return qpoint_data;
};
// 将 SuperCellTransformation 矩阵分解为 SuperCellDeformation 和 SuperCellMultiplier
auto decompose_transformation = [](Eigen::Matrix3i transformation)
-> std::pair<Eigen::Matrix3d, Eigen::Vector3i>
{
// 三种整数基础矩阵
struct Multiply { unsigned at; int multiply; };
struct Add { unsigned from, to; int multiply; };
struct Exchange { unsigned from, to; };
// 将 SuperCellTransformation 分解为一系列基础矩阵的乘积,并将这些基础矩阵从左到右输出
auto decompose = [](Eigen::Matrix3i matrix)
-> concurrencpp::generator<std::variant<Add, Exchange, Multiply>>
{
// 首先将第一列转变为只有一个元素不为零
while (true)
{
// 统计第一列零的个数,以及非零值中,绝对值最大和最小的行
std::multimap<unsigned, unsigned> values;
for (unsigned i = 0; i < 3; i++) if (matrix(i, 0) != 0)
values.insert({std::abs(matrix(i, 0)), i});
// 如果都是零,报错
if (values.size() == 0) [[unlikely]] throw std::runtime_error("Transformation matrix is singular.");
// 如果只有一个非零值,那么将它移到第一行
if (values.size() == 1)
{
if (auto i = values.begin()->second; i != 0)
{
auto transform = Eigen::Matrix3i::Identity().eval();
transform(0, 0) = 0;
transform(0, i) = 1;
transform(i, i) = 0;
transform(i, 0) = 1;
matrix = transform * matrix;
co_yield Exchange{0, i};
}
break;
}
// 否则,将最小值乘以整数倍,加到最大值上
else
{
auto i_max = values.rbegin()->second;
auto i_min = values.begin()->second;
auto multiply = -matrix(i_max, 0) / matrix(i_min, 0);
auto transform = Eigen::Matrix3i::Identity().eval();
transform(i_max, i_min) = multiply;
matrix = transform * matrix;
// 分解出来的矩阵需要是操作的逆
co_yield Add{i_min, i_max, -multiply};
}
}
// 然后将第二列后两行转变为只有一个元素不为零
while (true)
{
// 如果都是零,报错
if (matrix(1, 1) == 0 && matrix(2, 1) == 0) [[unlikely]]
throw std::runtime_error("Transformation matrix is singular.");
// 如果只有一个不是零,将它移到第二行
else if (matrix(2, 1) == 0) break;
else if (matrix(1, 1) == 0)
{
Eigen::Matrix3i transform{{1, 0, 0}, {0, 0, 1}, {0, 1, 0}};
matrix = transform * matrix;
co_yield Exchange{1, 2};
break;
}
// 否则,将最小值乘以整数倍,加到最大值上
else
{
unsigned i_max, i_min;
if (std::abs(matrix(1, 1)) > std::abs(matrix(2, 1))) { i_max = 1; i_min = 2; }
else { i_max = 2; i_min = 1; }
auto multiply = -matrix(i_max, 1) / matrix(i_min, 1);
auto transform = Eigen::Matrix3i::Identity().eval();
transform(i_max, i_min) = multiply;
matrix = transform * matrix;
co_yield Add{i_min, i_max, -multiply};
}
}
// 然后将第三行第三列元素化为 1
if (matrix(2, 2) == 0) [[unlikely]] throw std::runtime_error("Transformation matrix is singular.");
else if (matrix(2, 2) != 1)
{
co_yield Multiply{2, matrix(2, 2)};
matrix(2, 2) = 1;
}
// 将第三列的其它元素化为 0
if (matrix(0, 2) != 0)
{ co_yield Add{2, 0, matrix(0, 2)}; matrix(0, 2) = 0; }
if (matrix(1, 2) != 0)
{ co_yield Add{2, 1, matrix(1, 2)}; matrix(1, 2) = 0; }
// 将第二行第二列元素化为 1
if (matrix(1, 1) == 0) [[unlikely]] throw std::runtime_error("Transformation matrix is singular.");
else if (matrix(1, 1) != 1)
{ co_yield Multiply{1, matrix(1, 1)}; matrix(1, 1) = 1; }
// 将第一行第二列元素化为 0
if (matrix(0, 1) != 0)
{ co_yield Add{1, 0, matrix(0, 1)}; matrix(0, 1) = 0; }
// 将第一行第一列元素化为 1
if (matrix(0, 0) == 0) [[unlikely]] throw std::runtime_error("Transformation matrix is singular.");
else if (matrix(0, 0) != 1)
{ co_yield Multiply{0, matrix(0, 0)}; matrix(0, 0) = 1; }
};
auto deformatin = Eigen::Matrix3d::Identity().eval();
auto multiplier = Eigen::Vector3i::Ones().eval();
for (auto i : decompose(transformation))
{
if (std::holds_alternative<Multiply>(i))
{
auto [at, multiply] = std::get<Multiply>(i);
multiplier(at) *= multiply;
}
else if (std::holds_alternative<Add>(i))
{
auto [from, to, multiply] = std::get<Add>(i);
auto transform = Eigen::Matrix3d::Identity().eval();
transform(to, from) = static_cast<double>(multiply) / multiplier(from) * multiplier(to);
deformatin = deformatin * transform;
}
else if (std::holds_alternative<Exchange>(i))
{
auto [from, to] = std::get<Exchange>(i);
deformatin.col(from).swap(deformatin.col(to));
std::swap(multiplier(from), multiplier(to));
}
}
return {deformatin, multiplier};
};
// 构建基
// 每个 q 点对应一组 sub qpoint。不同的 q 点所对应的 sub qpoint 是不一样的,但 sub qpoint 与 q 点的相对位移在不同 q 点之间是相同的。
// 由于基只与这个相对位置有关(也就是说,不同 q 点的基是一样的),因此可以先计算出所有的基,这样降低计算量。
@ -245,9 +118,10 @@ void ufo::unfold(std::string config_file)
auto construct_basis = []
(
Eigen::Matrix3d primative_cell, Eigen::Vector3i super_cell_multiplier,
Eigen::Vector<unsigned, 3> primative_cell_basis_number, Eigen::MatrixX3d atom_position
Eigen::Vector<std::size_t, 3> primative_cell_basis_number, Eigen::MatrixX3d atom_position
)
{
biu::Logger::Guard log;
std::vector<std::vector<Eigen::VectorXcd>> basis(super_cell_multiplier.prod());
// diff_of_sub_qpoint 表示 sub qpoint 与 qpoint 的相对位置,单位为超胞的倒格矢
for (auto [diff_of_sub_qpoint_by_reciprocal_modified_super_cell, i_of_sub_qpoint]
@ -261,14 +135,6 @@ void ufo::unfold(std::string config_file)
auto diff_of_sub_qpoint_by_reciprocal_primative_cell = xyz_of_basis.cast<double>()
+ super_cell_multiplier.cast<double>().cwiseInverse().asDiagonal()
* diff_of_sub_qpoint_by_reciprocal_modified_super_cell.cast<double>();
// DiffOfSubQpoint
// = (DiffOfSubQpointByReciprocalPrimativeCell.transpose() * ReciprocalPrimativeCell).transpose()
// ReciprocalPrimativeCell = PrimativeCell.transpose().inverse()
// SuperCell = SuperCellTransformation * PrimativeCell
// ReciprocalSuperCell = SuperCell.transpose().inverse()
// AtomPosition = AtomPositionBySuperCell * SuperCell.transpose()
// 整理得到:
//
// 将单位转换为埃^-1
auto diff_of_sub_qpoint = (diff_of_sub_qpoint_by_reciprocal_primative_cell.transpose()
* (primative_cell.transpose().inverse())).transpose();
@ -287,7 +153,7 @@ void ufo::unfold(std::string config_file)
const std::vector<std::vector<Eigen::VectorXcd>>& basis,
// 实际上只需要其中的 AtomMovement
const std::vector<UnfoldOutput::MetaQpointDataType>& qpoint_data,
std::atomic<unsigned>& number_of_finished_modes
std::atomic<std::size_t>& number_of_finished_modes
)
{
// 将所有的模式取出,组成一个一维数组,稍后并行计算
@ -299,21 +165,20 @@ void ufo::unfold(std::string config_file)
// 对每个模式并行
std::transform
(
std::execution::par, mode_data.begin(), mode_data.end(),
std::execution::par_unseq, mode_data.begin(), mode_data.end(),
projection_coefficient.begin(), [&](const auto& mode_data)
{
// 这里, mode_data 和 projection_coefficient 均指对应于一个模式的数据
std::vector<double> projection_coefficient(basis.size());
for (unsigned i_of_sub_qpoint = 0; i_of_sub_qpoint < basis.size(); i_of_sub_qpoint++)
for (std::size_t i_of_sub_qpoint = 0; i_of_sub_qpoint < basis.size(); i_of_sub_qpoint++)
// 对于 basis 中, 对应于单胞倒格子的部分, 以及对应于不同方向的部分, 分别求内积, 然后求模方和
for (unsigned i_of_basis = 0; i_of_basis < basis[i_of_sub_qpoint].size(); i_of_basis++)
for (std::size_t i_of_basis = 0; i_of_basis < basis[i_of_sub_qpoint].size(); i_of_basis++)
projection_coefficient[i_of_sub_qpoint] +=
(basis[i_of_sub_qpoint][i_of_basis].transpose().conjugate() * mode_data.get())
.array().abs2().sum();
// 如果是严格地将向量分解到一组完备的基矢上, 那么不需要对计算得到的权重再做归一化处理
// 但这里并不是这样一个严格的概念. 因此对分解到各个 sub qpoint 上的权重做归一化处理
auto sum = std::accumulate
(projection_coefficient.begin(), projection_coefficient.end(), 0.);
auto sum = ranges::accumulate(projection_coefficient, 0.);
for (auto& _ : projection_coefficient) _ /= sum;
number_of_finished_modes++;
return projection_coefficient;
@ -324,8 +189,9 @@ void ufo::unfold(std::string config_file)
std::vector<std::vector<std::vector<double>>> projection_coefficient_output;
for
(
unsigned i_of_meta_qpoint = 0, num_of_mode_manipulated = 0;
i_of_meta_qpoint < qpoint_data.size(); i_of_meta_qpoint++
std::size_t i_of_meta_qpoint = 0, num_of_mode_manipulated = 0;
i_of_meta_qpoint < qpoint_data.size();
i_of_meta_qpoint++, num_of_mode_manipulated += qpoint_data[i_of_meta_qpoint].ModeData.size()
)
projection_coefficient_output.emplace_back
(
@ -339,8 +205,6 @@ void ufo::unfold(std::string config_file)
auto construct_output = []
(
const Input& input,
const Eigen::Vector3i& super_cell_multiplier,
const Eigen::Matrix3d& super_cell_deformation,
const std::vector<std::vector<std::vector<double>>>& projection_coefficient,
const std::vector<UnfoldOutput::MetaQpointDataType>& qpoint_data,
const std::optional<std::vector<std::size_t>>& selected_atoms
@ -348,31 +212,30 @@ void ufo::unfold(std::string config_file)
{
UnfoldOutput output;
output.PrimativeCell = input.PrimativeCell;
output.SuperCellTransformation = input.SuperCellTransformation;
output.SuperCellMultiplier = super_cell_multiplier;
output.SuperCellDeformation = super_cell_deformation;
output.SuperCellMultiplier = input.SuperCellMultiplier;
output.SuperCellDeformation = input.SuperCellDeformation;
output.SelectedAtoms = selected_atoms;
output.MetaQpointData = qpoint_data;
for (unsigned i_of_meta_qpoint = 0; i_of_meta_qpoint < qpoint_data.size(); i_of_meta_qpoint++)
for (std::size_t i_of_meta_qpoint = 0; i_of_meta_qpoint < qpoint_data.size(); i_of_meta_qpoint++)
{
// 如果需要投影到特定的原子上,需要先计算当前 meta qpoint 的不同模式的投影系数
std::optional<std::vector<double>> projection_coefficient_on_atoms;
if (selected_atoms)
{
projection_coefficient_on_atoms.emplace();
for (std::size_t i = 0; i < qpoint_data[i_of_meta_qpoint].ModeData.size(); i++)
for (std::size_t i_of_mode = 0; i_of_mode < qpoint_data[i_of_meta_qpoint].ModeData.size(); i_of_mode++)
{
projection_coefficient_on_atoms.value().emplace_back(0);
for (auto atom : *selected_atoms)
projection_coefficient_on_atoms.value().back()
+= qpoint_data[i_of_meta_qpoint].ModeData[i].AtomMovement.row(atom).array().abs2().sum();
+= qpoint_data[i_of_meta_qpoint].ModeData[i_of_mode].AtomMovement.row(atom).array().abs2().sum();
}
}
for
(
auto [diff_of_sub_qpoint_by_reciprocal_modified_super_cell, i_of_sub_qpoint]
: biu::sequence(super_cell_multiplier)
: biu::sequence(input.SuperCellMultiplier)
)
{
auto& _ = output.QpointData.emplace_back();
@ -399,10 +262,10 @@ void ufo::unfold(std::string config_file)
*/
auto sub_qpoint_by_reciprocal_primative_cell =
(
super_cell_multiplier.cast<double>().cwiseInverse().asDiagonal()
input.SuperCellMultiplier.cast<double>().cwiseInverse().asDiagonal()
* (
diff_of_sub_qpoint_by_reciprocal_modified_super_cell.cast<double>()
+ super_cell_deformation.inverse() * qpoint_data[i_of_meta_qpoint].Qpoint
+ input.SuperCellDeformation.inverse() * qpoint_data[i_of_meta_qpoint].Qpoint
)
).eval();
_.Qpoint = sub_qpoint_by_reciprocal_primative_cell.array()
@ -410,7 +273,7 @@ void ufo::unfold(std::string config_file)
_.Source = qpoint_data[i_of_meta_qpoint].Qpoint;
_.SourceIndex = i_of_meta_qpoint;
for (unsigned i_of_mode = 0; i_of_mode < qpoint_data[i_of_meta_qpoint].ModeData.size(); i_of_mode++)
for (std::size_t i_of_mode = 0; i_of_mode < qpoint_data[i_of_meta_qpoint].ModeData.size(); i_of_mode++)
{
auto& __ = _.ModeData.emplace_back();
__.Frequency = qpoint_data[i_of_meta_qpoint].ModeData[i_of_mode].Frequency;
@ -423,31 +286,31 @@ void ufo::unfold(std::string config_file)
return output;
};
std::clog << "Reading input file... " << std::flush;
biu::Logger::Guard log;
log.info("Reading input file... ");
auto input = YAML::LoadFile(config_file).as<Input>();
auto qpoint_data
= read_qpoint_data(input.QpointDataInputFile.value_or("band.hdf5"));
std::clog << "Done." << std::endl;
auto qpoint_data = read_qpoint_data(input.QpointDataInputFile.value_or("band.hdf5"));
log.info("Done.");
std::clog << "Constructing basis... " << std::flush;
auto [super_cell_deformation, super_cell_multiplier]
= decompose_transformation(input.SuperCellTransformation);
auto basis = construct_basis
(
input.PrimativeCell, super_cell_multiplier,
input.PrimativeCell, input.SuperCellMultiplier,
input.PrimativeCellBasisNumber,
input.AtomPositionBySuperCell
* (input.SuperCellTransformation.cast<double>() * input.PrimativeCell).transpose()
* (input.SuperCellDeformation * input.SuperCellMultiplier.cast<double>().asDiagonal() * input.PrimativeCell)
);
std::clog << "Done." << std::endl;
std::clog << "Calculating projection coefficient... " << std::flush;
// 用来在屏幕上输出进度的计数器和线程
std::atomic<unsigned> number_of_finished_modes(0);
std::atomic<std::size_t> number_of_finished_modes(0);
auto number_of_modes = ranges::accumulate
(
qpoint_data
| ranges::views::transform([](const auto& qpoint) { return qpoint.ModeData.size(); }),
| ranges::views::transform([](const auto& qpoint)
{ return qpoint.ModeData.size(); }),
0ul
);
std::atomic<bool> finished;
@ -471,10 +334,7 @@ void ufo::unfold(std::string config_file)
for (auto& output_file : input.QpointDataOutputFile)
{
auto output = construct_output
(
input, super_cell_multiplier, super_cell_deformation,
projection_coefficient, qpoint_data, output_file.SelectedAtoms
);
(input, projection_coefficient, qpoint_data, output_file.SelectedAtoms);
if (output_file.OutputAsYaml.value_or(false)) std::ofstream(output_file.Filename) << YAML::Node(output);
else std::ofstream(output_file.Filename, std::ios::binary) << biu::serialize<char>(output);
}

View File

@ -1,6 +1,7 @@
SuperCellTransformation:
- [ 3, 0, 0 ]
- [ 2, 4, 0 ]
SuperCellMultiplier: [3, 4, 1]
SuperCellDeformation:
- [ 1, 0, 0 ]
- [ 0.6666, 1, 0 ]
- [ 0, 0, 1 ]
Qpoints:
- [0, 0, 0]

View File

@ -1,45 +0,0 @@
Qpoints:
-
- 0
- 0
- 0
-
- 0.15000000000000002
- 0.10000000000000001
- 0
-
- 0.30000000000000004
- 0.20000000000000001
- 0
-
- 0.44999999999999996
- 0.29999999999999999
- 0
-
- 0.60000000000000009
- 0.40000000000000002
- 0
-
- 0.75
- 0.5
- 0
-
- 0.89999999999999991
- 0.59999999999999998
- 0
-
- 0.049999999999999822
- 0.69999999999999996
- 0
-
- 0.20000000000000018
- 0.80000000000000004
- 0
-
- 0.35000000000000009
- 0.90000000000000002
- 0
-
- 0.5
- 0
- 0